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Zhu Y, Hager KM, Manjari SR, Banavali NK, Chaturvedi V, Chaturvedi S. Development and Validation of TaqMan Chemistry Probe-Based Rapid Assay for the Detection of Echinocandin-Resistance in Candida auris. J Clin Microbiol 2023; 61:e0176722. [PMID: 36975998 PMCID: PMC10117040 DOI: 10.1128/jcm.01767-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/14/2023] [Indexed: 03/29/2023] Open
Abstract
Candida auris is a multidrug-resistant yeast pathogen causing outbreaks in health care facilities worldwide, and the emergence of echinocandin-resistant C. auris is a concern. Currently used Clinical and Laboratory Standards Institute (CLSI) and commercial antifungal susceptibility tests (AFST) are phenotype-based, slow, and not scalable, limiting their effectiveness in the surveillance of echinocandin-resistant C. auris. The urgent need for accurate and rapid methods of assessment of echinocandin resistance cannot be overstated, as this class of antifungal drugs is preferred for patient management. We report the development and validation of a TaqMan chemistry probe-based fluorescence melt curve analysis (FMCA) following asymmetric polymerase chain reaction (PCR) to assess mutations within the hot spot one (HS1) region of FKS1, the gene responsible for encoding 1,3-β-d-glucan synthase that is a target for echinocandins. The assay correctly identified F635C, F635Y, F635del, F635S, S639F or S639Y, S639P, and D642H/R645T mutations. Of these mutations, F635S and D642H/R645T were not involved in echinocandin resistance, while the rest were, as confirmed by AFST. Of 31 clinical cases, the predominant mutation conferring echinocandin resistance was S639F/Y (20 cases) followed by S639P (4 cases), F635del (4 cases), F635Y (2 cases), and F635C (1 case). The FMCA assay was highly specific and did not cross-react with closely and distantly related Candida and other yeast and mold species. Structural modeling of the Fks1 protein, its mutants, and docked conformations of three echinocandin drugs suggest a plausible Fks1 binding orientation for echinocandins. These findings lay the groundwork for future evaluations of additional FKS1 mutations and their impact on the development of drug resistance. The TaqMan chemistry probe-based FMCA would allow rapid, high throughput, and accurate detection of FKS1 mutations conferring echinocandin resistance in C. auris.
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Affiliation(s)
- YanChun Zhu
- Mycology Laboratory, Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kelli M. Hager
- Mycology Laboratory, Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Swati R. Manjari
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Nilesh K. Banavali
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - Vishnu Chaturvedi
- Westchester Medical Center, New York Medical College, Valhalla, New York, USA
| | - Sudha Chaturvedi
- Mycology Laboratory, Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
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Irumagawa S, Kobayashi K, Saito Y, Miyata T, Umetsu M, Kameda T, Arai R. Rational thermostabilisation of four-helix bundle dimeric de novo proteins. Sci Rep 2021; 11:7526. [PMID: 33824364 PMCID: PMC8024369 DOI: 10.1038/s41598-021-86952-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/22/2021] [Indexed: 11/29/2022] Open
Abstract
The stability of proteins is an important factor for industrial and medical applications. Improving protein stability is one of the main subjects in protein engineering. In a previous study, we improved the stability of a four-helix bundle dimeric de novo protein (WA20) by five mutations. The stabilised mutant (H26L/G28S/N34L/V71L/E78L, SUWA) showed an extremely high denaturation midpoint temperature (Tm). Although SUWA is a remarkably hyperstable protein, in protein design and engineering, it is an attractive challenge to rationally explore more stable mutants. In this study, we predicted stabilising mutations of WA20 by in silico saturation mutagenesis and molecular dynamics simulation, and experimentally confirmed three stabilising mutations of WA20 (N22A, N22E, and H86K). The stability of a double mutant (N22A/H86K, rationally optimised WA20, ROWA) was greatly improved compared with WA20 (ΔTm = 10.6 °C). The model structures suggested that N22A enhances the stability of the α-helices and N22E and H86K contribute to salt-bridge formation for protein stabilisation. These mutations were also added to SUWA and improved its Tm. Remarkably, the most stable mutant of SUWA (N22E/H86K, rationally optimised SUWA, ROSA) showed the highest Tm (129.0 °C). These new thermostable mutants will be useful as a component of protein nanobuilding blocks to construct supramolecular protein complexes.
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Affiliation(s)
- Shin Irumagawa
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano, 390-8621, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan
| | - Kaito Kobayashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
| | - Yutaka Saito
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, 169-8555, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Takeshi Miyata
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
| | - Ryoichi Arai
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan.
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano, 390-8621, Japan.
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan.
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Catapano MC, Parsons DS, Kotuniak R, Mladěnka P, Bal W, Maret W. Probing the Structure and Function of the Cytosolic Domain of the Human Zinc Transporter ZnT8 with Nickel(II) Ions. Int J Mol Sci 2021; 22:2940. [PMID: 33799326 PMCID: PMC8000985 DOI: 10.3390/ijms22062940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/30/2022] Open
Abstract
The human zinc transporter ZnT8 provides the granules of pancreatic β-cells with zinc (II) ions for assembly of insulin hexamers for storage. Until recently, the structure and function of human ZnTs have been modelled on the basis of the 3D structures of bacterial zinc exporters, which form homodimers with each monomer having six transmembrane α-helices harbouring the zinc transport site and a cytosolic domain with an α,β structure and additional zinc-binding sites. However, there are important differences in function as the bacterial proteins export an excess of zinc ions from the bacterial cytoplasm, whereas ZnT8 exports zinc ions into subcellular vesicles when there is no apparent excess of cytosolic zinc ions. Indeed, recent structural investigations of human ZnT8 show differences in metal binding in the cytosolic domain when compared to the bacterial proteins. Two common variants, one with tryptophan (W) and the other with arginine (R) at position 325, have generated considerable interest as the R-variant is associated with a higher risk of developing type 2 diabetes. Since the mutation is at the apex of the cytosolic domain facing towards the cytosol, it is not clear how it can affect zinc transport through the transmembrane domain. We expressed the cytosolic domain of both variants of human ZnT8 and have begun structural and functional studies. We found that (i) the metal binding of the human protein is different from that of the bacterial proteins, (ii) the human protein has a C-terminal extension with three cysteine residues that bind a zinc(II) ion, and (iii) there are small differences in stability between the two variants. In this investigation, we employed nickel(II) ions as a probe for the spectroscopically silent Zn(II) ions and utilised colorimetric and fluorimetric indicators for Ni(II) ions to investigate metal binding. We established Ni(II) coordination to the C-terminal cysteines and found differences in metal affinity and coordination in the two ZnT8 variants. These structural differences are thought to be critical for the functional differences regarding the diabetes risk. Further insight into the assembly of the metal centres in the cytosolic domain was gained from potentiometric investigations of zinc binding to synthetic peptides corresponding to N-terminal and C-terminal sequences of ZnT8 bearing the metal-coordinating ligands. Our work suggests the involvement of the C-terminal cysteines, which are part of the cytosolic domain, in a metal chelation and/or acquisition mechanism and, as now supported by the high-resolution structural work, provides the first example of metal-thiolate coordination chemistry in zinc transporters.
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Affiliation(s)
- Maria Carmen Catapano
- Departments of Biochemistry and Nutritional Sciences, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King’s College London, Franklin-Wilkins Bldg, 150 Stamford St., London SE1 9NH, UK; (M.C.C.); (D.S.P.)
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Douglas S. Parsons
- Departments of Biochemistry and Nutritional Sciences, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King’s College London, Franklin-Wilkins Bldg, 150 Stamford St., London SE1 9NH, UK; (M.C.C.); (D.S.P.)
- Department of Radiology, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - Radosław Kotuniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (R.K.); (W.B.)
| | - Přemysl Mladěnka
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic;
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (R.K.); (W.B.)
| | - Wolfgang Maret
- Departments of Biochemistry and Nutritional Sciences, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King’s College London, Franklin-Wilkins Bldg, 150 Stamford St., London SE1 9NH, UK; (M.C.C.); (D.S.P.)
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Kastano K, Mier P, Andrade-Navarro MA. The Role of Low Complexity Regions in Protein Interaction Modes: An Illustration in Huntingtin. Int J Mol Sci 2021; 22:1727. [PMID: 33572172 PMCID: PMC7915032 DOI: 10.3390/ijms22041727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
Low complexity regions (LCRs) are very frequent in protein sequences, generally having a lower propensity to form structured domains and tending to be much less evolutionarily conserved than globular domains. Their higher abundance in eukaryotes and in species with more cellular types agrees with a growing number of reports on their function in protein interactions regulated by post-translational modifications. LCRs facilitate the increase of regulatory and network complexity required with the emergence of organisms with more complex tissue distribution and development. Although the low conservation and structural flexibility of LCRs complicate their study, evolutionary studies of proteins across species have been used to evaluate their significance and function. To investigate how to apply this evolutionary approach to the study of LCR function in protein-protein interactions, we performed a detailed analysis for Huntingtin (HTT), a large protein that is a hub for interaction with hundreds of proteins, has a variety of LCRs, and for which partial structural information (in complex with HAP40) is available. We hypothesize that proteins RASA1, SYN2, and KAT2B may compete with HAP40 for their attachment to the core of HTT using similar LCRs. Our results illustrate how evolution might favor the interplay of LCRs with domains, and the possibility of detecting multiple modes of LCR-mediated protein-protein interactions with a large hub such as HTT when enough protein interaction data is available.
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Affiliation(s)
| | | | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany; (K.K.); (P.M.)
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Szała-Mendyk B, Molski A. Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study. Biomolecules 2020; 10:biom10101362. [PMID: 32987720 PMCID: PMC7598727 DOI: 10.3390/biom10101362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/02/2022] Open
Abstract
The precise kinetic pathways of peptide clustering and fibril formation are not fully understood. Here we study the initial clustering kinetics and transient cluster morphologies during aggregation of the heptapeptide fragment GNNQQNY from the yeast prion protein Sup35. We use a mid-resolution coarse-grained molecular dynamics model of Bereau and Deserno to explore the aggregation pathways from the initial random distribution of free monomers to the formation of large clusters. By increasing the system size to 72 peptides we could follow directly the molecular events leading to the formation of stable fibril-like structures. To quantify those structures we developed a new cluster helicity parameter. We found that the formation of fibril-like structures is a cooperative processes that requires a critical number of monomers, M⋆≈25, in a cluster. The terminal tyrosine residue is the structural determinant in the formation of helical fibril-like structures. This work supports and quantifies the two-step aggregation model where the initially formed amorphous clusters grow and, when they are large enough, rearrange into mature twisted structures. However, in addition to the nucleated fibrillation, growing aggregates undergo further internal reorganization, which leads to more compact structures of large aggregates.
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Zhang J, Teramoto T, Qiu C, Wine RN, Gonzalez LE, Baserga SJ, Tanaka Hall TM. Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA. RNA 2020; 26:1049-1059. [PMID: 32371454 PMCID: PMC7373996 DOI: 10.1261/rna.075416.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/29/2020] [Indexed: 05/04/2023]
Abstract
Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA-Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.
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Affiliation(s)
- Jun Zhang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Takamasa Teramoto
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Lauren E Gonzalez
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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Wen H, Geng Z, Gao Z, She Z, Dong Y. Characterization of the Pseudomonas aeruginosa T6SS PldB immunity proteins PA5086, PA5087 and PA5088 explains a novel stockpiling mechanism. Acta Crystallogr F Struct Biol Commun 2020; 76:222-227. [PMID: 32356524 PMCID: PMC7193511 DOI: 10.1107/s2053230x2000566x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/22/2020] [Indexed: 11/10/2022] Open
Abstract
The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic and eukaryotic cells. Three proteins, PA5086, PA5087 and PA5088, are employed to suppress the toxicity of PldB-family proteins. The structures of PA5087 and PA5088 have previously been reported, but the identification of further distinctions between these immunity proteins is needed. Here, the crystal structure of PA5086 is reported at 1.90 Å resolution. A structural comparison of the three PldB immunity proteins showed vast divergences in their electrostatic potential surfaces. This interesting phenomenon provides an explanation of the stockpiling mechanism of T6SS immunity proteins.
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Affiliation(s)
- Haiying Wen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Zhi Geng
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Zengqiang Gao
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Zhun She
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Yuhui Dong
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
- University of Chinese Academy of Sciences, People’s Republic of China
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Zhou J, Gao Z, Zhang H, Dong Y. Crystal structure of the nucleoid-associated protein Fis (PA4853) from Pseudomonas aeruginosa. Acta Crystallogr F Struct Biol Commun 2020; 76:209-215. [PMID: 32356522 PMCID: PMC7193516 DOI: 10.1107/s2053230x20005427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/18/2020] [Indexed: 11/10/2022] Open
Abstract
Factor for inversion stimulation (Fis) is a versatile bacterial nucleoid-associated protein that can directly bind and bend DNA to influence DNA topology. It also plays crucial roles in regulating bacterial virulence factors and in optimizing bacterial adaptation to various environments. Fis from Pseudomonas aeruginosa (PA4853, referred to as PaFis) has recently been found to be required for virulence by regulating the expression of type III secretion system (T3SS) genes. PaFis can specifically bind to the promoter region of exsA, which functions as a T3SS master regulator, to regulate its expression and plays an essential role in transcription elongation from exsB to exsA. Here, the crystal structure of PaFis, which is composed of a four-helix bundle and forms a homodimer, is reported. PaFis shows remarkable structural similarities to the well studied Escherichia coli Fis (EcFis), including an N-terminal flexible loop and a C-terminal helix-turn-helix (HTH) motif. However, the critical residues for Hin-catalyzed DNA inversion in the N-terminal loop of EcFis are not conserved in PaFis and further studies are required to investigate its exact role. A gel-electrophoresis mobility-shift assay showed that PaFis can efficiently bind to the promoter region of exsA. Structure-based mutagenesis revealed that several conserved basic residues in the HTH motif play essential roles in DNA binding. These structural and biochemical studies may help in understanding the role of PaFis in the regulation of T3SS expression and in virulence.
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Affiliation(s)
- Juan Zhou
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, People’s Republic of China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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Satoh T, Nishio M, Suzuki K, Yagi-Utsumi M, Kamiya Y, Mizushima T, Kato K. Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport. Acta Crystallogr F Struct Biol Commun 2020; 76:216-221. [PMID: 32356523 PMCID: PMC7193514 DOI: 10.1107/s2053230x20005452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/19/2020] [Indexed: 11/10/2022] Open
Abstract
The transmembrane intracellular lectin ER-Golgi intermediate compartment protein 53 (ERGIC-53) and the soluble EF-hand multiple coagulation factor deficiency protein 2 (MCFD2) form a complex that functions as a cargo receptor, trafficking various glycoproteins between the endoplasmic reticulum (ER) and the Golgi apparatus. It has been demonstrated that the carbohydrate-recognition domain (CRD) of ERGIC-53 (ERGIC-53CRD) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53CRD complexed with MCFD2 and mannosyl oligosaccharides have revealed protein-protein and protein-sugar binding modes. In contrast, the polypeptide-recognition mechanism of MCFD2 remains largely unknown. Here, a 1.60 Å resolution crystal structure of the ERGIC-53CRD-MCFD2 complex is reported, along with three other crystal forms. Comparison of these structures with those previously reported reveal that MCFD2, but not ERGIC-53-CRD, exhibits significant conformational plasticity that may be relevant to its accommodation of various polypeptide ligands.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Miho Nishio
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Kousuke Suzuki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Yukiko Kamiya
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Tsunehiro Mizushima
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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Abstract
The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ∼10-nm-diameter "L" and "V" shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.
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Affiliation(s)
- T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
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11
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Zhang M, Huang C, Wang Z, Lv H, Li X. In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract. BMC Mol Cell Biol 2020; 21:12. [PMID: 32143568 PMCID: PMC7060521 DOI: 10.1186/s12860-020-00252-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gap junction protein alpha 3 (GJA3), an important pathogenic gene of congenital cataracts, encodes the transmembrane protein connexin46, which functions as an intercellular channel for voltage and chemical gating by forming dodecamers. This study systematically collected nsSNP information for the GJA3 gene from SNP databases and literature and screened for nsSNPs with high risks of pathogenicity. RESULTS A total of 379 nsSNPs of GJA3 were identified. A total of 88 high-risk pathogenic GJA3 nsSNPs were found, including 31 published nsSNPs associated with congenital cataracts and 57 novel nsSNPs predicted by all eight online tools. The 88 high-risk pathogenic mutations, which are related to 67 amino acids in the wild-type sequences, cause a decrease in protein stability according to I-Mutant 3.0, MUpro and INPS. G2 and R33 were predicted to participate in post-translational modification and ligand binding by ModPred, RaptorX Binding and COACH. Additionally, high-risk mutations were likely to involve highly conserved sites, random coils, alpha helixes, and extracellular loops and were accompanied by changes in amino acid size, charge, hydrophobicity and spatial structure. CONCLUSIONS Eighty-eight high-risk pathogenic nsSNPs of GJA3 were screened out in the study, 57 of which were newly reported. The combination of multiple in silico tools is highly efficient for targeting pathogenic sites.
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Affiliation(s)
- Mingzhou Zhang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Chen Huang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
- Medical Research Center, Peking University Third Hospital, Beijing, China
| | - Zhenyu Wang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Huibin Lv
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xuemin Li
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China.
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12
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Abstract
Tooth agenesis is one of the most common developmental anomalies in humans and can affect dental occlusion and speech pronunciation. Research has identified an association between mutations in MSX1, PAX9, EDA, AXIN2, WNT10A, WNT10B and LRP6 and human tooth agenesis. Two unrelated individuals with non-syndromic tooth agenesis and their families were enrolled in this study. Using Sanger sequencing of the candidate genes, we identified two novel mutations: a missense mutation c.572 T>C and a frameshift mutation c.590_594 dup TGTCC, which were both detected in the homeodomain of MSX1. After identifying the mutations, structural modeling and bioinformatics analysis were used to predict the resulting conformational changes in the MSX1 homeodomain. Combined with 3D-structural analysis of other MSX1 mutations, we propose that there is a correlation between the observed phenotypes and alterations in hydrogen bond formation, thereby potentially affecting protein binding.
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Affiliation(s)
- Le Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei Province, China
| | - Jia Liang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei Province, China
| | - Haitang Yue
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei Province, China
| | - Zhuan Bian
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei Province, China
- * E-mail:
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13
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Lin Y, Sahoo BR, Ozawa D, Kinoshita M, Kang J, Lim MH, Okumura M, Huh YH, Moon E, Jang JH, Lee HJ, Ryu KY, Ham S, Won HS, Ryu KS, Sugiki T, Bang JK, Hoe HS, Fujiwara T, Ramamoorthy A, Lee YH. Diverse Structural Conversion and Aggregation Pathways of Alzheimer's Amyloid-β (1-40). ACS Nano 2019; 13:8766-8783. [PMID: 31310506 DOI: 10.1021/acsnano.9b01578] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Complex amyloid aggregation of amyloid-β (1-40) (Aβ1-40) in terms of monomer structures has not been fully understood. Herein, we report the microscopic mechanism and pathways of Aβ1-40 aggregation with macroscopic viewpoints through tuning its initial structure and solubility. Partial helical structures of Aβ1-40 induced by low solvent polarity accelerated cytotoxic Aβ1-40 amyloid fibrillation, while predominantly helical folds did not aggregate. Changes in the solvent polarity caused a rapid formation of β-structure-rich protofibrils or oligomers via aggregation-prone helical structures. Modulation of the pH and salt concentration transformed oligomers to protofibrils, which proceeded to amyloid formation. We reveal diverse molecular mechanisms underlying Aβ1-40 aggregation with conceptual energy diagrams and propose that aggregation-prone partial helical structures are key to inducing amyloidogenesis. We demonstrate that context-dependent protein aggregation is comprehensively understood using the macroscopic phase diagram, which provides general insights into differentiation of amyloid formation and phase separation from unfolded and folded structures.
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Affiliation(s)
- Yuxi Lin
- Department of Chemistry , Sookmyung Women's University , Cheongpa-ro 47-gil 100 , Yongsan-gu, Seoul 04310 , South Korea
| | - Bikash R Sahoo
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Daisaku Ozawa
- Department of Neurotherapeutics , Osaka University Graduate School of Medicine , 2-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Misaki Kinoshita
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8578 , Japan
| | - Juhye Kang
- Department of Chemistry , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea
- Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , South Korea
| | - Mi Hee Lim
- Department of Chemistry , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8578 , Japan
| | | | | | | | - Hyun-Ju Lee
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Ka-Young Ryu
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Sihyun Ham
- Department of Chemistry , Sookmyung Women's University , Cheongpa-ro 47-gil 100 , Yongsan-gu, Seoul 04310 , South Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute and College of Biomedical and Health Science , Konkuk University , Chungju , Chungbuk 27478 , South Korea
| | | | - Toshihiko Sugiki
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | | | - Hyang-Sook Hoe
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Toshimichi Fujiwara
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Young-Ho Lee
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
- Bio-Analytical Science , University of Science and Technology , Daejeon 34113 , South Korea
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14
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Topacio BR, Zatulovskiy E, Cristea S, Xie S, Tambo CS, Rubin SM, Sage J, Kõivomägi M, Skotheim JM. Cyclin D-Cdk4,6 Drives Cell-Cycle Progression via the Retinoblastoma Protein's C-Terminal Helix. Mol Cell 2019; 74:758-770.e4. [PMID: 30982746 PMCID: PMC6800134 DOI: 10.1016/j.molcel.2019.03.020] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 02/01/2019] [Accepted: 03/19/2019] [Indexed: 01/10/2023]
Abstract
The cyclin-dependent kinases Cdk4 and Cdk6 form complexes with D-type cyclins to drive cell proliferation. A well-known target of cyclin D-Cdk4,6 is the retinoblastoma protein Rb, which inhibits cell-cycle progression until its inactivation by phosphorylation. However, the role of Rb phosphorylation by cyclin D-Cdk4,6 in cell-cycle progression is unclear because Rb can be phosphorylated by other cyclin-Cdks, and cyclin D-Cdk4,6 has other targets involved in cell division. Here, we show that cyclin D-Cdk4,6 docks one side of an alpha-helix in the Rb C terminus, which is not recognized by cyclins E, A, and B. This helix-based docking mechanism is shared by the p107 and p130 Rb-family members across metazoans. Mutation of the Rb C-terminal helix prevents its phosphorylation, promotes G1 arrest, and enhances Rb's tumor suppressive function. Our work conclusively demonstrates that the cyclin D-Rb interaction drives cell division and expands the diversity of known cyclin-based protein docking mechanisms.
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Affiliation(s)
| | | | - Sandra Cristea
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shicong Xie
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Carrie S Tambo
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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15
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Semenyshyn R, Hentschel M, Stanglmair C, Teutsch T, Tarin C, Pacholski C, Giessen H, Neubrech F. In Vitro Monitoring Conformational Changes of Polypeptide Monolayers Using Infrared Plasmonic Nanoantennas. Nano Lett 2019; 19:1-7. [PMID: 30071729 DOI: 10.1021/acs.nanolett.8b02372] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Proteins and peptides play a predominant role in biochemical reactions of living cells. In these complex environments, not only the constitution of the molecules but also their three-dimensional configuration defines their functionality. This so-called secondary structure of proteins is crucial for understanding their function in living matter. Misfolding, for example, is suspected as the cause of neurodegenerative diseases such as Alzheimer's and Parkinson's disease. Ultimately, it is necessary to study a single protein and its folding dynamics. Here, we report a first step in this direction, namely ultrasensitive detection and discrimination of in vitro polypeptide folding and unfolding processes using resonant plasmonic nanoantennas for surface-enhanced vibrational spectroscopy. We utilize poly-l-lysine as a model system which has been functionalized on the gold surface. By in vitro infrared spectroscopy of a single molecular monolayer at the amide I vibrations we directly monitor the reversible conformational changes between α-helix and β-sheet states induced by controlled external chemical stimuli. Our scheme in combination with advanced positioning of the peptides and proteins and more brilliant light sources is highly promising for ultrasensitive in vitro studies down to the single protein level.
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Affiliation(s)
- Rostyslav Semenyshyn
- 4th Physics Institute and Research Center SCoPE , University of Stuttgart , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
- Center for Integrated Quantum Science and Technology , IQST , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
| | - Mario Hentschel
- 4th Physics Institute and Research Center SCoPE , University of Stuttgart , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
- Center for Integrated Quantum Science and Technology , IQST , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
| | - Christoph Stanglmair
- Max Planck Institute for Intelligent Systems, Heisenbergstraße 1 , 70569 Stuttgart , Germany
| | - Tanja Teutsch
- Institute for System Dynamics , University of Stuttgart , Waldburgstraße 17/19 , 70563 Stuttgart , Germany
| | - Cristina Tarin
- Institute for System Dynamics , University of Stuttgart , Waldburgstraße 17/19 , 70563 Stuttgart , Germany
| | - Claudia Pacholski
- Max Planck Institute for Intelligent Systems, Heisenbergstraße 1 , 70569 Stuttgart , Germany
- Institute of Chemistry , University of Potsdam , Am Mühlenberg 3 , 14476 Potsdam OT Golm , Germany
| | - Harald Giessen
- 4th Physics Institute and Research Center SCoPE , University of Stuttgart , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
- Center for Integrated Quantum Science and Technology , IQST , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
| | - Frank Neubrech
- 4th Physics Institute and Research Center SCoPE , University of Stuttgart , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
- Kirchhoff Institute for Physics , University of Heidelberg , Im Neuenheimer Feld 227 , 69120 Heidelberg , Germany
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16
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Khounlo R, Hawk BJ, Shin YK. EPR Lineshape Analysis to Investigate the SNARE Folding Intermediates. Methods Mol Biol 2019; 1860:33-51. [PMID: 30317497 PMCID: PMC6429964 DOI: 10.1007/978-1-4939-8760-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
SNARE complex formation, which is believed to drive intracellular membrane fusion, transits through multiple conformational states along the membrane fusion pathway. The SNARE intermediates are biologically important because they serve as targets for fusion regulators and clostridial neurotoxins. Spin-labeling EPR has contributed significantly to the understanding of the structures and the dynamics of SNARE intermediates. In particular, the EPR lineshape analysis, which is highly sensitive to protein conformational changes such as the local coil-to-helix transition, has revealed the sequential compacting steps leading to formation of the highly stable four-helix bundle.
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Affiliation(s)
- Ryan Khounlo
- Iowa State University, Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, 4138 Molecular Biology Building, 2437 Pammel Dr, Ames, IA 50011,
| | - Brenden J.D. Hawk
- Iowa State University, Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, 4138 Molecular Biology Building, 2437 Pammel Dr, Ames, IA 50011,
| | - Yeon-Kyun Shin
- Iowa State University, Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, 4152 Molecular Biology Building, 2437 Pammel Dr, Ames, IA 50011,
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17
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Thirumal Kumar D, Jerushah Emerald L, George Priya Doss C, Sneha P, Siva R, Charles Emmanuel Jebaraj W, Zayed H. Computational approach to unravel the impact of missense mutations of proteins (D2HGDH and IDH2) causing D-2-hydroxyglutaric aciduria 2. Metab Brain Dis 2018; 33:1699-1710. [PMID: 29987523 DOI: 10.1007/s11011-018-0278-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/20/2018] [Indexed: 01/28/2023]
Abstract
The 2-hydroxyglutaric aciduria (2-HGA) is a rare neurometabolic disorder that leads to the development of brain damage. It is classified into three categories: D-2-HGA, L-2-HGA, and combined D,L-2-HGA. The D-2-HGA includes two subtypes: type I and type II caused by the mutations in D2HGDH and IDH2 proteins, respectively. In this study, we studied six mutations, four in the D2HGDH (I147S, D375Y, N439D, and V444A) and two in the IDH2 proteins (R140G, R140Q). We performed in silico analysis to investigate the pathogenicity and stability changes of the mutant proteins using pathogenicity (PANTHER, PhD-SNP, SIFT, SNAP, and META-SNP) and stability (i-Mutant, MUpro, and iStable) predictors. All the mutations of both D2HGDH and IDH2 proteins were predicted as disease causing except V444A, which was predicted as neutral by SIFT. All the mutants were also predicted to be destabilizing the protein except the mutants D375Y and N439D. DSSP plugin of the PyMOL and Molecular Dynamics Simulations (MDS) were used to study the structural changes in the mutant proteins. In the case of D2HGDH protein, the mutations I147S and V444A that are positioned in the beta sheet region exhibited higher Root Mean Square Deviation (RMSD), decrease in compactness and number of intramolecular hydrogen bonds compared to the mutations N439D and D375Y that are positioned in the turn and loop region, respectively. While the mutants R140Q and R140QG that are positioned in the alpha helix region of the protein. MDS results revealed the mutation R140Q to be more destabilizing (higher RMSD values, decrease in compactness and number of intramolecular hydrogen bonds) compared to the mutation R140G of the IDH2 protein. This study is expected to serve as a platform for drug development against 2-HGA and pave the way for more accurate variant assessment and classification for patients with genetic diseases.
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Affiliation(s)
- D Thirumal Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - L Jerushah Emerald
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - P Sneha
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - R Siva
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - W Charles Emmanuel Jebaraj
- Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Medical College and Research Institute, Chennai, Tamil Nadu, 600116, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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18
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Thomas C, Waclawek M, Nutschan K, Pinske C, Sawers RG. The Extended C-Terminal α-Helix of the HypC Chaperone Restricts Recognition of Large Subunit Precursors by the Hyp-Scaffold Machinery during [NiFe]-Hydrogenase Maturation in Escherichia coli. J Mol Microbiol Biotechnol 2018; 28:87-97. [PMID: 29996137 DOI: 10.1159/000489929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/05/2018] [Indexed: 11/19/2022] Open
Abstract
Members of the HypC protein family are chaperone-like proteins that play a central role in the maturation of [NiFe]-hydrogenases (Hyd). Escherichia coli has a second copy of HypC, called HybG, and, as a component of the HypDEF maturation scaffold, these proteins help synthesize the NiFe-cofactor and guide the scaffold to its designated hydrogenase large subunit precursor. HypC is required to synthesize active Hyd-1 and Hyd-3, while HybG facilitates Hyd-2 and Hyd-1 synthesis. To identify determinants on HypC that allow it to discriminate against Hyd-2, we made amino acid exchanges in 3 variable regions, termed VR1, VR2, and VR3, of HypC, that make it more similar to HybG. Region VR3 includes a HypC-specific C-terminal α-helical extension, and this proved particularly important in preventing the maturation of Hyd-2 by HypC. Truncation of this extension on HypC increased Hyd-2 activity in the absence of HybG, while retaining maturation of Hyd-3 and Hyd-1. Combining this truncation with amino acid exchanges in VR1 and VR2 of HypC negatively affected the synthesis of active Hyd-1. The C-terminus of E. coli HypC is thus a key determinant in hindering Hyd-2 maturation, while VR1 and VR2 appear more important for Hyd-1 matu-ration.
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19
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Jiang CH, Huang CX, Chen YJ, Chuang YC, Huang BY, Yang CN. Molecular Modeling for Structural Insights Concerning the Activation Mechanisms of F1174L and R1275Q Mutations on Anaplastic Lymphoma Kinase. Molecules 2018; 23:molecules23071610. [PMID: 30004444 PMCID: PMC6100628 DOI: 10.3390/molecules23071610] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 11/29/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase involved in various cancers. In its basal state, the structure of ALK is in an autoinhibitory form stabilized by its A-loop, which runs from the N-lobe to the C-lobe of the kinase. Specifically, the A-loop adopts an inhibitory pose with its proximal A-loop helix (αAL-helix) to anchor the αC-helix orientation in an inactive form in the N-lobe; the distal portion of the A-loop is packed against the C-lobe to block the peptide substrate from binding. Upon phosphorylation of the first A-loop tyrosine (Y1278), the αAL-helix unfolds; the distal A-loop detaches from the C-lobe and reveals the P+1 pocket that accommodates the residues immediately after their phosphorylation, and ALK is activated accordingly. Recently, two neuroblastoma mutants, F1174L and R1275Q, have been determined to cause ALK activation without phosphorylation on Y1278. Notably, F1174 is located on the C-terminus of the αC-helix and away from the A-loop, whereas R1275 sits on the αAL-helix. In this molecular modeling study, we investigated the structural impacts of F1174L and R1275Q that lead to the gain-of-function event. Wild-type ALK and ALK with phosphorylated Y1278 were also modeled for comparison. Our modeling suggests that the replacement of F1174 with a smaller residue, namely leucine, moves the αC-helix and αAL-helix into closer contact and further distorts the distal portion of the A-loop. In wild-type ALK, R1275 assumes the dual role of maintaining the αAL-helix–αC-helix interaction in an inactive form and securing αAL-helix conformation through the D1276–R1275 interaction. Accordingly, mutating R1275 to a glutamine reorients the αC-helix to an active form and deforms the entire A-loop. In both F1174L and R1275Q mutants, the A-loop rearranges itself to expose the P+1 pocket, and kinase activity resumes.
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Affiliation(s)
- Cheng-Han Jiang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Chong-Xian Huang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Ya-Jyun Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Yu-Chung Chuang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Bo-Yen Huang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Chia-Ning Yang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
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20
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Mekkat A, Poppleton E, An B, Visse R, Nagase H, Kaplan DL, Brodsky B, Lin YS. Effects of flexibility of the α2 chain of type I collagen on collagenase cleavage. J Struct Biol 2018; 203:247-254. [PMID: 29763735 DOI: 10.1016/j.jsb.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 11/18/2022]
Abstract
Cleavage of collagen by collagenases such as matrix metalloproteinase 1 (MMP-1) is a key step in development, tissue remodeling, and tumor proliferation. The abundant heterotrimeric type I collagen composed of two α1(I) chains and one α2(I) chain is efficiently cleaved by MMP-1 at a unique site in the triple helix, a process which may be initiated by local unfolding within the peptide chains. Atypical homotrimers of the α1(I) chain, found in embryonic and cancer tissues, are very resistant to MMP cleavage. To investigate MMP-1 cleavage, recombinant homotrimers were constructed with sequences from the MMP cleavage regions of human collagen chains inserted into a host bacterial collagen protein system. All triple-helical constructs were cleaved by MMP-1, with α2(I) homotrimers cleaved efficiently at a rate similar to that seen for α1(II) and α1(III) homotrimers, while α1(I) homotrimers were cleaved at a much slower rate. The introduction of destabilizing Gly to Ser mutations within the human collagenase susceptible region of the α2(I) chain did not interfere with MMP-1 cleavage. Molecular dynamics simulations indicated a greater degree of transient hydrogen bond breaking in α2(I) homotrimers compared with α1(I) homotrimers at the MMP-1 cleavage site, and showed an extensive disruption of hydrogen bonding in the presence of a Gly to Ser mutation, consistent with chymotrypsin digestion results. This study indicates that α2(I) homotrimers are susceptible to MMP-1, proves that the presence of an α1(I) chain is not a requirement for α2(I) cleavage, and supports the importance of local unfolding of α2(I) in collagenase cleavage.
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Affiliation(s)
- Arya Mekkat
- Department of Chemistry, Tufts University, Medford, MA, USA
| | - Erik Poppleton
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Bo An
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Robert Visse
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Hideaki Nagase
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Barbara Brodsky
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA.
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA, USA.
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Fidler AL, Boudko SP, Rokas A, Hudson BG. The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution. J Cell Sci 2018; 131:jcs203950. [PMID: 29632050 PMCID: PMC5963836 DOI: 10.1242/jcs.203950] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution.
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Affiliation(s)
- Aaron L Fidler
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sergei P Boudko
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Billy G Hudson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Medical Education and Administration, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
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22
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Kranick JC, Chadalavada DM, Sahu D, Showalter SA. Engineering double-stranded RNA binding activity into the Drosha double-stranded RNA binding domain results in a loss of microRNA processing function. PLoS One 2017; 12:e0182445. [PMID: 28792523 PMCID: PMC5549741 DOI: 10.1371/journal.pone.0182445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/18/2017] [Indexed: 11/19/2022] Open
Abstract
Canonical processing of miRNA begins in the nucleus with the Microprocessor complex, which is minimally composed of the RNase III enzyme Drosha and two copies of its cofactor protein DGCR8. In structural analogy to most RNase III enzymes, Drosha possesses a modular domain with the double-stranded RNA binding domain (dsRBD) fold. Unlike the dsRBDs found in most members of the RNase III family, the Drosha-dsRBD does not display double-stranded RNA binding activity; perhaps related to this, the Drosha-dsRBD amino acid sequence does not conform well to the canonical patterns expected for a dsRBD. In this article, we investigate the impact on miRNA processing of engineering double-stranded RNA binding activity into Drosha's non-canonical dsRBD. Our findings corroborate previous studies that have demonstrated the Drosha-dsRBD is necessary for miRNA processing and suggest that the amino acid composition in the second α-helix of the domain is critical to support its evolved function.
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Affiliation(s)
- Joshua C. Kranick
- Department of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Durga M. Chadalavada
- Department of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Debashish Sahu
- Department of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Scott A. Showalter
- Department of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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Mulvaney EP, O'Meara F, Khan AR, O'Connell DJ, Kinsella BT. Identification of α-helix 4 (α4) of Rab11a as a novel Rab11-binding domain (RBD): Interaction of Rab11a with the Prostacyclin Receptor. Biochim Biophys Acta Mol Cell Res 2017; 1864:1819-1832. [PMID: 28739266 DOI: 10.1016/j.bbamcr.2017.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/28/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022]
Abstract
The cellular trafficking of numerous G protein-coupled receptors (GPCRs) is known to be regulated by Rab proteins that involves a direct protein:protein interaction between the receptor and the GTPase. In the case of the human prostacyclin receptor (hIP), it undergoes agonist-induced internalization and subsequent Rab11a-dependent recyclization involving an interaction between a Rab11-binding domain (RBD) localized within its carboxyl-tail domain with Rab11a. However, the GPCR-interacting domain on Rab11a itself is unknown. Hence, we sought to identify the region within Rab11a that mediates its interaction with the RBD of the hIP. The α4 helix region of Rab11 was identified as a novel binding domain for the hIP, a site entirely distinct from the Switch I/Switch II -regions that act as specific binding domain for most other Rab and Ras-like GTPase interactants. Specifically, Glu138 within α4 helix of Rab11a appears to contact with key residues (e.g. Lys304) within the RBD of the hIP, where such contacts differ depending on the agonist-activated versus -inactive status of the hIP. Through mutational studies, supported by in silico homology modelling of the inactive and active hIP:Rab11a complexes, a mechanism is proposed to explain both the constitutive and agonist-induced binding of Rab11a to regulate intracellular trafficking of the hIP. Collectively, these studies are not only the first to identify α4 helix of Rab11a as a protein binding domain on the GTPase but also reveal novel mechanistic insights into the intracellular trafficking of the hIP, and potentially of other members of the GPCR superfamily, involving Rab11-dependent mechanisms.
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Affiliation(s)
- Eamon P Mulvaney
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fergal O'Meara
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - David J O'Connell
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - B Therese Kinsella
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
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Kroeger JK, Hofmann SC, Leppert J, Has C, Franzke CW. Amino acid duplication in the coiled-coil structure of collagen XVII alters its maturation and trimerization causing mild junctional epidermolysis bullosa. Hum Mol Genet 2017; 26:479-488. [PMID: 28365758 DOI: 10.1093/hmg/ddw404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/21/2016] [Indexed: 12/16/2023] Open
Abstract
The function and stability of collagens depend on the accurate triple helix formation of three distinct polypeptide chains. Disruption of this triple-helical structure can result in connective-tissue disorders. Triple helix formation is thought to depend on three-stranded coiled-coil oligomerization sites within non-collagenous domains. However, only little is known about the physiological relevance of these coiled-coil structures. Transmembrane collagen XVII, also known as 180 kDa bullous pemphigoid antigen provides mechanical stability through the anchorage of epithelial cells to the basement membrane. Mutations in the collagen XVII gene, COL17A1, cause junctional epidermolysis bullosa (JEB), characterized by chronic trauma-induced skin blistering. Here we exploited a novel naturally occurring COL17A1 mutation, leading to an in-frame lysine duplication within the coiled-coil structure of the juxtamembranous NC16A domain of collagen XVII, which resulted in a mild phenotype of JEB due to reduced membrane-anchored collagen XVII molecules. This mutation causes structural changes in the mutant molecule and interferes with its maturation. The destabilized coiled-coil structure of the mutant collagen XVII unmasks a furin cleavage site that results in excessive and non-physiological ectodomain shedding during its maturation. Furthermore, it decreases its triple-helical stability due to defective coiled-coil oligomerization, which makes it highly susceptible to proteolytic degradation. As a consequence of altered maturation and decreased stability of collagen XVII trimers, reduced collagen XVII is incorporated into the cell membrane, resulting in compromised dermal-epidermal adhesion. Taken together, using this genetic model, we provide the first proof that alteration of the coiled-coil structure destabilizes oligomerization and impairs physiological shedding of collagen XVII in vivo.
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Affiliation(s)
- Jasmin K Kroeger
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Silke C Hofmann
- Center for Dermatology, Allergy and Dermatosurgery, HELIOS University Hospital Wuppertal, University Witten/Herdecke, Germany
| | - Juna Leppert
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Cristina Has
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Claus-Werner Franzke
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
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