1
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Fujiwara T, Mano E, Nango E. Structural basis for the minimal bifunctional alginate epimerase AlgE3 from Azotobacter chroococcum. FEBS Lett 2024; 598:1422-1437. [PMID: 38649293 DOI: 10.1002/1873-3468.14886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/15/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024]
Abstract
Among the epimerases specific to alginate, some of them in Azotobacter genera convert β-d-mannuronic acid to α-l-guluronic acid but also have lyase activity to degrade alginate. The remarkable characteristics of these epimerases make it a promising enzyme for tailoring alginates to meet specific demands. Here, we determined the structure of the bifunctional mannuronan C-5 epimerase AlgE3 from Azotobacter chroococcum (AcAlgE3) in complex with several mannuronic acid oligomers as well as in apo form, which allowed us to elucidate the binding manner of each mannuronic acid oligomer, and the structural plasticity, which is dependent on calcium ions. Moreover, a comprehensive analysis of the lyase activity profiles of AcAlgE3 combined with structural characteristics explained the preference for different chain length oligomers.
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Affiliation(s)
- Takaaki Fujiwara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Sayo-gun, Japan
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2
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Li S, Ge H, Li Y, Zhang K, Yu S, Cao H, Wang Y, Deng H, Li J, Dai J, Li LF, Luo Y, Sun Y, Geng Z, Dong Y, Zhang H, Qiu HJ. The E301R protein of African swine fever virus functions as a sliding clamp involved in viral genome replication. mBio 2023; 14:e0164523. [PMID: 37772878 PMCID: PMC10653895 DOI: 10.1128/mbio.01645-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/22/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Sliding clamp is a highly conserved protein in the evolution of prokaryotic and eukaryotic cells. The sliding clamp is required for genomic replication as a critical co-factor of DNA polymerases. However, the sliding clamp analogs in viruses remain largely unknown. We found that the ASFV E301R protein (pE301R) exhibited a sliding clamp-like structure and similar functions during ASFV replication. Interestingly, pE301R is assembled into a unique ring-shaped homotetramer distinct from sliding clamps or proliferating cell nuclear antigens (PCNAs) from other species. Notably, the E301R gene is required for viral life cycle, but the pE301R function can be partially restored by the porcine PCNA. This study not only highlights the functional role of the ASFV pE301R as a viral sliding clamp analog, but also facilitates the dissection of the complex replication mechanism of ASFV, which provides novel clues for developing antivirals against ASF.
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Affiliation(s)
- Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hailiang Ge
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- College of Animal Sciences, Yangtze University, Jingzhou, China
| | - Yanhua Li
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Kehui Zhang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shaoxiong Yu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongwei Cao
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yanjin Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hao Deng
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jiaqi Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jingwen Dai
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lian-Feng Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuzi Luo
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhi Geng
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Dong
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhang
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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3
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Wakui H, Yokoi Y, Horidome C, Ose T, Yao M, Tanaka Y, Hinou H, Nishimura SI. Structural and molecular insight into antibody recognition of dynamic neoepitopes in membrane tethered MUC1 of pancreatic cancer cells and secreted exosomes. RSC Chem Biol 2023; 4:564-572. [PMID: 37547453 PMCID: PMC10398351 DOI: 10.1039/d3cb00036b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/19/2023] [Indexed: 08/08/2023] Open
Abstract
Pancreatic cancer is highly metastatic and has poor prognosis, mainly due to delayed detection, often after metastasis has occurred. A novel method to enable early detection and disease intervention is strongly needed. Here we unveil for the first time that pancreatic cancer cells (PANC-1) and secreted exosomes express MUC1 bearing cancer-relevant dynamic epitopes recognized specifically by an anti-MUC1 antibody (SN-131), which binds specifically core 1 but not core 2 type O-glycans found in normal cells. Comprehensive assessment of the essential epitope for SN-131 indicates that PANC-1 cells produce dominantly MUC1 with aberrant O-glycoforms such as Tn, T, and sialyl T (ST) antigens. Importantly, SN-131 showed the highest affinity with MUC1 bearing ST antigen at the immunodominant DTR motif (KD = 1.58 nM) independent of the glycosylation states of other Ser/Thr residues in the MUC1 tandem repeats. The X-ray structure revealed that SN-131 interacts directly with Neu5Ac and root GalNAc of the ST antigen in addition to the proximal peptide region. Our results demonstrate that targeting O-glycosylated "dynamic neoepitopes" found in the membrane-tethered MUC1 is a promising therapeutic strategy for improving the treatment outcome of patients with pancreatic cancer.
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Affiliation(s)
- Hajime Wakui
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| | - Yasuhiro Yokoi
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| | - Chieko Horidome
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| | - Toyoyuki Ose
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N10 W8 Kita-ku Sapporo 060-0810 Japan
| | - Min Yao
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N10 W8 Kita-ku Sapporo 060-0810 Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University 2-1-1 Katahira Aoba-ku Sendai 980-8577 Japan
| | - Hiroshi Hinou
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| | - Shin-Ichiro Nishimura
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
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4
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Yang A, Jude KM, Lai B, Minot M, Kocyla AM, Glassman CR, Nishimiya D, Kim YS, Reddy ST, Khan AA, Garcia KC. Deploying synthetic coevolution and machine learning to engineer protein-protein interactions. Science 2023; 381:eadh1720. [PMID: 37499032 PMCID: PMC10403280 DOI: 10.1126/science.adh1720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/16/2023] [Indexed: 07/29/2023]
Abstract
Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.
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Affiliation(s)
- Aerin Yang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ben Lai
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Mason Minot
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Anna M. Kocyla
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caleb R. Glassman
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daisuke Nishimiya
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yoon Seok Kim
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Aly A. Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
- Departments of Pathology, and Family Medicine, University of Chicago, Chicago, IL 60637, USA
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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5
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Khavani M, Mehranfar A, Mofrad MRK. On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation. Virus Res 2023; 326:199050. [PMID: 36682462 DOI: 10.1016/j.virusres.2023.199050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/21/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibitor for this virus is of great medical and public health importance. With this goal in mind, we investigate the affinity of different sialic acid-based compounds (ligands) against the hemagglutinin-neuraminidase (HN) protein of the mumps virus, using a combination of molecular dynamics (MD) simulations and quantum chemistry calculations. Our MD simulation results indicate that the ligands form stable complexes with the HN protein through a combination of electrostatic, van der Waals (vdW), and hydrogen bond (H-bond) interactions, which the electrostatic interactions play a more important role in the complexation process. Based on the obtained results from the structural analysis Arg381, Arg291, and Arg49 play a key role in the binding site interactions with the different ligands, in comparison with other residues. There are some candidates such as Neu5Acα2-6Galβ1-4GlcNAcβ, Neu5Acα2-3Galβ1-3GlcNacβ1-3Galβ1-4Glc, and Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4Glc that form more stable complexes with the HN than the α2-3-Sialyllactose confirmed by the calculated Gibbs binding energies (-39.65, -46.93, and -36.49 kcal.mol-1, respectively). To investigate the relationship between the molecular properties of the selected compounds and their affinity to the HN receptor, density functional theory dispersion corrected (DFT-D3) calculations were employed. According to our DFT-D3 results, neutral sialic acid-based compounds have lower reactivity to the mumps virus than the negativity charge structures. Moreover, by increasing the electronic chemical potential (μ) the vdW and H-bond interactions between drugs and the HN protein increase. In other words, by elevating the electron tendency of the selected ligands their affinity to the mumps virus increases. Our quantum chemistry calculations reveal that in addition to the structural features the molecular properties of the drugs can play important roles in their affinity and reactivity against the virus. The results of this study can provide useful details to design new compounds or improve their properties against the mumps virus.
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Affiliation(s)
- Mohammad Khavani
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Aliyeh Mehranfar
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mohammad R K Mofrad
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA.
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6
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Chavarria-Smith J, Chiu CPC, Jackman JK, Yin J, Zhang J, Hackney JA, Lin WY, Tyagi T, Sun Y, Tao J, Dunlap D, Morton WD, Ghodge SV, Maun HR, Li H, Hernandez-Barry H, Loyet KM, Chen E, Liu J, Tam C, Yaspan BL, Cai H, Balazs M, Arron JR, Li J, Wittwer AJ, Pappu R, Austin CD, Lee WP, Lazarus RA, Sudhamsu J, Koerber JT, Yi T. Dual antibody inhibition of KLK5 and KLK7 for Netherton syndrome and atopic dermatitis. Sci Transl Med 2022; 14:eabp9159. [PMID: 36516271 DOI: 10.1126/scitranslmed.abp9159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The epidermis is a barrier that prevents water loss while keeping harmful substances from penetrating the host. The impermeable cornified layer of the stratum corneum is maintained by balancing continuous turnover driven by epidermal basal cell proliferation, suprabasal cell differentiation, and corneal shedding. The epidermal desquamation process is tightly regulated by balance of the activities of serine proteases of the Kallikrein-related peptidases (KLK) family and their cognate inhibitor lymphoepithelial Kazal type-related inhibitor (LEKTI), which is encoded by the serine peptidase inhibitor Kazal type 5 gene. Imbalance of proteolytic activity caused by a deficiency of LEKTI leads to excessive desquamation due to increased activities of KLK5, KLK7, and KLK14 and results in Netherton syndrome (NS), a debilitating condition with an unmet clinical need. Increased activity of KLKs may also be pathological in other dermatoses such as atopic dermatitis (AD). Here, we describe the discovery of inhibitory antibodies against murine KLK5 and KLK7 that could compensate for the deficiency of LEKTI in NS. These antibodies are protective in mouse models of NS and AD and, when combined, promote improved skin barrier integrity and reduced inflammation. To translate these findings, we engineered a humanized bispecific antibody capable of potent inhibition of human KLK5 and KLK7. A crystal structure of KLK5 bound to the inhibitory Fab revealed that the antibody binds distal to its active site and uses a relatively unappreciated allosteric inhibition mechanism. Treatment with the bispecific anti-KLK5/7 antibody represents a promising therapy for clinical development in NS and other inflammatory dermatoses.
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Affiliation(s)
- Joseph Chavarria-Smith
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cecilia P C Chiu
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janet K Jackman
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jianping Yin
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- Department of Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wei-Yu Lin
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tulika Tyagi
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yonglian Sun
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janet Tao
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Debra Dunlap
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - William D Morton
- Confluence Discovery Technologies Inc., 4320 Duncan Ave, Suite 400, St. Louis, MO 63108, USA
| | - Swapnil V Ghodge
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Henry R Maun
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hong Li
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hilda Hernandez-Barry
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly M Loyet
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Emily Chen
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Liu
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christine Tam
- Department of Biomolecular Resources, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hao Cai
- Department of Preclinical and Translational Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mercedesz Balazs
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jing Li
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Arthur J Wittwer
- Confluence Discovery Technologies Inc., 4320 Duncan Ave, Suite 400, St. Louis, MO 63108, USA
| | - Rajita Pappu
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cary D Austin
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Robert A Lazarus
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - James T Koerber
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tangsheng Yi
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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7
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Takahashi D, Fujiwara I, Sasajima Y, Narita A, Imada K, Miyata M. ATP-dependent polymerization dynamics of bacterial actin proteins involved in Spiroplasma swimming. Open Biol 2022; 12:220083. [PMID: 36285441 PMCID: PMC9597168 DOI: 10.1098/rsob.220083] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MreB is a bacterial protein belonging to the actin superfamily. This protein polymerizes into an antiparallel double-stranded filament that determines cell shape by maintaining cell wall synthesis. Spiroplasma eriocheiris, a helical wall-less bacterium, has five MreB homologous (SpeMreB1-5) that probably contribute to swimming motility. Here, we investigated the structure, ATPase activity and polymerization dynamics of SpeMreB3 and SpeMreB5. SpeMreB3 polymerized into a double-stranded filament with possible antiparallel polarity, while SpeMreB5 formed sheets which contained the antiparallel filament, upon nucleotide binding. SpeMreB3 showed slow Pi release owing to the lack of an amino acid motif conserved in the catalytic centre of MreB family proteins. Our SpeMreB3 crystal structures and analyses of SpeMreB3 and SpeMreB5 variants showed that the amino acid motif probably plays a role in eliminating a nucleophilic water proton during ATP hydrolysis. Sedimentation assays suggest that SpeMreB3 has a lower polymerization activity than SpeMreB5, though their polymerization dynamics are qualitatively similar to those of other actin superfamily proteins, in which pre-ATP hydrolysis and post-Pi release states are unfavourable for them to remain as filaments.
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Affiliation(s)
- Daichi Takahashi
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan
| | - Ikuko Fujiwara
- Graduate School of Science, Osaka City University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan,Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yuya Sasajima
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan
| | - Akihiro Narita
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Katsumi Imada
- Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
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8
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Gilzer D, Schreiner M, Niemann HH. Direct interaction of a chaperone-bound type III secretion substrate with the export gate. Nat Commun 2022; 13:2858. [PMID: 35654781 PMCID: PMC9163089 DOI: 10.1038/s41467-022-30487-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/29/2022] [Indexed: 12/12/2022] Open
Abstract
Several gram-negative bacteria employ type III secretion systems (T3SS) to inject effector proteins into eukaryotic host cells directly from the bacterial cytoplasm. The export gate SctV (YscV in Yersinia) binds substrate:chaperone complexes such as YscX:YscY, which are essential for formation of a functional T3SS. Here, we present structures of the YscX:YscY complex alone and bound to nonameric YscV. YscX binds its chaperone YscY at two distinct sites, resembling the heterotrimeric complex of the T3SS needle subunit with its chaperone and co-chaperone. In the ternary complex the YscX N-terminus, which mediates YscX secretion, occupies a binding site within one YscV that is also used by flagellar chaperones, suggesting the interaction's importance for substrate recognition. The YscX C-terminus inserts between protomers of the YscV ring where the stalk protein binds to couple YscV to the T3SS ATPase. This primary YscV-YscX interaction is essential for the formation of a secretion-competent T3SS.
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Affiliation(s)
- Dominic Gilzer
- Department of Chemistry, Bielefeld University, Universitaetstrasse 25, 33615, Bielefeld, Germany
| | - Madeleine Schreiner
- Department of Chemistry, Bielefeld University, Universitaetstrasse 25, 33615, Bielefeld, Germany
| | - Hartmut H Niemann
- Department of Chemistry, Bielefeld University, Universitaetstrasse 25, 33615, Bielefeld, Germany.
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9
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Maunders EA, Ngu DHY, Ganio K, Hossain SI, Lim BYJ, Leeming MG, Luo Z, Tan A, Deplazes E, Kobe B, McDevitt CA. The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis. Front Microbiol 2022; 13:903146. [PMID: 35685933 PMCID: PMC9171197 DOI: 10.3389/fmicb.2022.903146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Acquisition of the trace-element molybdenum via the high-affinity ATP-binding cassette permease ModABC is essential for Pseudomonas aeruginosa respiration in anaerobic and microaerophilic environments. This study determined the X-ray crystal structures of the molybdenum-recruiting solute-binding protein ModA from P. aeruginosa PAO1 in the metal-free state and bound to the group 6 metal oxyanions molybdate, tungstate, and chromate. Pseudomonas aeruginosa PAO1 ModA has a non-contiguous dual-hinged bilobal structure with a single metal-binding site positioned between the two domains. Metal binding results in a 22° relative rotation of the two lobes with the oxyanions coordinated by four residues, that contribute six hydrogen bonds, distinct from ModA orthologues that feature an additional oxyanion-binding residue. Analysis of 485 Pseudomonas ModA sequences revealed conservation of the metal-binding residues and β-sheet structural elements, highlighting their contribution to protein structure and function. Despite the capacity of ModA to bind chromate, deletion of modA did not affect P. aeruginosa PAO1 sensitivity to chromate toxicity nor impact cellular accumulation of chromate. Exposure to sub-inhibitory concentrations of chromate broadly perturbed P. aeruginosa metal homeostasis and, unexpectedly, was associated with an increase in ModA-mediated molybdenum uptake. Elemental analyses of the proteome from anaerobically grown P. aeruginosa revealed that, despite the increase in cellular molybdenum upon chromate exposure, distribution of the metal within the proteome was substantially perturbed. This suggested that molybdoprotein cofactor acquisition may be disrupted, consistent with the potent toxicity of chromate under anaerobic conditions. Collectively, these data reveal a complex relationship between chromate toxicity, molybdenum homeostasis and anaerobic respiration.
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Affiliation(s)
- Eve A. Maunders
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Dalton H. Y. Ngu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sheikh I. Hossain
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Bryan Y. J. Lim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Michael G. Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Aimee Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Boštjan Kobe,
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Christopher A. McDevitt,
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10
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Yen M, Ren J, Liu Q, Glassman CR, Sheahan TP, Picton LK, Moreira FR, Rustagi A, Jude KM, Zhao X, Blish CA, Baric RS, Su LL, Garcia KC. Facile discovery of surrogate cytokine agonists. Cell 2022; 185:1414-1430.e19. [PMID: 35325595 PMCID: PMC9021867 DOI: 10.1016/j.cell.2022.02.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/11/2022] [Accepted: 02/22/2022] [Indexed: 12/26/2022]
Abstract
Cytokines are powerful immune modulators that initiate signaling through receptor dimerization, but natural cytokines have structural limitations as therapeutics. We present a strategy to discover cytokine surrogate agonists by using modular ligands that exploit induced proximity and receptor dimer geometry as pharmacological metrics amenable to high-throughput screening. Using VHH and scFv to human interleukin-2/15, type-I interferon, and interleukin-10 receptors, we generated combinatorial matrices of single-chain bispecific ligands that exhibited diverse spectrums of functional activities, including potent inhibition of SARS-CoV-2 by surrogate interferons. Crystal structures of IL-2R:VHH complexes revealed that variation in receptor dimer geometries resulted in functionally diverse signaling outputs. This modular platform enabled engineering of surrogate ligands that compelled assembly of an IL-2R/IL-10R heterodimer, which does not naturally exist, that signaled through pSTAT5 on T and natural killer (NK) cells. This "cytokine med-chem" approach, rooted in principles of induced proximity, is generalizable for discovery of diversified agonists for many ligand-receptor systems.
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Affiliation(s)
- Michelle Yen
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Junming Ren
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Qingxiang Liu
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caleb R Glassman
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy P Sheahan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lora K Picton
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fernando R Moreira
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiang Zhao
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leon L Su
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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11
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Shisaka Y, Sakakibara E, Suzuki K, Stanfield JK, Onoda H, Ueda G, Hatano M, Sugimoto H, Shoji O. Tetraphenylporphyrin Enters the Ring: First Example of a Complex Between Highly Bulky Porphyrins and a Protein. Chembiochem 2022; 23:e202200095. [PMID: 35352458 DOI: 10.1002/cbic.202200095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Indexed: 11/08/2022]
Abstract
Tetraphenylporphyrin (TPP) is a symmetrically substituted synthetic porphyrin whose properties can be readily modified, providing it with significant advantages over naturally occurring porphyrins. Herein, we report the first example of a stable complex between a native biomolecule, the haemoprotein HasA, and TPP as well as its derivatives. The X-ray crystal structures of nine different HasA-TPP complexes were solved at high resolutions. HasA capturing TPP derivatives was also demonstrated to inhibit growth of the opportunistic pathogen Pseudomonas aeruginosa . Mutant variants of HasA binding FeTPP were shown to possess a different mode of coordination, permitting the cyclopropanation of styrene.
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Affiliation(s)
- Yuma Shisaka
- Nagoya University, Chemistry, Furo-cho, Chikusa-ku, 464-8602, Nagoya, JAPAN
| | - Erika Sakakibara
- Nagoya University, Chemistry, Furo-cho, Chikusa-ku, 464-8602, Nagoya, JAPAN
| | - Kazuto Suzuki
- Nagoya University, Chemistry, Furo-cho, Chikusa-ku, 464-8602, Nagoya, JAPAN
| | | | - Hiroki Onoda
- Nagoya University, Chemistry, Furo-cho, Chikusa-ku, 464-8602, Nagoya, JAPAN
| | - Garyo Ueda
- Nagoya University, Chemistry, Furo-cho, Chikusa-ku, 464-8602, Nagoya, JAPAN
| | - Miu Hatano
- Nagoya University, Chemistry, Furo-cho, Chikusa-ku, 464-8602, Nagoya, JAPAN
| | - Hiroshi Sugimoto
- RIKEN: Rikagaku Kenkyujo, SPring-8 Centre, 1-1-1 Kouto, 679-5148, Sayo, JAPAN
| | - Osami Shoji
- Nagoya University, Graduate School of Science, Furo, Chikusa,, 464-8602, Nagoya, JAPAN
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12
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Schweininger J, Kriegel M, Häge S, Conrad M, Alkhashrom S, Lösing J, Weiler S, Tillmanns J, Egerer-Sieber C, Decker A, Lenac Roviš T, Eichler J, Sticht H, Marschall M, Muller YA. The crystal structure of the varicella-zoster Orf24-Orf27 nuclear egress complex spotlights multiple determinants of herpesvirus subfamily specificity. J Biol Chem 2022; 298:101625. [PMID: 35074430 PMCID: PMC8867122 DOI: 10.1016/j.jbc.2022.101625] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
Varicella-zoster virus (VZV) is a human pathogen from the α-subfamily of herpesviruses. The VZV Orf24-Orf27 complex represents the essential viral core nuclear egress complex (NEC) that orchestrates the egress of the preassembled virus capsids from the nucleus. While previous studies have primarily emphasized that the architecture of core NEC complexes is highly conserved among herpesviruses, the present report focuses on subfamily-specific structural and functional features that help explain the differences in the autologous versus nonautologous interaction patterns observed for NEC formation across herpesviruses. Here, we describe the crystal structure of the Orf24-Orf27 complex at 2.1 Å resolution. Coimmunoprecipitation and confocal imaging data show that Orf24-Orf27 complex formation displays some promiscuity in a herpesvirus subfamily-restricted manner. At the same time, analysis of thermodynamic parameters of NEC formation of three prototypical α-, β-, and γ herpesviruses, i.e., VZV, human cytomegalovirus (HCMV), and Epstein–Barr virus (EBV), revealed highly similar binding affinities for the autologous interaction with specific differences in enthalpy and entropy. Computational alanine scanning, structural comparisons, and mutational data highlight intermolecular interactions shared among α-herpesviruses that are clearly distinct from those seen in β- and γ-herpesviruses, including a salt bridge formed between Orf24-Arg167 and Orf27-Asp126. This interaction is located outside of the hook-into-groove interface and contributes significantly to the free energy of complex formation. Combined, these data explain distinct properties of specificity and permissivity so far observed in herpesviral NEC interactions. These findings will prove valuable in attempting to target multiple herpesvirus core NECs with selective or broad-acting drug candidates.
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13
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Rahman S, Wineman-Fisher V, Nagy PR, Al-Hamdani Y, Tkatchenko A, Varma S. Methyl-Induced Polarization Destabilizes the Noncovalent Interactions of N-Methylated Lysines. Chemistry 2021; 27:11005-11014. [PMID: 33999467 PMCID: PMC9830558 DOI: 10.1002/chem.202100644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Indexed: 01/12/2023]
Abstract
Lysine methylation can modify noncovalent interactions by altering lysine's hydrophobicity as well as its electronic structure. Although the ramifications of the former are documented, the effects of the latter remain largely unknown. Understanding the electronic structure is important for determining how biological methylation modulates protein-protein binding, and the impact of artificial methylation experiments in which methylated lysines are used as spectroscopic probes and protein crystallization facilitators. The benchmarked first-principles calculations undertaken here reveal that methyl-induced polarization weakens the electrostatic attraction of amines with protein functional groups - salt bridges, hydrogen bonds and cation-π interactions weaken by as much as 10.3, 7.9 and 3.5 kT, respectively. Multipole analysis shows that weakened electrostatics is due to the altered inductive effects, which overcome increased attraction from methyl-enhanced polarizability and dispersion. Due to their fundamental nature, these effects are expected to be present in many cases. A survey of methylated lysines in protein structures reveals several cases in which methyl-induced polarization is the primary driver of altered noncovalent interactions; in these cases, destabilizations are found to be in the 0.6-4.7 kT range. The clearest case of where methyl-induced polarization plays a dominant role in regulating biological function is that of the PHD1-PHD2 domain, which recognizes lysine-methylated states on histones. These results broaden our understanding of how methylation modulates noncovalent interactions.
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Affiliation(s)
- Sanim Rahman
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, FL-33620, USA,Current Address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD-21205, USA
| | - Vered Wineman-Fisher
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, FL-33620, USA
| | - Péter R. Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, H-1521 Budapest, P.O.Box 91, Hungary
| | - Yasmine Al-Hamdani
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, FL-33620, USA,Department of Physics, University of South Florida, 4202 E. Fowler Ave., Tampa, FL-33620, USA
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14
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Kim S, Yoon I, Kim S, Hwang KY. Protocol for improving diffraction quality of leucyl-tRNA synthetase 1 with methylation and post-crystallization soaking and cooling in cryoprotectants. STAR Protoc 2021; 2:100642. [PMID: 34258600 PMCID: PMC8260868 DOI: 10.1016/j.xpro.2021.100642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Leucyl-tRNA synthetase 1 (LARS1) synthesizes Leu-tRNALeu for protein synthesis and plays an important role in mTORC1 activation by sensing intracellular leucine concentrations. Here, we describe a protocol for the purification, reductive methylation, binding affinity measurement by microscale thermophoresis, T i value measurement by Tycho, and post-crystallization soaking and cooling in cryoprotectants to improve crystallization of LARS1. Collectively, this allowed us to build the RagD binding domain, which was shown to be a dynamic region of LARS1 refractory to crystallization. For complete details on the use and execution of this protocol, please refer to Kim et al. (2021).
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Affiliation(s)
- Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea,Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Republic of Korea,Corresponding author
| | - Ina Yoon
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea,Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Republic of Korea,Corresponding author
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15
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Kim S, Yoon I, Son J, Park J, Kim K, Lee JH, Park SY, Kang BS, Han JM, Hwang KY, Kim S. Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation. Cell Rep 2021; 35:109031. [PMID: 33910001 DOI: 10.1016/j.celrep.2021.109031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 12/18/2020] [Accepted: 04/02/2021] [Indexed: 01/07/2023] Open
Abstract
Leucyl-tRNA synthetase 1 (LARS1) mediates activation of leucine-dependent mechanistic target of rapamycin complex 1 (mTORC1) as well as ligation of leucine to its cognate tRNAs, yet its mechanism of leucine sensing is poorly understood. Here we describe leucine binding-induced conformational changes of LARS1. We determine different crystal structures of LARS1 complexed with leucine, ATP, and a reaction intermediate analog, leucyl-sulfamoyl-adenylate (Leu-AMS), and find two distinct functional states of LARS1 for mTORC1 activation. Upon leucine binding to the synthetic site, H251 and R517 in the connective polypeptide and 50FPYPY54 in the catalytic domain change the hydrogen bond network, leading to conformational change in the C-terminal domain, correlating with RagD association. Leucine binding to LARS1 is increased in the presence of ATP, further augmenting leucine-dependent interaction of LARS1 and RagD. Thus, this work unveils the structural basis for leucine-dependent long-range communication between the catalytic and RagD-binding domains of LARS1 for mTORC1 activation.
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Affiliation(s)
- Sulhee Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ina Yoon
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea
| | - Jonghyeon Son
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Junga Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Kibum Kim
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea; Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji-Ho Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Beom Sik Kang
- School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung Min Han
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea; Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea.
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16
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Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. SCIENCE ADVANCES 2021; 7:eabf8711. [PMID: 33853786 PMCID: PMC8046379 DOI: 10.1126/sciadv.abf8711] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/24/2021] [Indexed: 05/19/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate-ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Iris D Young
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Luan Carvalho Martins
- Biochemistry Department, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Dominique H Smith
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Tristan W Owens
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ishan Deshpande
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Gregory E Merz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Aye C Thwin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Justin T Biel
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jessica K Peters
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michelle Moritz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadia Herrera
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Huong T Kratochvil
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - James M Bennett
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
| | - Jose Brandao Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
| | - Matteo P Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Martin R Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Tyler J Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - James M Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Tobias Krojer
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - George Meigs
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ailsa J Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | | | - Victor L Rangel
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, São Paulo, Brazil
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Rachael E Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexei S Soares
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jennifer L Wierman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Peter O'Brien
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Natalia Jura
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, San Francisco, CA 94158, USA
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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17
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Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S. Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Mol Cell 2021; 81:599-613.e8. [PMID: 33373584 PMCID: PMC8183676 DOI: 10.1016/j.molcel.2020.11.047] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/17/2020] [Accepted: 11/23/2020] [Indexed: 01/28/2023]
Abstract
RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryoelectron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement may apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses suggest not only conserved substrates for TRIM proteins but also, unexpectedly, deep evolutionary connections between TRIM proteins and RNA helicases, linking ubiquitin and RNA biology throughout animal evolution.
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MESH Headings
- Cryoelectron Microscopy
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/metabolism
- DEAD Box Protein 58/ultrastructure
- Epitopes
- Evolution, Molecular
- HEK293 Cells
- Humans
- Immunity, Innate
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/metabolism
- Interferon-Induced Helicase, IFIH1/ultrastructure
- Models, Molecular
- Phylogeny
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Interaction Domains and Motifs
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/ultrastructure
- Tripartite Motif Proteins/genetics
- Tripartite Motif Proteins/metabolism
- Tripartite Motif Proteins/ultrastructure
- Ubiquitin-Protein Ligases/genetics
- Ubiquitin-Protein Ligases/metabolism
- Ubiquitin-Protein Ligases/ultrastructure
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Affiliation(s)
- Kazuki Kato
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xin Mu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sehoon Park
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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18
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Smith RHB, Khan ZM, Ung PMU, Scopton AP, Silber L, Mack SM, Real AM, Schlessinger A, Dar AC. Type II Binders Targeting the "GLR-Out" Conformation of the Pseudokinase STRADα. Biochemistry 2021; 60:289-302. [PMID: 33440120 DOI: 10.1021/acs.biochem.0c00714] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pseudokinases play important roles in signal transduction and cellular processes similar to those of catalytically competent kinases. However, pseudokinase pharmacological tractability and conformational space accessibility are poorly understood. Pseudokinases have only recently been suggested to adopt "inactive" conformations or interact with conformation-specific kinase inhibitors (e.g., type II compounds). In this work, the heavily substituted pseudokinase STRADα, which possesses a DFG → GLR substitution in the catalytic site that permits nucleotide binding while impairing divalent cation coordination, is used as a test case to demonstrate the potential applicability of conformation-specific, type II compounds to pseudokinase pharmacology. Integrated structural modeling is employed to generate a "GLR-out" conformational ensemble. Likely interacting type II compounds are identified through virtual screening against this ensemble model. Biophysical validation of compound binding is demonstrated through protein thermal stabilization and ATP competition. Localization of a top-performing compound through surface methylation strongly suggests that STRADα can adopt the "GLR-out" conformation and interact with compounds that comply with the standard type II pharmacophore. These results suggest that, despite a loss of catalytic function, some pseudokinases, including STRADα, may retain the conformational switching properties of conventional protein kinases.
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Affiliation(s)
- Ryan H B Smith
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Zaigham M Khan
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Peter Man-Un Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Alex P Scopton
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Lisa Silber
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Seshat M Mack
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Alexander M Real
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Arvin C Dar
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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19
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Chowdhury R, Abboud MI, McAllister TE, Banerji B, Bhushan B, Sorensen JL, Kawamura A, Schofield CJ. Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2. Sci Rep 2020; 10:21964. [PMID: 33319810 PMCID: PMC7738489 DOI: 10.1038/s41598-020-76307-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
Crystallization is the bottleneck in macromolecular crystallography; even when a protein crystallises, crystal packing often influences ligand-binding and protein-protein interaction interfaces, which are the key points of interest for functional and drug discovery studies. The human hypoxia-inducible factor prolyl hydroxylase 2 (PHD2) readily crystallises as a homotrimer, but with a sterically blocked active site. We explored strategies aimed at altering PHD2 crystal packing by protein modification and molecules that bind at its active site and elsewhere. Following the observation that, despite weak inhibition/binding in solution, succinamic acid derivatives readily enable PHD2 crystallization, we explored methods to induce crystallization without active site binding. Cyclic peptides obtained via mRNA display bind PHD2 tightly away from the active site. They efficiently enable PHD2 crystallization in different forms, both with/without substrates, apparently by promoting oligomerization involving binding to the C-terminal region. Although our work involves a specific case study, together with those of others, the results suggest that mRNA display-derived cyclic peptides may be useful in challenging protein crystallization cases.
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Affiliation(s)
- Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Tom E McAllister
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Biswadip Banerji
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Bhaskar Bhushan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - John L Sorensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.
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20
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Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, Aimon A, Bennett JM, Neto JB, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs M, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.24.393405. [PMID: 33269349 PMCID: PMC7709169 DOI: 10.1101/2020.11.24.393405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, CA, USA
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, CA, USA
| | - Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, CA, USA
| | - Iris D. Young
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Luan Carvalho Martins
- Biochemistry Department, Institute for Biological Sciences, Federal University of Minas Gerais. Belo Horizonte, Brazil
| | - Dominique H. Smith
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA, USA
| | - Ursula Schulze-Gahmen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Tristan W. Owens
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Ishan Deshpande
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Gregory E. Merz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Aye C. Thwin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Justin T. Biel
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Jessica K. Peters
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Michelle Moritz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Nadia Herrera
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Huong T. Kratochvil
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - QCRG Structural Biology Consortium
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James M. Bennett
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
| | - Jose Brandao Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Tyler J. Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Tobias Krojer
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - George Meigs
- Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ailsa J. Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | | | - Victor L Rangel
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, São Paulo, Brazil
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Rachael E. Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | | | - Jennifer L. Wierman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Natalia Jura
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA, USA
| | - John Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California Merced, CA, USA
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
- Institute for Neurodegenerative Disease, University of California San Francisco, CA, USA
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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21
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Javitt G, Cao Z, Resnick E, Gabizon R, Bulleid NJ, Fass D. Structure and Electron-Transfer Pathway of the Human Methionine Sulfoxide Reductase MsrB3. Antioxid Redox Signal 2020; 33:665-678. [PMID: 32517586 PMCID: PMC7475093 DOI: 10.1089/ars.2020.8037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aims: The post-translational oxidation of methionine to methionine sulfoxide (MetSO) is a reversible process, enabling the repair of oxidative damage to proteins and the use of sulfoxidation as a regulatory switch. MetSO reductases catalyze the stereospecific reduction of MetSO. One of the mammalian MetSO reductases, MsrB3, has a signal sequence for entry into the endoplasmic reticulum (ER). In the ER, MsrB3 is expected to encounter a distinct redox environment compared with its paralogs in the cytosol, nucleus, and mitochondria. We sought to determine the location and arrangement of MsrB3 redox-active cysteines, which may couple MsrB3 activity to other redox events in the ER. Results: We determined the human MsrB3 structure by using X-ray crystallography. The structure revealed that a disulfide bond near the protein amino terminus is distant in space from the active site. Nevertheless, biochemical assays showed that these amino-terminal cysteines are oxidized by the MsrB3 active site after its reaction with MetSO. Innovation: This study reveals a mechanism to shuttle oxidizing equivalents from the primary MsrB3 active site toward the enzyme surface, where they would be available for further dithiol-disulfide exchange reactions. Conclusion: Conformational changes must occur during the MsrB3 catalytic cycle to transfer oxidizing equivalents from the active site to the amino-terminal redox-active disulfide. The accessibility of this exposed disulfide may help couple MsrB3 activity to other dithiol-disulfide redox events in the secretory pathway.
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Affiliation(s)
- Gabriel Javitt
- Department of Structural Biology and Weizmann Institute of Science, Rehovot, Israel
| | - Zhenbo Cao
- Institute of Molecular, Cellular and Systems Biology, CMVLS, University of Glasgow, Glasgow, United Kingdom
| | - Efrat Resnick
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ronen Gabizon
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Neil J Bulleid
- Institute of Molecular, Cellular and Systems Biology, CMVLS, University of Glasgow, Glasgow, United Kingdom
| | - Deborah Fass
- Department of Structural Biology and Weizmann Institute of Science, Rehovot, Israel
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22
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The Structure of the Cysteine-Rich Domain of Plasmodium falciparum P113 Identifies the Location of the RH5 Binding Site. mBio 2020; 11:mBio.01566-20. [PMID: 32900802 PMCID: PMC7482062 DOI: 10.1128/mbio.01566-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Malaria is a deadly infectious disease primarily caused by the parasite Plasmodium falciparum. It remains a major global health problem, and there is no highly effective vaccine. A parasite protein called RH5 is centrally involved in the invasion of host red blood cells, making it—and the other parasite proteins it interacts with—promising vaccine targets. We recently identified a protein called P113 that binds RH5, suggesting that it anchors RH5 to the parasite surface. In this paper, we use structural biology to locate and characterize the RH5 binding region on P113. These findings will be important to guide the development of new antimalarial vaccines to ultimately prevent this disease, which affects some of the poorest people on the planet. Plasmodium falciparum RH5 is a secreted parasite ligand that is essential for erythrocyte invasion through direct interaction with the host erythrocyte receptor basigin. RH5 forms a tripartite complex with two other secreted parasite proteins, CyRPA and RIPR, and is tethered to the surface of the parasite through membrane-anchored P113. Antibodies against RH5, CyRPA, and RIPR can inhibit parasite invasion, suggesting that vaccines containing these three components have the potential to prevent blood-stage malaria. To further explore the role of the P113-RH5 interaction, we selected monoclonal antibodies against P113 that were either inhibitory or noninhibitory for RH5 binding. Using a Fab fragment as a crystallization chaperone, we determined the crystal structure of the RH5 binding region of P113 and showed that it is composed of two domains with structural similarities to rhamnose-binding lectins. We identified the RH5 binding site on P113 by using a combination of hydrogen-deuterium exchange mass spectrometry and site-directed mutagenesis. We found that a monoclonal antibody to P113 that bound to this interface and inhibited the RH5-P113 interaction did not inhibit parasite blood-stage growth. These findings provide further structural information on the protein interactions of RH5 and will be helpful in guiding the development of blood-stage malaria vaccines that target RH5.
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23
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Crystallization of Recombinant Fimbrial Proteins of Porphyromonas gingivalis. Methods Mol Biol 2020. [PMID: 32815130 DOI: 10.1007/978-1-0716-0939-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Porphyromonas gingivalis fimbriae play a critical role in colonization. Elucidation of the fimbrial structure in atomic detail is important for understanding the colonization mechanism and to provide means to combat periodontitis. X-ray crystallography is a technique that is used to obtain detailed information of proteins along with bound ligands and ions. Crystallization of the protein of interest is the first step toward structure determination. Unfortunately it is not possible to predict the crystallization condition of a certain protein or even if the protein can be crystallized. Protein crystallization is, on the contrary, a matter of trial and error. However, the best strategy for success is to focus on the protein purification step to obtain a sample that is pure, stable, homogeneous and of high concentration. This chapter addresses general methods for crystallization of fimbrial proteins.
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24
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Malinauskas T, Peer TV, Bishop B, Mueller TD, Siebold C. Repulsive guidance molecules lock growth differentiation factor 5 in an inhibitory complex. Proc Natl Acad Sci U S A 2020; 117:15620-15631. [PMID: 32576689 PMCID: PMC7354924 DOI: 10.1073/pnas.2000561117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Repulsive guidance molecules (RGMs) are cell surface proteins that regulate the development and homeostasis of many tissues and organs, including the nervous, skeletal, and immune systems. They control fundamental biological processes, such as migration and differentiation by direct interaction with the Neogenin (NEO1) receptor and function as coreceptors for the bone morphogenetic protein (BMP)/growth differentiation factor (GDF) family. We determined crystal structures of all three human RGM family members in complex with GDF5, as well as the ternary NEO1-RGMB-GDF5 assembly. Surprisingly, we show that all three RGMs inhibit GDF5 signaling, which is in stark contrast to RGM-mediated enhancement of signaling observed for other BMPs, like BMP2. Despite their opposite effect on GDF5 signaling, RGMs occupy the BMP type 1 receptor binding site similar to the observed interactions in RGM-BMP2 complexes. In the NEO1-RGMB-GDF5 complex, RGMB physically bridges NEO1 and GDF5, suggesting cross-talk between the GDF5 and NEO1 signaling pathways. Our crystal structures, combined with structure-guided mutagenesis of RGMs and BMP ligands, binding studies, and cellular assays suggest that RGMs inhibit GDF5 signaling by competing with GDF5 type 1 receptors. While our crystal structure analysis and in vitro binding data initially pointed towards a simple competition mechanism between RGMs and type 1 receptors as a possible basis for RGM-mediated GDF5 inhibition, further experiments utilizing BMP2-mimicking GDF5 variants clearly indicate a more complex mechanism that explains how RGMs can act as a functionality-changing switch for two structurally and biochemically similar signaling molecules.
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Affiliation(s)
- Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom;
| | - Tina V Peer
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute, University of Würzburg, 97082 Würzburg, Germany
| | - Benjamin Bishop
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Thomas D Mueller
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute, University of Würzburg, 97082 Würzburg, Germany
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom;
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25
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Large-Scale Expression and Purification of Mumps Virus Hemagglutinin-Neuraminidase for Structural Analyses and Glycan-Binding Assays. Methods Mol Biol 2020. [PMID: 32306363 DOI: 10.1007/978-1-0716-0430-4_55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Many viruses utilize cell-surface glycans as receptors for host cell entry. Viral surface glycoproteins specifically interact with glycan motifs, which strongly contributes to viral tropism. Recently, the interactions between host cell glycan receptors and the mumps virus (MuV) hemagglutinin-neuraminidase (MuV-HN) protein were characterized by determining the co-crystal structure of MuV-HN in complex with glycan receptors. Here, we describe protocols for large-scale expression, purification and crystallization of MuV-HN proteins for structural analyses and glycan-binding assays with the overarching goal of investigating glycan-protein interactions.
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26
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Tang C, Deng Z, Li X, Yang M, Tian Z, Chen Z, Wang G, Wu W, Feng WH, Zhang G, Chen Z. Helicase of Type 2 Porcine Reproductive and Respiratory Syndrome Virus Strain HV Reveals a Unique Structure. Viruses 2020; 12:v12020215. [PMID: 32075207 PMCID: PMC7077220 DOI: 10.3390/v12020215] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 02/11/2020] [Indexed: 12/18/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is prevalent throughout the world and has caused great economic losses to the swine industry. Nonstructural protein 10 (nsp10) is a superfamily 1 helicase participating in multiple processes of virus replication and one of the three most conserved proteins in nidoviruses. Here we report three high resolution crystal structures of highly pathogenic PRRSV nsp10. PRRSV nsp10 has multiple domains, including an N-terminal zinc-binding domain (ZBD), a β-barrel domain, a helicase core with two RecA-like domains, and a C-terminal domain (CTD). The CTD adopts a novel fold and is required for the overall structure and enzymatic activities. Although each domain except the CTD aligns well with its homologs, PRRSV nsp10 adopts an unexpected extended overall structure in crystals and solution. Moreover, structural and functional analyses of PRRSV nsp10 versus its closest homolog, equine arteritis virus nsp10, suggest that DNA binding might induce a profound conformational change of PRRSV nsp10 to exert functions, thus shedding light on the mechanisms of activity regulation of this helicase.
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Affiliation(s)
- Chenjun Tang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Zengqin Deng
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Xiaorong Li
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Meiting Yang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Zizi Tian
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Zhenhang Chen
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Guoguo Wang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Wei Wu
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Wen-hai Feng
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
| | - Gongyi Zhang
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA;
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (C.T.); (Z.D.); (X.L.); (M.Y.); (Z.T.); (Z.C.); (G.W.); (W.W.); (W.-h.F.)
- Correspondence: ; Tel.: +86-10-6273-4078
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27
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Kumar Megta A, Palva A, von Ossowski I, Krishnan V. SpaB, an atypically adhesive basal pilin from the lactobacillar SpaCBA pilus: crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun 2019; 75:731-737. [PMID: 31797814 PMCID: PMC6891582 DOI: 10.1107/s2053230x19015358] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
The SpaB pilin is recognized as the basal subunit of the sortase-dependent SpaCBA pilus, which is known to be produced by the Gram-positive Lactobacillus rhamnosus GG, a gut-adapted commensal advocated to have health benefits. Despite seeming to function as an archetypal basal pilin by serving as the terminal subunit in pilus assembly, SpaB also assumes an atypical role as a mucoadhesive protein. To shed light on the structural factors that contribute to this dual functional behaviour, a recombinant form of the L. rhamnosus GG SpaB pilin was produced and purified for crystallization and X-ray diffraction experiments. The crystallization of SpaB remained particularly challenging until the implementation of a three-pronged crystallization approach involving C-terminal tail truncation, surface lysine methylation and magnesium additives. Ultimately, hexagonal crystals of SpaB were produced and were able to diffract to a resolution of 2.4 Å. This crystal form belonged to space group P6522 or P6122, with unit-cell parameters a = b = 51.53, c = 408.22 Å, α = β = 90.0, γ = 120.0°. Obtaining an interpretable electron-density map via single-wavelength anomalous diffraction (SAD) using iodide-derivative data sets did not succeed owing to the weak anomalous signal. As an alternative, attempts to provide phases by molecular replacement using the iodide-SAD data from SpaB and a collection of distant homology models (<28% sequence identity) are in progress.
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Affiliation(s)
- Abhin Kumar Megta
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India
- School of Biotechnology, KIIT University, Odisha 751 024, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Vengadesan Krishnan
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India
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28
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Tan K, Zhou M, Ahrendt AJ, Duke NEC, Tabaja N, Ball WJ, Kirley TL, Norman AB, Joachimiak A, Schiffer M, Wilton R, Pokkuluri PR. Structural analysis of free and liganded forms of the Fab fragment of a high-affinity anti-cocaine antibody, h2E2. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:697-706. [PMID: 31702583 DOI: 10.1107/s2053230x19013608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/05/2019] [Indexed: 01/04/2023]
Abstract
A high-affinity anti-cocaine monoclonal antibody, designated h2E2, is entering phase 1 clinical trials for cocaine abuse therapy. To gain insight into the molecular details of its structure that are important for binding cocaine and cocaine metabolites, the Fab fragment was generated and crystallized with and without ligand. Structures of the unliganded Fab and the Fab fragment bound to benzoylecgonine were determined, and were compared with each other and with other crystallized anti-cocaine antibodies. The affinity of the h2E2 antibody for cocaine is 4 nM, while that of the cocaine metabolite benzoylecgonine is 20 nM. Both are higher than the reported affinity for cocaine of the two previously crystallized anti-cocaine antibodies. Consistent with cocaine fluorescent quenching binding studies for the h2E2 mAb, four aromatic residues in the CDR regions of the Fab (TyrL32, TyrL96, TrpL91 and TrpH33) were found to be involved in ligand binding. The aromatic side chains surround and trap the tropane moiety of the ligand in the complex structure, forming significant van der Waals interactions which may account for the higher affinity observed for the h2E2 antibody. A water molecule mediates hydrogen bonding between the antibody and the carbonyl group of the benzoyl ester. The affinity of binding to h2E2 of benzoylecgonine differs only by a factor of five compared with that of cocaine; therefore, it is suggested that h2E2 would bind cocaine in the same way as observed in the Fab-benzoylecgonine complex, with minor rearrangements of some hypervariable segments of the antibody.
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Affiliation(s)
- Kemin Tan
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Min Zhou
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Angela J Ahrendt
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Norma E C Duke
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Nassif Tabaja
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - William J Ball
- Department of Pharmacology and Systems Physiology, College of Medicine and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Terence L Kirley
- Department of Pharmacology and Systems Physiology, College of Medicine and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Andrew B Norman
- Department of Pharmacology and Systems Physiology, College of Medicine and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Marianne Schiffer
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Rosemarie Wilton
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - P Raj Pokkuluri
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
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29
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Arora K, Corbett KD. The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding. Nucleic Acids Res 2019; 47:2365-2376. [PMID: 30566683 PMCID: PMC6411835 DOI: 10.1093/nar/gky1273] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 01/24/2023] Open
Abstract
In eukaryotic meiosis, generation of haploid gametes depends on the formation of inter-homolog crossovers, which enable the pairing, physical linkage, and eventual segregation of homologs in the meiosis I division. A class of conserved meiosis-specific proteins, collectively termed ZMMs, are required for formation and spatial control of crossovers throughout eukaryotes. Here, we show that three Saccharomyces cerevisiae ZMM proteins-Zip2, Zip4 and Spo16-interact with one another and form a DNA-binding complex critical for crossover formation and control. We determined the crystal structure of a Zip2:Spo16 subcomplex, revealing a heterodimer structurally related to the XPF:ERCC1 endonuclease complex. Zip2:Spo16 lacks an endonuclease active site, but binds specific DNA structures found in early meiotic recombination intermediates. Mutations in multiple DNA-binding surfaces on Zip2:Spo16 severely compromise DNA binding, supporting a model in which the complex's central and HhH domains cooperate to bind DNA. Overall, our data support a model in which the Zip2:Zip4:Spo16 complex binds and stabilizes early meiotic recombination intermediates, then coordinates additional factors to promote crossover formation and license downstream events including synaptonemal complex assembly.
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Affiliation(s)
- Kanika Arora
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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30
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Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR. Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nat Commun 2019; 10:4127. [PMID: 31511507 PMCID: PMC6739347 DOI: 10.1038/s41467-019-11931-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/13/2019] [Indexed: 02/06/2023] Open
Abstract
Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.
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Affiliation(s)
- Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India
- Institute of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Giuseppe Cannone
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nainesh Katagihallimath
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India
| | - Subramanian Ramaswamy
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India.
| | - Kutti R Vinothkumar
- National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India.
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31
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Alanine DGW, Quinkert D, Kumarasingha R, Mehmood S, Donnellan FR, Minkah NK, Dadonaite B, Diouf A, Galaway F, Silk SE, Jamwal A, Marshall JM, Miura K, Foquet L, Elias SC, Labbé GM, Douglas AD, Jin J, Payne RO, Illingworth JJ, Pattinson DJ, Pulido D, Williams BG, de Jongh WA, Wright GJ, Kappe SHI, Robinson CV, Long CA, Crabb BS, Gilson PR, Higgins MK, Draper SJ. Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies. Cell 2019; 178:216-228.e21. [PMID: 31204103 PMCID: PMC6602525 DOI: 10.1016/j.cell.2019.05.025] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 03/05/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022]
Abstract
The Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) is the leading target for next-generation vaccines against the disease-causing blood-stage of malaria. However, little is known about how human antibodies confer functional immunity against this antigen. We isolated a panel of human monoclonal antibodies (mAbs) against PfRH5 from peripheral blood B cells from vaccinees in the first clinical trial of a PfRH5-based vaccine. We identified a subset of mAbs with neutralizing activity that bind to three distinct sites and another subset of mAbs that are non-functional, or even antagonistic to neutralizing antibodies. We also identify the epitope of a novel group of non-neutralizing antibodies that significantly reduce the speed of red blood cell invasion by the merozoite, thereby potentiating the effect of all neutralizing PfRH5 antibodies as well as synergizing with antibodies targeting other malaria invasion proteins. Our results provide a roadmap for structure-guided vaccine development to maximize antibody efficacy against blood-stage malaria.
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Affiliation(s)
- Daniel G W Alanine
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Doris Quinkert
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | | | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Francesca R Donnellan
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Nana K Minkah
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Bernadeta Dadonaite
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Sarah E Silk
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Abhishek Jamwal
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jennifer M Marshall
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Lander Foquet
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Sean C Elias
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Geneviève M Labbé
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Alexander D Douglas
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Jing Jin
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Ruth O Payne
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Joseph J Illingworth
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - David J Pattinson
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - David Pulido
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Barnabas G Williams
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Willem A de Jongh
- ExpreS(2)ion Biotechnologies, SCION-DTU Science Park, Agern Allé 1, Hørsholm 2970, Denmark
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Carole A Long
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Brendan S Crabb
- Burnet Institute, 85 Commercial Road, Melbourne, VIC 3004, Australia
| | - Paul R Gilson
- Burnet Institute, 85 Commercial Road, Melbourne, VIC 3004, Australia
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Simon J Draper
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
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32
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Crystal structure of a mammalian Wnt–frizzled complex. Nat Struct Mol Biol 2019; 26:372-379. [DOI: 10.1038/s41594-019-0216-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/27/2019] [Indexed: 11/08/2022]
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33
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Ganesh D, Torigoe K, Kumano-Kuramochi M, Machida S, Kobori T. Microplate-based Assay for Screening of Advanced Glycation End Products Binding to Its Receptor. ANAL SCI 2019; 35:237-240. [PMID: 30643096 DOI: 10.2116/analsci.18c021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Advanced Glycation End products (AGEs) are a group of amino-acid modifications produced with sugars or di-carbonyls. Some AGEs are known to affect health through binding to the receptor of AGEs (RAGE). Here, we propose a method for screening RAGE-binding AGEs by a competitive assay using purified RAGE and AGEs-specific antibody. This method has clarified that at least carboxyethyl lysine and pentosidine among methylglyoxal-derived AGEs are involved in RAGE binding, suggesting that this would be a promising method for classifying RAGE-binding AGEs.
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Affiliation(s)
- Deepak Ganesh
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Kyoko Torigoe
- Food Research Institute, National Agriculture and Food Research Organization
| | | | - Sachiko Machida
- Food Research Institute, National Agriculture and Food Research Organization
| | - Toshiro Kobori
- Graduate School of Life and Environmental Sciences, University of Tsukuba.,Food Research Institute, National Agriculture and Food Research Organization
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34
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Gao C, Pallett MA, Croll TI, Smith GL, Graham SC. Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55. J Biol Chem 2019; 294:6416-6429. [PMID: 30819806 PMCID: PMC6484134 DOI: 10.1074/jbc.ra118.006561] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
BTB-Kelch proteins are substrate-specific adaptors for cullin-3 (Cul3) RING-box-based E3 ubiquitin ligases, mediating protein ubiquitylation for subsequent proteasomal degradation. Vaccinia virus encodes three BTB-Kelch proteins: A55, C2, and F3. Viruses lacking A55 or C2 have altered cytopathic effects in cultured cells and altered pathology in vivo Previous studies have shown that the ectromelia virus orthologue of A55 interacts with Cul3 in cells. We report that the N-terminal BTB-BACK (BB) domain of A55 binds directly to the Cul3 N-terminal domain (Cul3-NTD), forming a 2:2 complex in solution. We solved the structure of an A55BB/Cul3-NTD complex from anisotropic crystals diffracting to 2.3/3.7 Å resolution in the best/worst direction, revealing that the overall interaction and binding interface closely resemble the structures of cellular BTB/Cul3-NTD complexes, despite low sequence identity between A55 and cellular BTB domains. Surprisingly, despite this structural similarity, the affinity of Cul3-NTD for A55BB was stronger than for cellular BTB proteins. Glutamate substitution of the A55 residue Ile-48, adjacent to the canonical φX(D/E) Cul3-binding motif, reduced affinity of A55BB for Cul3-NTD by at least 2 orders of magnitude. Moreover, Ile-48 and the φX(D/E) motif are conserved in A55 orthologues from other poxviruses, but not in the vaccinia virus proteins C2 or F3. The high-affinity interaction between A55BB and Cul3-NTD suggests that, in addition to directing the Cul3-RING E3 ligase complex to degrade cellular/viral target proteins that are normally unaffected, A55 may also sequester Cul3 from cellular adaptor proteins, thereby protecting substrates of these cellular adaptors from ubiquitylation and degradation.
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Affiliation(s)
- Chen Gao
- From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and
| | - Mitchell A Pallett
- From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and
| | - Tristan I Croll
- the Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, United Kingdom
| | - Geoffrey L Smith
- From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and
| | - Stephen C Graham
- From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and
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35
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Zhou Y, Liu Z, Zhang J, Dou T, Chen J, Ge G, Zhu S, Wang F. Prediction of ligand modulation patterns on membrane receptors via lysine reactivity profiling. Chem Commun (Camb) 2019; 55:4311-4314. [DOI: 10.1039/c9cc00520j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A mass spectrometry-based lysine reactivity profiling strategy for the prediction of the ligand modulation patterns on neuronal membrane receptors.
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Affiliation(s)
- Ye Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Jinbao Zhang
- Institute of Neuroscience
- CAS Center for Excellence in Brain Science and Intelligence Technology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai
| | - Tongyi Dou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Jin Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Guangbo Ge
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Shujia Zhu
- Institute of Neuroscience
- CAS Center for Excellence in Brain Science and Intelligence Technology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
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36
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Larsen NB, Gao AO, Sparks JL, Gallina I, Wu RA, Mann M, Räschle M, Walter JC, Duxin JP. Replication-Coupled DNA-Protein Crosslink Repair by SPRTN and the Proteasome in Xenopus Egg Extracts. Mol Cell 2018; 73:574-588.e7. [PMID: 30595436 PMCID: PMC6375733 DOI: 10.1016/j.molcel.2018.11.024] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/20/2018] [Accepted: 11/15/2018] [Indexed: 01/19/2023]
Abstract
DNA-protein crosslinks (DPCs) are bulky lesions that interfere with DNA metabolism and therefore threaten genomic integrity. Recent studies implicate the metalloprotease SPRTN in S phase removal of DPCs, but how SPRTN is targeted to DPCs during DNA replication is unknown. Using Xenopus egg extracts that recapitulate replication-coupled DPC proteolysis, we show that DPCs can be degraded by SPRTN or the proteasome, which act as independent DPC proteases. Proteasome recruitment requires DPC polyubiquitylation, which is partially dependent on the ubiquitin ligase activity of TRAIP. In contrast, SPRTN-mediated DPC degradation does not require DPC polyubiquitylation but instead depends on nascent strand extension to within a few nucleotides of the lesion, implying that polymerase stalling at the DPC activates SPRTN on both leading and lagging strand templates. Our results demonstrate that SPRTN and proteasome activities are coupled to DNA replication by distinct mechanisms that promote replication across immovable protein barriers.
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Affiliation(s)
- Nicolai B Larsen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Alan O Gao
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Justin L Sparks
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Irene Gallina
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthias Mann
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Markus Räschle
- Department of Molecular Biotechnology and Systems Biology, Technical University of Kaiserslautern, 67653 Kaiserslautern, Germany
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Julien P Duxin
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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37
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Ye F, Huang Y, Li J, Ma Y, Xie C, Liu Z, Deng X, Wan J, Xue T, Liu W, Zhang M. An unexpected INAD PDZ tandem-mediated plcβ binding in Drosophila photo receptors. eLife 2018; 7:41848. [PMID: 30526850 PMCID: PMC6300352 DOI: 10.7554/elife.41848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/08/2018] [Indexed: 01/08/2023] Open
Abstract
INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. However, the molecular mechanism that governs the interaction between INAD and NORPA (phospholipase Cβ, PLCβ), a key step for the fast kinetics of the light signaling, is not known. Here, we show that the NORPA C-terminal coiled-coil domain and PDZ-binding motif (CC-PBM) synergistically bind to INAD PDZ45 tandem with an unexpected mode and unprecedented high affinity. Guided by the structure of the INAD-NORPA complex, we discover that INADL is probably a mammalian counterpart of INAD. The INADL PDZ89 tandem specifically binds to PLCβ4 with a mode that is strikingly similar to that of the INAD-NORPA complex, as revealed by the structure of the INADL PDZ89-PLCβ4 CC-PBM complex. Therefore, our study suggests that the highly specific PDZ tandem - PLCβ interactions are an evolutionarily conserved mechanism in PLCβ signaling in the animal kingdom.
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Affiliation(s)
- Fei Ye
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yuxin Huang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jianchao Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yuqian Ma
- Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chensu Xie
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zexu Liu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoying Deng
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Tian Xue
- Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
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38
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Liu B, Sureda-Gómez M, Zhen Y, Amador V, Reverter D. A quaternary tetramer assembly inhibits the deubiquitinating activity of USP25. Nat Commun 2018; 9:4973. [PMID: 30478318 PMCID: PMC6255862 DOI: 10.1038/s41467-018-07510-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 11/01/2018] [Indexed: 01/13/2023] Open
Abstract
USP25 deubiquitinating enzyme is a key member of the ubiquitin system, which acts as a positive regulator of the Wnt/β-catenin signaling by promoting the deubiquitination and stabilization of tankyrases. USP25 is characterized by the presence of a long insertion in the middle of the conserved catalytic domain. The crystal structure of USP25 displays an unexpected homotetrameric quaternary assembly that is directly involved in the inhibition of its enzymatic activity. The tetramer is assembled by the association of two dimers and includes contacts between the coiled-coil insertion domain and the ubiquitin-binding pocket at the catalytic domain, revealing a distinctive autoinhibitory mechanism. Biochemical and kinetic assays with dimer, tetramer and truncation constructs of USP25 support this mechanism, displaying higher catalytic activity in the dimer assembly. Moreover, the high stabilization of tankyrases in cultured cells by ectopic expression of a constitutive dimer of USP25 supports a biological relevance of this tetramerization/inhibition mechanism. USP25 is a deubiquitinating enzyme and a positive regulator of Wnt/β-catenin signaling. Here the authors present the crystal structure of USP25 in a tetrameric inactive state and their biochemical and kinetic assays support an USP25 autoinhibitory mechanism that is mediated through a dimer to tetramerization transition.
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Affiliation(s)
- Bing Liu
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Dept. de Bioquímica i Biologia Molecular, Serra Hunter Fellow, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Marta Sureda-Gómez
- Institut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona, 08036, Spain
| | - Yang Zhen
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Dept. de Bioquímica i Biologia Molecular, Serra Hunter Fellow, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Virginia Amador
- Institut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona, 08036, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain. .,Dept. de Bioquímica i Biologia Molecular, Serra Hunter Fellow, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
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39
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Pakharukova N, McKenna S, Tuittila M, Paavilainen S, Malmi H, Xu Y, Parilova O, Matthews S, Zavialov AV. Archaic and alternative chaperones preserve pilin folding energy by providing incomplete structural information. J Biol Chem 2018; 293:17070-17080. [PMID: 30228191 DOI: 10.1074/jbc.ra118.004170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/14/2018] [Indexed: 11/06/2022] Open
Abstract
Adhesive pili are external component of fibrous adhesive organelles and help bacteria attach to biotic or abiotic surfaces. The biogenesis of adhesive pili via the chaperone-usher pathway (CUP) is independent of external energy sources. In the classical CUP, chaperones transport assembly-competent pilins in a folded but expanded conformation. During donor-strand exchange, pilins subsequently collapse, producing a tightly packed hydrophobic core and releasing the necessary free energy to drive fiber formation. Here, we show that pilus biogenesis in non-classical, archaic, and alternative CUPs uses a different source of conformational energy. High-resolution structures of the archaic Csu-pili system from Acinetobacter baumannii revealed that non-classical chaperones employ a short donor strand motif that is insufficient to fully complement the pilin fold. This results in chaperone-bound pilins being trapped in a substantially unfolded intermediate. The exchange of this short motif with the longer donor strand from adjacent pilin provides the full steric information essential for folding, and thereby induces a large unfolded-to-folded conformational transition to drive assembly. Our findings may inform the development of anti-adhesion drugs (pilicides) to combat bacterial infections.
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Affiliation(s)
- Natalia Pakharukova
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Sophie McKenna
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Minna Tuittila
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Sari Paavilainen
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Henri Malmi
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Yingqi Xu
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Olena Parilova
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Steve Matthews
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Anton V Zavialov
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
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40
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Persson K, Backman L. Crystallization of Recombinant α-Actinin and Related Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1721:95-103. [PMID: 29423850 DOI: 10.1007/978-1-4939-7546-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
When it comes to crystallization each protein is unique. It can never be predicted beforehand in which condition the particular protein will crystallize or even if it is possible to crystallize. Still, by following some simple checkpoints the chances of obtaining crystals are increased. The primary checkpoints are purity, stability, concentration, and homogeneity. High-quality protein crystals are needed. This protocol will allow an investigator to: clone, express, and crystallize a protein of interest.
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Affiliation(s)
- Karina Persson
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Lars Backman
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.
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41
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Application of the immunoregulatory receptor LILRB1 as a crystallisation chaperone for human class I MHC complexes. J Immunol Methods 2018; 464:47-56. [PMID: 30365927 DOI: 10.1016/j.jim.2018.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/02/2018] [Accepted: 10/22/2018] [Indexed: 12/24/2022]
Abstract
X-ray crystallographic studies of class I peptide-MHC molecules (pMHC) continue to provide important insights into immune recognition, however their success depends on generation of diffraction-quality crystals, which remains a significant challenge. While protein engineering techniques such as surface-entropy reduction and lysine methylation have proven utility in facilitating and/or improving protein crystallisation, they risk affecting the conformation and biochemistry of the class I MHC antigen binding groove. An attractive alternative is the use of noncovalent crystallisation chaperones, however these have not been developed for pMHC. Here we describe a method for promoting class I pMHC crystallisation, by exploiting its natural ligand interaction with the immunoregulatory receptor LILRB1 as a novel crystallisation chaperone. First, focussing on a model HIV-1-derived HLA-A2-restricted peptide, we determined a 2.4 Å HLA-A2/LILRB1 structure, which validated that co-crystallisation with LILRB1 does not alter conformation of the antigenic peptide. We then demonstrated that addition of LILRB1 enhanced the crystallisation of multiple peptide-HLA-A2 complexes, and identified a generic condition for initial co-crystallisation. LILRB1 chaperone-based crystallisation enabled structure determination for HLA-A2 complexes previously intransigent to crystallisation, including both conventional and post-translationally-modified peptides, of diverse lengths. Since both the LILRB1 recognition interface on the HLA-A2 α3 domain molecule and HLA-A2-mediated crystal contacts are predominantly conserved across class I MHC molecules, the approach we outline could prove applicable to a diverse range of class I pMHC. LILRB1 chaperone-mediated crystallisation should expedite molecular insights into the immunobiology of diverse immune-related diseases and immunotherapeutic strategies, particularly involving class I pMHC complexes that are challenging to crystallise.
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42
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Pivovarova Y, Liu J, Lesigang J, Koldyka O, Rauschmeier R, Hu K, Dong G. Structure of a Novel Dimeric SET Domain Methyltransferase that Regulates Cell Motility. J Mol Biol 2018; 430:4209-4229. [PMID: 30148980 PMCID: PMC7141177 DOI: 10.1016/j.jmb.2018.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 11/21/2022]
Abstract
Lysine methyltransferases (KMTs) were initially associated with transcriptional control through their methylation of histones and other nuclear proteins, but have since been found to regulate many other cellular activities. The apical complex lysine (K) methyltransferase (AKMT) of the human parasite Toxoplasma gondii was recently shown to play a critical role in regulating cellular motility. Here we report a 2.1-Å resolution crystal structure of the conserved and functional C-terminal portion (aa289-709) of T. gondii AKMT. AKMT dimerizes via a unique intermolecular interface mediated by the C-terminal tetratricopeptide repeat-like domain together with a specific zinc-binding motif that is absent from all other KMTs. Disruption of AKMT dimerization impaired both its enzyme activity and parasite egress from infected host cells in vivo. Structural comparisons reveal that AKMT is related to the KMTs in the SMYD family, with, however, a number of distinct structural features in addition to the unusual dimerization interface. These features are conserved among the apicomplexan parasites and their free-living relatives, but not found in any known KMTs in animals. AKMT therefore is the founding member of a new subclass of KMT that has important implications for the evolution of the apicomplexans.
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Affiliation(s)
- Yulia Pivovarova
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Jun Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Johannes Lesigang
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | | | - Rene Rauschmeier
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Ke Hu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Gang Dong
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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43
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Wang H, Feng L, Webb GI, Kurgan L, Song J, Lin D. Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity. Brief Bioinform 2018; 19:838-852. [PMID: 28334201 PMCID: PMC6171492 DOI: 10.1093/bib/bbx018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/19/2017] [Indexed: 12/11/2022] Open
Abstract
X-ray crystallography is the main tool for structural determination of proteins. Yet, the underlying crystallization process is costly, has a high attrition rate and involves a series of trial-and-error attempts to obtain diffraction-quality crystals. The Structural Genomics Consortium aims to systematically solve representative structures of major protein-fold classes using primarily high-throughput X-ray crystallography. The attrition rate of these efforts can be improved by selection of proteins that are potentially easier to be crystallized. In this context, bioinformatics approaches have been developed to predict crystallization propensities based on protein sequences. These approaches are used to facilitate prioritization of the most promising target proteins, search for alternative structural orthologues of the target proteins and suggest designs of constructs capable of potentially enhancing the likelihood of successful crystallization. We reviewed and compared nine predictors of protein crystallization propensity. Moreover, we demonstrated that integrating selected outputs from multiple predictors as candidate input features to build the predictive model results in a significantly higher predictive performance when compared to using these predictors individually. Furthermore, we also introduced a new and accurate predictor of protein crystallization propensity, Crysf, which uses functional features extracted from UniProt as inputs. This comprehensive review will assist structural biologists in selecting the most appropriate predictor, and is also beneficial for bioinformaticians to develop a new generation of predictive algorithms.
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Affiliation(s)
- Huilin Wang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, China
| | | | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Australia
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, USA
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Monash University, Australia
| | - Donghai Lin
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, China
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44
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Architecture of the native major royal jelly protein 1 oligomer. Nat Commun 2018; 9:3373. [PMID: 30135511 PMCID: PMC6105727 DOI: 10.1038/s41467-018-05619-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/19/2018] [Indexed: 01/07/2023] Open
Abstract
Honeybee caste development is nutritionally regulated by royal jelly (RJ). Major royal jelly protein 1 (MRJP1), the most abundant glycoprotein among soluble royal jelly proteins, plays pivotal roles in honeybee nutrition and larvae development, and exhibits broad pharmacological activities in humans. However, its structure has long remained unknown. Herein, we identify and report a 16-molecule architecture of native MRJP1 oligomer containing four MRJP1, four apisimin, and eight unanticipated 24-methylenecholesterol molecules at 2.65 Å resolution. MRJP1 has a unique six-bladed β-propeller fold with three disulfide bonds, and it interacts with apisimin mainly by hydrophobic interaction. Every four 24-methylenecholesterol molecules are packaged by two MRJP1 and two apisimin molecules. This assembly dimerizes to form an H-shaped MRJP14-apisimin4-24-methylenecholesterol8 complex via apisimin in a conserved and pH-dependent fashion. Our findings offer a structural basis for understanding the pharmacological effects of MRJPs and 24-methylenecholesterol, and provide insights into their unique physiological roles in bees.
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45
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Fan C, Fan M, Orlando BJ, Fastman NM, Zhang J, Xu Y, Chambers MG, Xu X, Perry K, Liao M, Feng L. X-ray and cryo-EM structures of the mitochondrial calcium uniporter. Nature 2018; 559:575-579. [PMID: 29995856 DOI: 10.1038/s41586-018-0330-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 05/17/2018] [Indexed: 01/01/2023]
Abstract
Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium signalling, and cell death. This uptake is mediated by a highly selective calcium channel called the mitochondrial calcium uniporter (MCU). Here, we determined the structures of the pore-forming MCU proteins from two fungi by X-ray crystallography and single-particle cryo-electron microscopy. The stoichiometry, overall architecture, and individual subunit structure differed markedly from those described in the recent nuclear magnetic resonance structure of Caenorhabditis elegans MCU. We observed a dimer-of-dimer architecture across species and chemical environments, which was corroborated by biochemical experiments. Structural analyses and functional characterization uncovered the roles of key residues in the pore. These results reveal a new ion channel architecture, provide insights into calcium coordination, selectivity and conduction, and establish a structural framework for understanding the mechanism of mitochondrial calcium uniporter function.
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Affiliation(s)
- Chao Fan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Minrui Fan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Nathan M Fastman
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Biophysics Program, Stanford University, Stanford, CA, USA
| | - Jinru Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yan Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Xiaofang Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Kay Perry
- NE-CAT and Dept. of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,Biophysics Program, Stanford University, Stanford, CA, USA.
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46
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Kubitza C, Ginsel C, Bittner F, Havemeyer A, Clement B, Scheidig AJ. T4 lysozyme-facilitated crystallization of the human molybdenum cofactor-dependent enzyme mARC. Acta Crystallogr F Struct Biol Commun 2018; 74:337-344. [PMID: 29870017 PMCID: PMC5987741 DOI: 10.1107/s2053230x18006921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/04/2018] [Indexed: 12/12/2022] Open
Abstract
The human mitochondrial amidoxime reducing component (hmARC) is a molybdenum cofactor-dependent enzyme that is involved in the reduction of a diverse range of N-hydroxylated compounds of either physiological or xenobiotic origin. In this study, the use of a fusion-protein approach with T4 lysozyme (T4L) to determine the structure of this hitherto noncrystallizable enzyme by X-ray crystallography is described. A set of four different hmARC-T4L fusion proteins were designed. Two of them contained either an N-terminal or a C-terminal T4L moiety fused to hmARC, while the other two contained T4L as an internal fusion partner tethered to the hmARC enzyme between two predicted secondary-structure elements. One of these internal fusion constructs could be expressed and crystallized successfully. The hmARC-T4L crystals diffracted to 1.7 Å resolution using synchrotron radiation and belonged to space group P212121 with one molecule in the asymmetric unit. Initial attempts to solve the structure by molecular replacement using T4L did not result in electron-density distributions that were sufficient for model building and interpretation of the hmARC moiety. However, this study emphasizes the utility of the T4L fusion-protein approach, which can be used for the crystallization and structure determination of membrane-bound proteins as well as soluble proteins.
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Affiliation(s)
- Christian Kubitza
- Structural Biology, Zoological Institute, Kiel University, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Carsten Ginsel
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Florian Bittner
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Antje Havemeyer
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Bernd Clement
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Axel J. Scheidig
- Structural Biology, Zoological Institute, Kiel University, Am Botanischen Garten 1–9, 24118 Kiel, Germany
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47
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Cossé MM, Barta ML, Fisher DJ, Oesterlin LK, Niragire B, Perrinet S, Millot GA, Hefty PS, Subtil A. The Loss of Expression of a Single Type 3 Effector (CT622) Strongly Reduces Chlamydia trachomatis Infectivity and Growth. Front Cell Infect Microbiol 2018; 8:145. [PMID: 29868501 PMCID: PMC5962693 DOI: 10.3389/fcimb.2018.00145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/20/2018] [Indexed: 12/20/2022] Open
Abstract
Invasion of epithelial cells by the obligate intracellular bacterium Chlamydia trachomatis results in its enclosure inside a membrane-bound compartment termed an inclusion. The bacterium quickly begins manipulating interactions between host intracellular trafficking and the inclusion interface, diverging from the endocytic pathway and escaping lysosomal fusion. We have identified a previously uncharacterized protein, CT622, unique to the Chlamydiaceae, in the absence of which most bacteria failed to establish a successful infection. CT622 is abundant in the infectious form of the bacteria, in which it associates with CT635, a putative novel chaperone protein. We show that CT622 is translocated into the host cytoplasm via type three secretion throughout the developmental cycle of the bacteria. Two separate domains of roughly equal size have been identified within CT622 and a 1.9 Å crystal structure of the C-terminal domain has been determined. Genetic disruption of ct622 expression resulted in a strong bacterial growth defect, which was due to deficiencies in proliferation and in the generation of infectious bacteria. Our results converge to identify CT622 as a secreted protein that plays multiple and crucial roles in the initiation and support of the C. trachomatis growth cycle. They reveal that genetic disruption of a single effector can deeply affect bacterial fitness.
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Affiliation(s)
- Mathilde M Cossé
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Michael L Barta
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Derek J Fisher
- Department of Microbiology, Southern Illinois University, Carbondale, IL, United States
| | - Lena K Oesterlin
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique UMR 144, Molecular Mechanisms of Intracellular Transport, Paris, France
| | - Béatrice Niragire
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France
| | - Stéphanie Perrinet
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France
| | - Gaël A Millot
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR3756 IP Centre National de la Recherche Scientifique, Paris, France
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Agathe Subtil
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France
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48
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Bräuning B, Bertosin E, Praetorius F, Ihling C, Schatt A, Adler A, Richter K, Sinz A, Dietz H, Groll M. Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. Nat Commun 2018; 9:1806. [PMID: 29728606 PMCID: PMC5935710 DOI: 10.1038/s41467-018-04139-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 04/02/2018] [Indexed: 01/30/2023] Open
Abstract
Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA-YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures.
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Affiliation(s)
- Bastian Bräuning
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Chair of Biochemistry, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany.
| | - Eva Bertosin
- Center for Integrated Protein Science Munich (CIPSM), Department of Physics, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Florian Praetorius
- Center for Integrated Protein Science Munich (CIPSM), Department of Physics, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Christian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str.4, 06120, Halle/Saale, Germany
| | - Alexandra Schatt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str.4, 06120, Halle/Saale, Germany
| | - Agnes Adler
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Chair of Biochemistry, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Klaus Richter
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Chair of Biotechnology, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str.4, 06120, Halle/Saale, Germany
| | - Hendrik Dietz
- Center for Integrated Protein Science Munich (CIPSM), Department of Physics, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Chair of Biochemistry, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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49
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Crystal Structure of NisI in a Lipid-Free Form, the Nisin Immunity Protein, from Lactococcus lactis. Antimicrob Agents Chemother 2018; 62:AAC.01966-17. [PMID: 29311076 DOI: 10.1128/aac.01966-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/18/2017] [Indexed: 11/20/2022] Open
Abstract
Nisin is a lantibiotic, a member of a family of polypeptides containing lanthionine with antimicrobial activity. Nisin-producing microorganisms require immunity proteins for self-protection from nisin itself. Lactococcus lactis, a microorganism that synthesizes nisin, has an integral NisFEG ABC transporter and an NisI lipoprotein that function in nisin immunity. Here, we present the crystal structure of the full length of NisI22-C, a lipid-free form of NisI, determined at 1.9-Å resolution. As with the nuclear magnetic resonance (NMR) structures of the N- and C-terminal domains of NisI, NisI22-C is composed of N- and C-terminal domains, both of which display a fold similar to that found in SpaI, a lipoprotein with immunity against subtilin in Bacillus subtilis The full-length structure of NisI22-c reveals a large, deep cleft by the interdomain association, one side of which is occupied by the residues important for immunity. Opposite the cleft, a shallow groove is found where nisin-interacting residues are distributed in the periphery composed of the C-terminal negative patch. Based on a sulfate ion found in the large and deep cleft, a model of NisI in complex with a farnesyl diphosphate backbone of lipid II is proposed, suggesting a mechanism for increasing the chances of encountering nisin.
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50
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Kim HT, Na BK, Chung J, Kim S, Kwon SK, Cha H, Son J, Cho JM, Hwang KY. Structural Basis for Inhibitor-Induced Hydrogen Peroxide Production by Kynurenine 3-Monooxygenase. Cell Chem Biol 2018; 25:426-438.e4. [PMID: 29429898 DOI: 10.1016/j.chembiol.2018.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/17/2017] [Accepted: 01/08/2018] [Indexed: 11/18/2022]
Abstract
Kynurenine 3-monooxygenase (KMO) inhibitors have been developed for the treatment of neurodegenerative disorders. The mechanisms of flavin reduction and hydrogen peroxide production by KMO inhibitors are unknown. Herein, we report the structure of human KMO and crystal structures of Saccharomyces cerevisiae (sc) and Pseudomonas fluorescens (pf) KMO with Ro 61-8048. Proton transfer in the hydrogen bond network triggers flavin reduction in p-hydroxybenzoate hydroxylase, but the mechanism triggering flavin reduction in KMO is different. Conformational changes via π-π interactions between the loop above the flavin and substrate or non-substrate effectors lead to disorder of the C-terminal α helix in scKMO and shifts of domain III in pfKMO, stimulating flavin reduction. Interestingly, Ro 61-8048 has two different binding modes. It acts as a competitive inhibitor in scKMO and as a non-substrate effector in pfKMO. These findings provide understanding of the catalytic cycle of KMO and insight for structure-based drug design of KMO inhibitors.
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Affiliation(s)
- Hyun Tae Kim
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Byeong Kwan Na
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Jiwoung Chung
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Sool Ki Kwon
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Hyunju Cha
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Jonghyeon Son
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Joong Myung Cho
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea.
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea.
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