1
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Sun X, Alfermann J, Li H, Watkins MB, Chen YT, Morrell TE, Mayerthaler F, Wang CY, Komatsuzaki T, Chu JW, Ando N, Mootz HD, Yang H. Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases. Nat Chem 2024; 16:259-268. [PMID: 38049653 PMCID: PMC11227371 DOI: 10.1038/s41557-023-01361-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
Abstract
Many peptide-derived natural products are produced by non-ribosomal peptide synthetases (NRPSs) in an assembly-line fashion. Each amino acid is coupled to a designated peptidyl carrier protein (PCP) through two distinct reactions catalysed sequentially by the single active site of the adenylation domain (A-domain). Accumulating evidence suggests that large-amplitude structural changes occur in different NRPS states; yet how these molecular machines orchestrate such biochemical sequences has remained elusive. Here, using single-molecule Förster resonance energy transfer, we show that the A-domain of gramicidin S synthetase I adopts structurally extended and functionally obligatory conformations for alternating between adenylation and thioester-formation structures during enzymatic cycles. Complementary biochemical, computational and small-angle X-ray scattering studies reveal interconversion among these three conformations as intrinsic and hierarchical where intra-A-domain organizations propagate to remodel inter-A-PCP didomain configurations during catalysis. The tight kinetic coupling between structural transitions and enzymatic transformations is quantified, and how the gramicidin S synthetase I A-domain utilizes its inherent conformational dynamics to drive directional biosynthesis with a flexibly linked PCP domain is revealed.
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Affiliation(s)
- Xun Sun
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonas Alfermann
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Hao Li
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology; Institute of Molecular Medicine and Bioengineering; Department of Biological Science and Technology; Centre for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Thomas E Morrell
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | | | - Chia-Ying Wang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tamiki Komatsuzaki
- Research Centre of Mathematics for Social Creativity, Research Institute for Electronic Science; The Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Japan
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology; Institute of Molecular Medicine and Bioengineering; Department of Biological Science and Technology; Centre for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Henning D Mootz
- Institute of Biochemistry, University of Münster, Münster, Germany.
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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2
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Trudeau SJ, Hwang H, Mathur D, Begum K, Petrey D, Murray D, Honig B. PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions. Protein Sci 2023; 32:e4594. [PMID: 36776141 PMCID: PMC10019447 DOI: 10.1002/pro.4594] [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: 09/13/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
We describe the Predicting Protein-Compound Interactions (PrePCI) database which comprises over 5 billion predicted interactions between 6.8 million chemical compounds and 19,797 human proteins. PrePCI relies on a proteome-wide database of structural models based on both traditional modeling techniques and the AlphaFold Protein Structure Database. Sequence- and structural similarity-based metrics are established between template proteins, T, in the Protein Data Bank that bind compounds, C, and query proteins in the model database, Q. When the metrics exceed threshold values, it is assumed that C also binds to Q with a likelihood ratio (LR) derived from machine learning. If the relationship is based on structural similarity, the LR is based on a scoring function that measures the extent to which C is compatible with the binding site of Q as described in the LT-scanner algorithm. For every predicted complex derived in this way, chemical similarity based on the Tanimoto coefficient identifies other small molecules that may bind to Q. An overall LR for the binding of C to Q is obtained from Naive Bayesian statistics. The PrePCI database can be queried by entering a UniProt ID or gene name for a protein to obtain a list of compounds predicted to bind to it along with associated LRs. Alternatively, entering an identifier for the compound outputs a list of proteins it is predicted to bind. Specific applications of the database to lead discovery, elucidation of drug mechanism of action, and biological function annotation are described.
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Affiliation(s)
- Stephen J. Trudeau
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Integrated Graduate Program in Cellular, Molecular and Biomedical Studies (CMBS), Columbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Howook Hwang
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Schrodinger, Inc.New YorkNew YorkUSA
| | - Deepika Mathur
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Kamrun Begum
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Donald Petrey
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Diana Murray
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Barry Honig
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of MedicineColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain and Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
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3
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Zhu Z, Deng Z, Wang Q, Wang Y, Zhang D, Xu R, Guo L, Wen H. Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design. Front Pharmacol 2022; 13:939555. [PMID: 35837274 PMCID: PMC9275593 DOI: 10.3389/fphar.2022.939555] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue. An explosion in high-resolution ion channel structures paved way for structure-based rational drug design and the state-of-the-art simulation and machine learning techniques dramatically improved the efficiency and effectiveness of computer-aided drug design. Here we present an overview of how simulation and machine learning-based methods fundamentally changed the ion channel-related drug design at different levels, as well as the emerging trends in the field.
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Affiliation(s)
- Zhengdan Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Institute of Big Data Research, Beijing, China
| | - Zhenfeng Deng
- DP Technology, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | | | - Duo Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- DP Technology, Beijing, China
| | - Ruihan Xu
- DP Technology, Beijing, China
- National Engineering Research Center of Visual Technology, Peking University, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
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4
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Soto-Ospina A, Araque Marín P, Bedoya G, Sepulveda-Falla D, Villegas Lanau A. Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer's Disease on the Orthosteric Site. Front Mol Biosci 2021; 8:649990. [PMID: 34150846 PMCID: PMC8206637 DOI: 10.3389/fmolb.2021.649990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease pathology is characterized by β-amyloid plaques and neurofibrillary tangles. Amyloid precursor protein is processed by β and γ secretase, resulting in the production of β-amyloid peptides with a length ranging from 38 to 43 amino acids. Presenilin 1 (PS1) is the catalytic unit of γ-secretase, and more than 200 PS1 pathogenic mutations have been identified as causative for Alzheimer's disease. A complete monocrystal structure of PS1 has not been determined so far due to the presence of two flexible domains. We have developed a complete structural model of PS1 using a computational approach with structure prediction software. Missing fragments Met1-Glut72 and Ser290-Glu375 were modeled and validated by their energetic and stereochemical characteristics. Then, with the complete structure of PS1, we defined that these fragments do not have a direct effect in the structure of the pore. Next, we used our hypothetical model for the analysis of the functional effects of PS1 mutations Ala246GLu, Leu248Pro, Leu248Arg, Leu250Val, Tyr256Ser, Ala260Val, and Val261Phe, localized in the catalytic pore. For this, we used a quantum mechanics/molecular mechanics (QM/MM) hybrid method, evaluating modifications in the topology, potential surface density, and electrostatic potential map of mutated PS1 proteins. We found that each mutation exerts changes resulting in structural modifications of the active site and in the shape of the pore. We suggest this as a valid approach for functional studies of PS1 in view of the possible impact in substrate processing and for the design of targeted therapeutic strategies.
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Affiliation(s)
- Alejandro Soto-Ospina
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
| | - Pedronel Araque Marín
- School of Life Sciences, Research and Innovation in Chemistry Formulations Group, EIA University, Envigado, Colombia
| | - Gabriel Bedoya
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
| | - Diego Sepulveda-Falla
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrés Villegas Lanau
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
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5
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He J, Huang SY. Full-length de novo protein structure determination from cryo-EM maps using deep learning. Bioinformatics 2021; 37:3480-3490. [PMID: 33978686 DOI: 10.1093/bioinformatics/btab357] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/03/2021] [Accepted: 05/08/2021] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Advances in microscopy instruments and image processing algorithms have led to an increasing number of cryo-EM maps. However, building accurate models for the EM maps at 3-5 Å resolution remains a challenging and time-consuming process. With the rapid growth of deposited EM maps, there is an increasing gap between the maps and reconstructed/modeled 3-dimensional (3D) structures. Therefore, automatic reconstruction of atomic-accuracy full-atomstructures fromEMmaps is pressingly needed. RESULTS We present a semi-automatic de novo structure determination method using a deep learningbased framework, named as DeepMM, which builds atomic-accuracy all-atom models from cryo-EM maps at near-atomic resolution. In our method, the main-chain and Cα positions as well as their amino acid and secondary structure types are predicted in the EM map using Densely Connected Convolutional Networks. DeepMM was extensively validated on 40 simulated maps at 5 Å resolution and 30 experimental maps at 2.6-4.8 Å resolution as well as an EMDB-wide data set of 2931 experimental maps at 2.6-4.9 Å resolution, and compared with state-of-the-art algorithms including RosettaES, MAINMAST, and Phenix. Overall, our DeepMM algorithm obtained a significant improvement over existing methods in terms of both accuracy and coverage in building full-length protein structures on all test sets, demonstrating the efficacy and general applicability of DeepMM. AVAILABILITY http://huanglab.phys.hust.edu.cn/DeepMM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiahua He
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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6
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Juvonen RO, Ahinko M, Jokinen EM, Huuskonen J, Raunio H, Pentikäinen OT. Substrate Selectivity of Coumarin Derivatives by Human CYP1 Enzymes: In Vitro Enzyme Kinetics and In Silico Modeling. ACS OMEGA 2021; 6:11286-11296. [PMID: 34056284 PMCID: PMC8153946 DOI: 10.1021/acsomega.1c00123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/08/2021] [Indexed: 05/05/2023]
Abstract
Of the three enzymes in the human cytochrome P450 family 1, CYP1A2 is an important enzyme mediating metabolism of xenobiotics including drugs in the liver, while CYP1A1 and CYP1B1 are expressed in extrahepatic tissues. Currently used CYP substrates, such as 7-ethoxycoumarin and 7-ethoxyresorufin, are oxidized by all individual CYP1 forms. The main aim of this study was to find profluorescent coumarin substrates that are more selective for the individual CYP1 forms. Eleven 3-phenylcoumarin derivatives were synthetized, their enzyme kinetic parameters were determined, and their interactions in the active sites of CYP1 enzymes were analyzed by docking and molecular dynamic simulations. All coumarin derivatives and 7-ethoxyresorufin and 7-pentoxyresorufin were oxidized by at least one CYP1 enzyme. 3-(3-Methoxyphenyl)-6-methoxycoumarin (19) was 7-O-demethylated by similar high efficiency [21-30 ML/(min·mol CYP)] by all CYP1 forms and displayed similar binding in the enzyme active sites. 3-(3-Fluoro-4-acetoxyphenyl)coumarin (14) was selectively 7-O-demethylated by CYP1A1, but with low efficiency [0.16 ML/(min mol)]. This was explained by better orientation and stronger H-bond interactions in the active site of CYP1A1 than that of CYP1A2 and CYP1B1. 3-(4-Acetoxyphenyl)-6-chlorocoumarin (20) was 7-O-demethylated most efficiently by CYP1B1 [53 ML/(min·mol CYP)], followed by CYP1A1 [16 ML/(min·mol CYP)] and CYP1A2 [0.6 ML/(min·mol CYP)]. Variations in stabilities of complexes between 20 and the individual CYP enzymes explained these differences. Compounds 14, 19, and 20 are candidates to replace traditional substrates in measuring activity of human CYP1 enzymes.
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Affiliation(s)
- Risto O. Juvonen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Box 1627, 70211 Kuopio, Finland
| | - Mira Ahinko
- Department
of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014 Jyvaskyla, Finland
| | - Elmeri M. Jokinen
- Institute
of Biomedicine, Faculty of Medicine, Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Juhani Huuskonen
- Department
of Chemistry, University of Jyvaskyla, P.O. Box 35, FI-40014 Jyvaskyla, Finland
| | - Hannu Raunio
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Box 1627, 70211 Kuopio, Finland
| | - Olli T. Pentikäinen
- Department
of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014 Jyvaskyla, Finland
- Institute
of Biomedicine, Faculty of Medicine, Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
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7
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Xing S, Zhu R, Cheng K, Cai Y, Hu Y, Li C, Zeng X, Zhu Q, He L. Gene Expression, Biochemical Characterization of a sn-1, 3 Extracellular Lipase From Aspergillus niger GZUF36 and Its Model-Structure Analysis. Front Microbiol 2021; 12:633489. [PMID: 33776965 PMCID: PMC7994357 DOI: 10.3389/fmicb.2021.633489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, a sn-1, 3 extracellular lipases from Aspergillus niger GZUF36 (PEXANL1) was expressed in Pichia pastoris, characterized, and the predicted structural model was analyzed. The optimized culture conditions of P. pastoris showed that the highest lipase activity of 66.5 ± 1.4 U/mL (P < 0.05) could be attained with 1% methanol and 96 h induction time. The purified PEXANL1 exhibited the highest activity at pH 4.0 and 40°C temperature, and its original activity remained unaltered in the majority of the organic solvents (20% v/v concentration). Triton X-100, Tween 20, Tween 80, and SDS at a concentration of 0.01% (w/v) enhanced, and all the metal ions tested inhibited activity of purified PEXANL. The results of ultrasound-assisted PEXANL1 catalyzed synthesis of 1,3-diaglycerides showed that the content of 1,3-diglycerides was rapidly increased to 36.90% with 25 min of ultrasound duration (P < 0.05) and later decreased to 19.93% with 35 min of ultrasound duration. The modeled structure of PEXANL1 by comparative modeling showed α/β hydrolase fold. Structural superposition and molecular docking results validated that Ser162, His274, and Asp217 residues of PEXANL1 were involved in the catalysis. Small-angle X-ray scattering analysis indicated the monomer properties of PEXANL1 in solution. The ab initio model of PEXANL1 overlapped with its modeling structure. This work presents a reliable structural model of A. niger lipase based on homology modeling and small-angle X-ray scattering. Besides, the data from this study will benefit the rational design of suitable crystalline lipase variants in the future.
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Affiliation(s)
- Shuqi Xing
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Ruonan Zhu
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Kai Cheng
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Yangyang Cai
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Yuedan Hu
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Cuiqin Li
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, China
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, Guizhou University, Guiyang, China
| | - Xuefeng Zeng
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, Guizhou University, Guiyang, China
| | - Qiujin Zhu
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, Guizhou University, Guiyang, China
| | - Laping He
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guizhou University, Guiyang, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, Guizhou University, Guiyang, China
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8
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Yu M, Zhang T, Zhang W, Sun Q, Li H, Li JP. Elucidating the Interactions Between Heparin/Heparan Sulfate and SARS-CoV-2-Related Proteins-An Important Strategy for Developing Novel Therapeutics for the COVID-19 Pandemic. Front Mol Biosci 2021; 7:628551. [PMID: 33569392 PMCID: PMC7868326 DOI: 10.3389/fmolb.2020.628551] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Owing to the high mortality and the spread rate, the infectious disease caused by SARS-CoV-2 has become a major threat to public health and social economy, leading to over 70 million infections and 1. 6 million deaths to date. Since there are currently no effective therapeutic or widely available vaccines, it is of urgent need to look for new strategies for the treatment of SARS-CoV-2 infection diseases. Binding of a viral protein onto cell surface heparan sulfate (HS) is generally the first step in a cascade of interaction that is required for viral entry and the initiation of infection. Meanwhile, interactions of selectins and cytokines (e.g., IL-6 and TNF-α) with HS expressed on endothelial cells are crucial in controlling the recruitment of immune cells during inflammation. Thus, structurally defined heparin/HS and their mimetics might serve as potential drugs by competing with cell surface HS for the prevention of viral adhesion and modulation of inflammatory reaction. In this review, we will elaborate coronavirus invasion mechanisms and summarize the latest advances in HS-protein interactions, especially proteins relevant to the process of coronavirus infection and subsequent inflammation. Experimental and computational techniques involved will be emphasized.
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Affiliation(s)
- Mingjia Yu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Tianji Zhang
- Division of Chemistry and Analytical Science, National Institute of Metrology, Beijing, China
| | - Wei Zhang
- Division of Chemistry and Analytical Science, National Institute of Metrology, Beijing, China
| | - Qianyun Sun
- Division of Chemistry, Shandong Institute of Metrology, Jinan, China
| | - Hongmei Li
- Division of Chemistry and Analytical Science, National Institute of Metrology, Beijing, China
| | - Jin-ping Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Uppsala, Sweden
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9
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Negative Image-Based Screening: Rigid Docking Using Cavity Information. Methods Mol Biol 2021; 2266:125-140. [PMID: 33759124 DOI: 10.1007/978-1-0716-1209-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Rational drug discovery relies heavily on molecular docking-based virtual screening, which samples flexibly the ligand binding poses against the target protein's structure. The upside of flexible docking is that the geometries of the generated docking poses are adjusted to match the residue alignment inside the target protein's ligand-binding pocket. The downside is that the flexible docking requires plenty of computing resources and, regardless, acquiring a decent level of enrichment typically demands further rescoring or post-processing. Negative image-based screening is a rigid docking technique that is ultrafast and computationally light but also effective as proven by vast benchmarking and screening experiments. In the NIB screening, the target protein cavity's shape/electrostatics is aligned and compared against ab initio-generated ligand 3D conformers. In this chapter, the NIB methodology is explained at the practical level and both its weaknesses and strengths are discussed candidly.
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10
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Lasso G, Honig B, Shapira SD. A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. Cell Syst 2020; 12:82-91.e3. [PMID: 33053371 PMCID: PMC7552982 DOI: 10.1016/j.cels.2020.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/03/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022]
Abstract
Viruses deploy genetically encoded strategies to coopt host machinery and support viral replicative cycles. Here, we use protein structure similarity to scan for molecular mimicry, manifested by structural similarity between viral and endogenous host proteins, across thousands of cataloged viruses and hosts spanning broad ecological niches and taxonomic range, including bacteria, plants and fungi, invertebrates, and vertebrates. This survey identified over 6,000,000 instances of structural mimicry; more than 70% of viral mimics cannot be discerned through protein sequence alone. We demonstrate that the manner and degree to which viruses exploit molecular mimicry varies by genome size and nucleic acid type and identify 158 human proteins that are mimicked by coronaviruses, providing clues about cellular processes driving pathogenesis. Our observations point to molecular mimicry as a pervasive strategy employed by viruses and indicate that the protein structure space used by a given virus is dictated by the host proteome. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Gorka Lasso
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA; Zuckerman Mind Brain Behavior Institute, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University, New York, NY, USA
| | - Sagi D Shapira
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.
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11
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Wang SH, Wu TJ, Lee CW, Yu J. Dissecting the conformation of glycans and their interactions with proteins. J Biomed Sci 2020; 27:93. [PMID: 32900381 PMCID: PMC7487937 DOI: 10.1186/s12929-020-00684-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
The use of in silico strategies to develop the structural basis for a rational optimization of glycan-protein interactions remains a great challenge. This problem derives, in part, from the lack of technologies to quantitatively and qualitatively assess the complex assembling between a glycan and the targeted protein molecule. Since there is an unmet need for developing new sugar-targeted therapeutics, many investigators are searching for technology platforms to elucidate various types of molecular interactions within glycan-protein complexes and aid in the development of glycan-targeted therapies. Here we discuss three important technology platforms commonly used in the assessment of the complex assembly of glycosylated biomolecules, such as glycoproteins or glycosphingolipids: Biacore analysis, molecular docking, and molecular dynamics simulations. We will also discuss the structural investigation of glycosylated biomolecules, including conformational changes of glycans and their impact on molecular interactions within the glycan-protein complex. For glycoproteins, secreted protein acidic and rich in cysteine (SPARC), which is associated with various lung disorders, such as chronic obstructive pulmonary disease (COPD) and lung cancer, will be taken as an example showing that the core fucosylation of N-glycan in SPARC regulates protein-binding affinity with extracellular matrix collagen. For glycosphingolipids (GSLs), Globo H ceramide, an important tumor-associated GSL which is being actively investigated as a target for new cancer immunotherapies, will be used to demonstrate how glycan structure plays a significant role in enhancing angiogenesis in tumor microenvironments.
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Affiliation(s)
- Sheng-Hung Wang
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, 333, Taiwan
| | - Tsai-Jung Wu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, 333, Taiwan
| | - Chien-Wei Lee
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, 333, Taiwan
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, 333, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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12
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Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis. Hum Genet 2020; 139:1443-1454. [PMID: 32514796 PMCID: PMC7519902 DOI: 10.1007/s00439-020-02188-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022]
Abstract
Dilated cardiomyopathy (DCM) belongs to the most frequent forms of cardiomyopathy mainly characterized by cardiac dilatation and reduced systolic function. Although most cases of DCM are classified as sporadic, 20–30% of cases show a heritable pattern. Familial forms of DCM are genetically heterogeneous, and mutations in several genes have been identified that most commonly play a role in cytoskeleton and sarcomere-associated processes. Still, a large number of familial cases remain unsolved. Here, we report five individuals from three independent families who presented with severe dilated cardiomyopathy during the neonatal period. Using whole-exome sequencing (WES), we identified causative, compound heterozygous missense variants in RPL3L (ribosomal protein L3-like) in all the affected individuals. The identified variants co-segregated with the disease in each of the three families and were absent or very rare in the human population, in line with an autosomal recessive inheritance pattern. They are located within the conserved RPL3 domain of the protein and were classified as deleterious by several in silico prediction software applications. RPL3L is one of the four non-canonical riboprotein genes and it encodes the 60S ribosomal protein L3-like protein that is highly expressed only in cardiac and skeletal muscle. Three-dimensional homology modeling and in silico analysis of the affected residues in RPL3L indicate that the identified changes specifically alter the interaction of RPL3L with the RNA components of the 60S ribosomal subunit and thus destabilize its binding to the 60S subunit. In conclusion, we report that bi-allelic pathogenic variants in RPL3L are causative of an early-onset, severe neonatal form of dilated cardiomyopathy, and we show for the first time that cytoplasmic ribosomal proteins are involved in the pathogenesis of non-syndromic cardiomyopathies.
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13
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Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules 2020; 25:molecules25112467. [PMID: 32466409 PMCID: PMC7321371 DOI: 10.3390/molecules25112467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 11/24/2022] Open
Abstract
We discuss the use of the regularized linear discriminant analysis (LDA) as a model reduction technique combined with particle swarm optimization (PSO) in protein tertiary structure prediction, followed by structure refinement based on singular value decomposition (SVD) and PSO. The algorithm presented in this paper corresponds to the category of template-based modeling. The algorithm performs a preselection of protein templates before constructing a lower dimensional subspace via a regularized LDA. The protein coordinates in the reduced spaced are sampled using a highly explorative optimization algorithm, regressive–regressive PSO (RR-PSO). The obtained structure is then projected onto a reduced space via singular value decomposition and further optimized via RR-PSO to carry out a structure refinement. The final structures are similar to those predicted by best structure prediction tools, such as Rossetta and Zhang servers. The main advantage of our methodology is that alleviates the ill-posed character of protein structure prediction problems related to high dimensional optimization. It is also capable of sampling a wide range of conformational space due to the application of a regularized linear discriminant analysis, which allows us to expand the differences over a reduced basis set.
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14
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Avram S, Mernea M, Limban C, Borcan F, Chifiriuc C. Potential Therapeutic Approaches to Alzheimer's Disease By Bioinformatics, Cheminformatics And Predicted Adme-Tox Tools. Curr Neuropharmacol 2020; 18:696-719. [PMID: 31885353 PMCID: PMC7536829 DOI: 10.2174/1570159x18666191230120053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/24/2019] [Accepted: 12/28/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is considered a severe, irreversible and progressive neurodegenerative disorder. Currently, the pharmacological management of AD is based on a few clinically approved acethylcholinesterase (AChE) and N-methyl-D-aspartate (NMDA) receptor ligands, with unclear molecular mechanisms and severe side effects. METHODS Here, we reviewed the most recent bioinformatics, cheminformatics (SAR, drug design, molecular docking, friendly databases, ADME-Tox) and experimental data on relevant structurebiological activity relationships and molecular mechanisms of some natural and synthetic compounds with possible anti-AD effects (inhibitors of AChE, NMDA receptors, beta-secretase, amyloid beta (Aβ), redox metals) or acting on multiple AD targets at once. We considered: (i) in silico supported by experimental studies regarding the pharmacological potential of natural compounds as resveratrol, natural alkaloids, flavonoids isolated from various plants and donepezil, galantamine, rivastagmine and memantine derivatives, (ii) the most important pharmacokinetic descriptors of natural compounds in comparison with donepezil, memantine and galantamine. RESULTS In silico and experimental methods applied to synthetic compounds led to the identification of new AChE inhibitors, NMDA antagonists, multipotent hybrids targeting different AD processes and metal-organic compounds acting as Aβ inhibitors. Natural compounds appear as multipotent agents, acting on several AD pathways: cholinesterases, NMDA receptors, secretases or Aβ, but their efficiency in vivo and their correct dosage should be determined. CONCLUSION Bioinformatics, cheminformatics and ADME-Tox methods can be very helpful in the quest for an effective anti-AD treatment, allowing the identification of novel drugs, enhancing the druggability of molecular targets and providing a deeper understanding of AD pathological mechanisms.
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Affiliation(s)
| | - Maria Mernea
- Address correspondence to this author at the Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95th Spl. Independentei, Bucharest, Romania; Tel/Fax: ++4-021-318-1573; E-mail:
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15
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Mirza MU, Vanmeert M, Ali A, Iman K, Froeyen M, Idrees M. Perspectives towards antiviral drug discovery against Ebola virus. J Med Virol 2019; 91:2029-2048. [PMID: 30431654 PMCID: PMC7166701 DOI: 10.1002/jmv.25357] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/04/2018] [Indexed: 12/18/2022]
Abstract
Ebola virus disease (EVD), caused by Ebola viruses, resulted in more than 11 500 deaths according to a recent 2018 WHO report. With mortality rates up to 90%, it is nowadays one of the most deadly infectious diseases. However, no Food and Drug Administration‐approved Ebola drugs or vaccines are available yet with the mainstay of therapy being supportive care. The high fatality rate and absence of effective treatment or vaccination make Ebola virus a category‐A biothreat pathogen. Fortunately, a series of investigational countermeasures have been developed to control and prevent this global threat. This review summarizes the recent therapeutic advances and ongoing research progress from research and development to clinical trials in the development of small‐molecule antiviral drugs, small‐interference RNA molecules, phosphorodiamidate morpholino oligomers, full‐length monoclonal antibodies, and vaccines. Moreover, difficulties are highlighted in the search for effective countermeasures against EVD with additional focus on the interplay between available in silico prediction methods and their evidenced potential in antiviral drug discovery.
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Affiliation(s)
- Muhammad Usman Mirza
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, KU Leuven, Leuven, Belgium
| | - Michiel Vanmeert
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, KU Leuven, Leuven, Belgium
| | - Amjad Ali
- Department of Genetics, Hazara University, Mansehra, Pakistan.,Molecular Virology Laboratory, Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory (BIRL), Department of Biology, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Matheus Froeyen
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, KU Leuven, Leuven, Belgium
| | - Muhammad Idrees
- Molecular Virology Laboratory, Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan.,Hazara University Mansehra, Khyber Pakhtunkhwa Pakistan
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16
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Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women. Int J Mol Sci 2019; 20:ijms20194828. [PMID: 31569399 PMCID: PMC6801521 DOI: 10.3390/ijms20194828] [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] [Received: 09/02/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/25/2022] Open
Abstract
This study suggests that two newly discovered variants in the MSH2 gene, which codes for a DNA mismatch repair (MMR) protein, can be associated with a high risk of breast cancer. While variants in the MSH2 gene are known to be linked with an elevated cancer risk, the MSH2 gene is not a part of the standard kit for testing patients for elevated breast cancer risk. Here we used the results of genetic testing of women diagnosed with breast cancer, but who did not have variants in BRCA1 and BRCA2 genes. Instead, the test identified four variants with unknown significance (VUS) in the MSH2 gene. Here, we carried in silico analysis to develop a classifier that can distinguish pathogenic from benign mutations in MSH2 genes taken from ClinVar. The classifier was then used to classify VUS in MSH2 genes, and two of them, p.Ala272Val and p.Met592Val, were predicted to be pathogenic mutations. These two mutations were found in women with breast cancer who did not have mutations in BRCA1 and BRCA2 genes, and thus they are suggested to be considered as new bio-markers for the early detection of elevated breast cancer risk. However, before this is done, an in vitro validation of mutation pathogenicity is needed and, moreover, the presence of these mutations should be demonstrated in a higher number of patients or in families with breast cancer history.
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17
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Lasso G, Mayer SV, Winkelmann ER, Chu T, Elliot O, Patino-Galindo JA, Park K, Rabadan R, Honig B, Shapira SD. A Structure-Informed Atlas of Human-Virus Interactions. Cell 2019; 178:1526-1541.e16. [PMID: 31474372 PMCID: PMC6736651 DOI: 10.1016/j.cell.2019.08.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/17/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022]
Abstract
While knowledge of protein-protein interactions (PPIs) is critical for understanding virus-host relationships, limitations on the scalability of high-throughput methods have hampered their identification beyond a number of well-studied viruses. Here, we implement an in silico computational framework (pathogen host interactome prediction using structure similarity [P-HIPSTer]) that employs structural information to predict ∼282,000 pan viral-human PPIs with an experimental validation rate of ∼76%. In addition to rediscovering known biology, P-HIPSTer has yielded a series of new findings: the discovery of shared and unique machinery employed across human-infecting viruses, a likely role for ZIKV-ESR1 interactions in modulating viral replication, the identification of PPIs that discriminate between human papilloma viruses (HPVs) with high and low oncogenic potential, and a structure-enabled history of evolutionary selective pressure imposed on the human proteome. Further, P-HIPSTer enables discovery of previously unappreciated cellular circuits that act on human-infecting viruses and provides insight into experimentally intractable viruses.
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Affiliation(s)
- Gorka Lasso
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Sandra V Mayer
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Evandro R Winkelmann
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Tim Chu
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Oliver Elliot
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | | | - Kernyu Park
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA; Zuckerman Mind Brain Behavior Institute, Columbia University Medical Center, New York, NY, USA; Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA.
| | - Sagi D Shapira
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.
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18
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Haataja TJK, Capoulade R, Lecointe S, Hellman M, Merot J, Permi P, Pentikäinen U. Critical Structural Defects Explain Filamin A Mutations Causing Mitral Valve Dysplasia. Biophys J 2019; 117:1467-1475. [PMID: 31542223 DOI: 10.1016/j.bpj.2019.08.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022] Open
Abstract
Mitral valve diseases affect ∼3% of the population and are the most common reasons for valvular surgery because no drug-based treatments exist. Inheritable genetic mutations have now been established as the cause of mitral valve insufficiency, and four different missense mutations in the filamin A gene (FLNA) have been found in patients suffering from nonsyndromic mitral valve dysplasia (MVD). The filamin A (FLNA) protein is expressed, in particular, in endocardial endothelia during fetal valve morphogenesis and is key in cardiac development. The FLNA-MVD-causing mutations are clustered in the N-terminal region of FLNA. How the mutations in FLNA modify its structure and function has mostly remained elusive. In this study, using NMR spectroscopy and interaction assays, we investigated FLNA-MVD-causing V711D and H743P mutations. Our results clearly indicated that both mutations almost completely destroyed the folding of the FLNA5 domain, where the mutation is located, and also affect the folding of the neighboring FLNA4 domain. The structure of the neighboring FLNA6 domain was not affected by the mutations. These mutations also completely abolish FLNA's interactions with protein tyrosine phosphatase nonreceptor type 12, which has been suggested to contribute to the pathogenesis of FLNA-MVD. Taken together, our results provide an essential structural and molecular framework for understanding the molecular bases of FLNA-MVD, which is crucial for the development of new therapies to replace surgery.
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Affiliation(s)
- Tatu J K Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland; Institute of Biomedicine, University of Turku, Turku, Finland; Turku Bioscience Centre, University of Turku, 20520 Turku, Finland
| | - Romain Capoulade
- l'institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - Simon Lecointe
- l'institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - Maarit Hellman
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland; Department of Chemistry and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Jean Merot
- l'institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland; Department of Chemistry and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Turku, Finland; Turku Bioscience Centre, University of Turku, 20520 Turku, Finland.
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19
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Moroz OV, Blagova E, Reiser V, Saikia R, Dalal S, Jørgensen CI, Bhatia VK, Baunsgaard L, Andersen B, Svendsen A, Wilson KS. Novel Inhibitory Function of the Rhizomucor miehei Lipase Propeptide and Three-Dimensional Structures of Its Complexes with the Enzyme. ACS OMEGA 2019; 4:9964-9975. [PMID: 31460089 PMCID: PMC6648591 DOI: 10.1021/acsomega.9b00612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/13/2019] [Indexed: 06/10/2023]
Abstract
Many proteins are synthesized as precursors, with propeptides playing a variety of roles such as assisting in folding or preventing them from being active within the cell. While the precise role of the propeptide in fungal lipases is not completely understood, it was previously reported that mutations in the propeptide region of the Rhizomucor miehei lipase have an influence on the activity of the mature enzyme, stressing the importance of the amino acid composition of this region. We here report two structures of this enzyme in complex with its propeptide, which suggests that the latter plays a role in the correct maturation of the enzyme. Most importantly, we demonstrate that the propeptide shows inhibition of lipase activity in standard lipase assays and propose that an important role of the propeptide is to ensure that the enzyme is not active during its expression pathway in the original host.
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Affiliation(s)
- Olga V. Moroz
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Elena Blagova
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Verena Reiser
- Novozymes
A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Rakhi Saikia
- Novozymes
A/S, Plot No. 32, 47-50,
Genisys Building, Whitefield, EPIP Zone, Brookefield, Bengaluru, Karnataka 560066, India
| | - Sohel Dalal
- Novozymes
A/S, Plot No. 32, 47-50,
Genisys Building, Whitefield, EPIP Zone, Brookefield, Bengaluru, Karnataka 560066, India
| | | | | | | | | | - Allan Svendsen
- Novozymes
A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Keith S. Wilson
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
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20
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Wong ETC, Gsponer J. Predicting Protein-Protein Interfaces that Bind Intrinsically Disordered Protein Regions. J Mol Biol 2019; 431:3157-3178. [PMID: 31207240 DOI: 10.1016/j.jmb.2019.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022]
Abstract
A long-standing goal in biology is the complete annotation of function and structure on all protein-protein interactions, a large fraction of which is mediated by intrinsically disordered protein regions (IDRs). However, knowledge derived from experimental structures of such protein complexes is disproportionately small due, in part, to challenges in studying interactions of IDRs. Here, we introduce IDRBind, a computational method that by combining gradient boosted trees and conditional random field models predicts binding sites of IDRs with performance approaching state-of-the-art globular interface predictions, making it suitable for proteome-wide applications. Although designed and trained with a focus on molecular recognition features, which are long interaction-mediating-elements in IDRs, IDRBind also predicts the binding sites of short peptides more accurately than existing specialized predictors. Consistent with IDRBind's specificity, a comparison of protein interface categories uncovered uniform trends in multiple physicochemical properties, positioning molecular recognition feature interfaces between peptide and globular interfaces.
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Affiliation(s)
- Eric T C Wong
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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21
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Morrell TE, Rafalska-Metcalf IU, Yang H, Chu JW. Compound Molecular Logic in Accessing the Active Site of Mycobacterium tuberculosis Protein Tyrosine Phosphatase B. J Am Chem Soc 2018; 140:14747-14752. [PMID: 30301350 DOI: 10.1021/jacs.8b08070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein tyrosine phosphatase B (PtpB) from Mycobacterium tuberculosis (Mtb) extends the bacteria's survival in hosts and hence is a potential target for Mtb-specific drugs. To study how Mtb-specific sequence insertions in PtpB may regulate access to its active site through large-amplitude conformational changes, we performed free-energy calculations using an all-atom explicit solvent model. Corroborated by biochemical assays, the results show that PtpB's active site is controlled via an "either/or" compound conformational gating mechanism, an unexpected discovery that Mtb has evolved to bestow a single enzyme with such intricate logical operations. In addition to providing unprecedented insights for its active-site surroundings, the findings also suggest new ways of inactivating PtpB.
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Affiliation(s)
- Thomas E Morrell
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | | | - Haw Yang
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, and Institute of Molecular Medicine and Bioengineering , National Chiao Tung University , Hsinchu , Taiwan 30068 , ROC
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22
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Navigating Among Known Structures in Protein Space. Methods Mol Biol 2018. [PMID: 30298400 DOI: 10.1007/978-1-4939-8736-8_12] [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
Present-day protein space is the result of 3.7 billion years of evolution, constrained by the underlying physicochemical qualities of the proteins. It is difficult to differentiate between evolutionary traces and effects of physicochemical constraints. Nonetheless, as a rule of thumb, instances of structural reuse, or focusing on structural similarity, are likely attributable to physicochemical constraints, whereas sequence reuse, or focusing on sequence similarity, may be more indicative of evolutionary relationships. Both types of relationships have been studied and can provide meaningful insights to protein biophysics and evolution, which in turn can lead to better algorithms for protein search, annotation, and maybe even design.In broad strokes, studies of protein space vary in the entities they represent, the similarity measure comparing these entities, and the representation used. The entities can be, for example, protein chains, domains, supra-domains, or smaller protein sub-parts denoted themes. The measures of similarity between the entities can be based on sequence, structure, function, or any combination of these. The representation can be global, encompassing the whole space, or local, focusing on a particular region surrounding protein(s) of interest. Global representations include lists of grouped proteins, protein networks, and maps. Networks are the abstraction that is derived most directly from the similarity data: each node is the protein entity (e.g., a domain), and edges connect similar domains. Selecting the entities, the similarity measure, and the abstraction are three intertwined decisions: the similarity measures allow us to identify the entities, and the selection of entities influences what is a meaningful similarity measure. Similarly, we seek entities that are related to each other in a way, for which a simple representation describes their relationships succinctly and accurately. This chapter will cover studies that rely on different entities, similarity measures, and a range of representations to better understand protein structure space. Scholars may use publicly available navigators offering a global representation, and in particular the hierarchical classifications SCOP, CATH, and ECOD, or a local representation, which encompass structural alignment algorithms. Alternatively, scholars can configure their own navigator using existing tools. To demonstrate this DIY (do it yourself) approach for navigating in protein space, we investigate substrate-binding proteins. By presenting sequence similarities among this large and diverse protein family as a network, we can infer that one member (pdb ID 4ntl; of yet unknown function) may bind methionine and suggest a putative binding mechanism.
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23
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Muhammed MT, Aki-Yalcin E. Homology modeling in drug discovery: Overview, current applications, and future perspectives. Chem Biol Drug Des 2018; 93:12-20. [PMID: 30187647 DOI: 10.1111/cbdd.13388] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/29/2018] [Accepted: 08/04/2018] [Indexed: 02/06/2023]
Abstract
Homology modeling is one of the computational structure prediction methods that are used to determine protein 3D structure from its amino acid sequence. It is considered to be the most accurate of the computational structure prediction methods. It consists of multiple steps that are straightforward and easy to apply. There are many tools and servers that are used for homology modeling. There is no single modeling program or server which is superior in every aspect to others. Since the functionality of the model depends on the quality of the generated protein 3D structure, maximizing the quality of homology modeling is crucial. Homology modeling has many applications in the drug discovery process. Since drugs interact with receptors that consist mainly of proteins, protein 3D structure determination, and thus homology modeling is important in drug discovery. Accordingly, there has been the clarification of protein interactions using 3D structures of proteins that are built with homology modeling. This contributes to the identification of novel drug candidates. Homology modeling plays an important role in making drug discovery faster, easier, cheaper, and more practical. As new modeling methods and combinations are introduced, the scope of its applications widens.
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Affiliation(s)
- Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta, Turkey.,Department of Basic Biotechnology, Institute of Biotechnology, Ankara University, Ankara, Turkey
| | - Esin Aki-Yalcin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
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24
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Goldstein T, Anthony SJ, Gbakima A, Bird BH, Bangura J, Tremeau-Bravard A, Belaganahalli MN, Wells HL, Dhanota JK, Liang E, Grodus M, Jangra RK, DeJesus VA, Lasso G, Smith BR, Jambai A, Kamara BO, Kamara S, Bangura W, Monagin C, Shapira S, Johnson CK, Saylors K, Rubin EM, Chandran K, Lipkin WI, Mazet JAK. The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses. Nat Microbiol 2018; 3:1084-1089. [PMID: 30150734 PMCID: PMC6557442 DOI: 10.1038/s41564-018-0227-2] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/25/2018] [Indexed: 11/08/2022]
Abstract
Here we describe the complete genome of a new ebolavirus, Bombali virus (BOMV) detected in free-tailed bats in Sierra Leone (little free-tailed (Chaerephon pumilus) and Angolan free-tailed (Mops condylurus)). The bats were found roosting inside houses, indicating the potential for human transmission. We show that the viral glycoprotein can mediate entry into human cells. However, further studies are required to investigate whether exposure has actually occurred or if BOMV is pathogenic in humans.
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Affiliation(s)
- Tracey Goldstein
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Simon J Anthony
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
- EcoHealth Alliance, New York, NY, USA.
| | - Aiah Gbakima
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Brian H Bird
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - James Bangura
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Alexandre Tremeau-Bravard
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Manjunatha N Belaganahalli
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Heather L Wells
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jasjeet K Dhanota
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Eliza Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- EcoHealth Alliance, New York, NY, USA
| | - Michael Grodus
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Veronica A DeJesus
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Gorka Lasso
- Department of Systems Biology, Irving Cancer Research Center, Columbia University, New York, NY, USA
| | - Brett R Smith
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Amara Jambai
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Sorie Kamara
- Livestock and Veterinary Services Division, Ministry of Agriculture, Forestry and Food Security, Freetown, Sierra Leone
| | - William Bangura
- Forestry and Wildlife Division, Ministry of Agriculture, Forestry and Food Security, Freetown, Sierra Leone
| | - Corina Monagin
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
- Metabiota, Inc., San Francisco, CA, USA
| | - Sagi Shapira
- Department of Systems Biology, Irving Cancer Research Center, Columbia University, New York, NY, USA
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Christine K Johnson
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | | | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jonna A K Mazet
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
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25
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Structural motifs in the RGS RZ subfamily combine to attenuate interactions with Gα subunits. Biochem Biophys Res Commun 2018; 503:2736-2741. [DOI: 10.1016/j.bbrc.2018.08.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/03/2018] [Indexed: 11/20/2022]
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26
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Interplay between negative and positive design elements in Gα helical domains of G proteins determines interaction specificity toward RGS2. Biochem J 2018; 475:2293-2304. [PMID: 29925530 DOI: 10.1042/bcj20180285] [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: 04/11/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 01/26/2023]
Abstract
Regulators of G protein signaling (RGS) proteins inactivate Gα subunits, thereby controlling G protein-coupled signaling networks. Among all RGS proteins, RGS2 is unique in interacting only with the Gαq but not with the Gαi subfamily. Previous studies suggested that this specificity is determined by the RGS domain and, in particular, by three RGS2-specific residues that lead to a unique mode of interaction with Gαq This interaction was further proposed to act through contacts with the Gα GTPase domain. Here, we combined energy calculations and GTPase activity measurements to determine which Gα residues dictate specificity toward RGS2. We identified putative specificity-determining residues in the Gα helical domain, which among G proteins is found only in Gα subunits. Replacing these helical domain residues in Gαi with their Gαq counterparts resulted in a dramatic specificity switch toward RGS2. We further show that Gα-RGS2 specificity is set by Gαi residues that perturb interactions with RGS2, and by Gαq residues that enhance these interactions. These results show, for the first time, that the Gα helical domain is central to dictating specificity toward RGS2, suggesting that this domain plays a general role in governing Gα-RGS specificity. Our insights provide new options for manipulating RGS-G protein interactions in vivo, for better understanding of their 'wiring' into signaling networks, and for devising novel drugs targeting such interactions.
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27
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Giovanola M, Vollero A, Cinquetti R, Bossi E, Forrest LR, Di Cairano ES, Castagna M. Threonine 67 is a key component in the coupling of the NSS amino acid transporter KAAT1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1179-1186. [PMID: 29409909 DOI: 10.1016/j.bbamem.2018.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 01/30/2023]
Affiliation(s)
- M Giovanola
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Trentacoste 2, 20134, Milano, Italy
| | - A Vollero
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
| | - R Cinquetti
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
| | - E Bossi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
| | - L R Forrest
- Computational Structural Biology Section, NIH NINDS, 35 Convent Drive, Bethesda, MD 20892-3761, USA
| | - E S Di Cairano
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Trentacoste 2, 20134, Milano, Italy
| | - M Castagna
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Trentacoste 2, 20134, Milano, Italy.
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28
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Jończyk J, Malawska B, Bajda M. Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification. PLoS One 2017; 12:e0186108. [PMID: 28982153 PMCID: PMC5629032 DOI: 10.1371/journal.pone.0186108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/25/2017] [Indexed: 12/18/2022] Open
Abstract
The crucial role of G-protein coupled receptors and the significant achievements associated with a better understanding of the spatial structure of known receptors in this family encouraged us to undertake a study on the histamine H3 receptor, whose crystal structure is still unresolved. The latest literature data and availability of different software enabled us to build homology models of higher accuracy than previously published ones. The new models are expected to be closer to crystal structures; and therefore, they are much more helpful in the design of potential ligands. In this article, we describe the generation of homology models with the use of diverse tools and a hybrid assessment. Our study incorporates a hybrid assessment connecting knowledge-based scoring algorithms with a two-step ligand-based docking procedure. Knowledge-based scoring employs probability theory for global energy minimum determination based on information about native amino acid conformation from a dataset of experimentally determined protein structures. For a two-step docking procedure two programs were applied: GOLD was used in the first step and Glide in the second. Hybrid approaches offer advantages by combining various theoretical methods in one modeling algorithm. The biggest advantage of hybrid methods is their intrinsic ability to self-update and self-refine when additional structural data are acquired. Moreover, the diversity of computational methods and structural data used in hybrid approaches for structure prediction limit inaccuracies resulting from theoretical approximations or fuzziness of experimental data. The results of docking to the new H3 receptor model allowed us to analyze ligand-receptor interactions for reference compounds.
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Affiliation(s)
- Jakub Jończyk
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Barbara Malawska
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
- * E-mail:
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29
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Najafabadi HS, Garton M, Weirauch MT, Mnaimneh S, Yang A, Kim PM, Hughes TR. Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. Genome Biol 2017; 18:167. [PMID: 28877740 PMCID: PMC5588721 DOI: 10.1186/s13059-017-1287-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/14/2017] [Indexed: 02/07/2023] Open
Abstract
Background The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. Results Here, we show that the C2H2-ZF expansion in metazoans is facilitated by contribution of non-base-contacting residues to DNA binding energy, allowing base-contacting specificity residues to mutate without catastrophic loss of DNA binding. In contrast, C2H2-ZF DNA binding in fungi, plants, and other lineages is constrained by reliance on base-contacting residues for DNA-binding functionality. Reconstructions indicate that virtually every DNA triplet was recognized by at least one C2H2-ZF domain in the common progenitor of placental mammals, but that extant C2H2-ZF domains typically bind different sequences from these ancestral domains, with changes facilitated by non-base-contacting residues. Conclusions Our results suggest that the evolution of C2H2-ZFs in metazoans was expedited by the interaction of non-base-contacting residues with the DNA backbone. We term this phenomenon “kaleidoscopic evolution,” to reflect the diversity of both binding motifs and binding motif transitions and the facilitation of their diversification. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1287-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Michael Garton
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Sanie Mnaimneh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada. .,Canadian Institute for Advanced Research, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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30
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Horitani M, Offenbacher AR, Carr CAM, Yu T, Hoeke V, Cutsail GE, Hammes-Schiffer S, Klinman JP, Hoffman BM. 13C ENDOR Spectroscopy of Lipoxygenase-Substrate Complexes Reveals the Structural Basis for C-H Activation by Tunneling. J Am Chem Soc 2017; 139:1984-1997. [PMID: 28121140 PMCID: PMC5322796 DOI: 10.1021/jacs.6b11856] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Indexed: 12/20/2022]
Abstract
In enzymatic C-H activation by hydrogen tunneling, reduced barrier width is important for efficient hydrogen wave function overlap during catalysis. For native enzymes displaying nonadiabatic tunneling, the dominant reactive hydrogen donor-acceptor distance (DAD) is typically ca. 2.7 Å, considerably shorter than normal van der Waals distances. Without a ground state substrate-bound structure for the prototypical nonadiabatic tunneling system, soybean lipoxygenase (SLO), it has remained unclear whether the requisite close tunneling distance occurs through an unusual ground state active site arrangement or by thermally sampling conformational substates. Herein, we introduce Mn2+ as a spin-probe surrogate for the SLO Fe ion; X-ray diffraction shows Mn-SLO is structurally faithful to the native enzyme. 13C ENDOR then reveals the locations of 13C10 and reactive 13C11 of linoleic acid relative to the metal; 1H ENDOR and molecular dynamics simulations of the fully solvated SLO model using ENDOR-derived restraints give additional metrical information. The resulting three-dimensional representation of the SLO active site ground state contains a reactive (a) conformer with hydrogen DAD of ∼3.1 Å, approximately van der Waals contact, plus an inactive (b) conformer with even longer DAD, establishing that stochastic conformational sampling is required to achieve reactive tunneling geometries. Tunneling-impaired SLO variants show increased DADs and variations in substrate positioning and rigidity, confirming previous kinetic and theoretical predictions of such behavior. Overall, this investigation highlights the (i) predictive power of nonadiabatic quantum treatments of proton-coupled electron transfer in SLO and (ii) sensitivity of ENDOR probes to test, detect, and corroborate kinetically predicted trends in active site reactivity and to reveal unexpected features of active site architecture.
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Affiliation(s)
- Masaki Horitani
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Adam R. Offenbacher
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Cody A. Marcus Carr
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Tao Yu
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Veronika Hoeke
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - George E. Cutsail
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Judith P. Klinman
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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31
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Caprari S, Minervini G, Brandi V, Polticelli F. In silico study of the structure and function of Streptococcus mutans plasmidic proteins. BIO-ALGORITHMS AND MED-SYSTEMS 2017. [DOI: 10.1515/bams-2017-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe Gram-positive bacterium
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32
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Li H, Lyu Q, Cheng J. A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning. ACTA ACUST UNITED AC 2016; 9:306-313. [PMID: 29081613 PMCID: PMC5658031 DOI: 10.4172/jpb.1000419] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Protein structure prediction is an important problem in computational biology, and is widely applied to various biomedical problems such as protein function study, protein design, and drug design. In this work, we developed a novel deep learning approach based on a deeply stacked denoising autoencoder for protein structure reconstruction. We applied our approach to a template-based protein structure prediction using only the 3D structural coordinates of homologous template proteins as input. The templates were identified for a target protein by a PSI-BLAST search. 3DRobot (a program that automatically generates diverse and well-packed protein structure decoys) was used to generate initial decoy models for the target from the templates. A stacked denoising autoencoder was trained on the decoys to obtain a deep learning model for the target protein. The trained deep model was then used to reconstruct the final structural model for the target sequence. With target proteins that have highly similar template proteins as benchmarks, the GDT-TS score of the predicted structures is greater than 0.7, suggesting that the deep autoencoder is a promising method for protein structure reconstruction.
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Affiliation(s)
- Haiou Li
- Department of Computer Science and Technology, Soochow University, Suzhou, 215006, China.,Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Qiang Lyu
- Department of Computer Science and Technology, Soochow University, Suzhou, 215006, China
| | - Jianlin Cheng
- Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
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33
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Ripoll DR, Khavrutskii I, Wallqvist A, Chaudhury S. Modeling the Role of Epitope Arrangement on Antibody Binding Stoichiometry in Flaviviruses. Biophys J 2016; 111:1641-1654. [PMID: 27760352 DOI: 10.1016/j.bpj.2016.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 02/03/2023] Open
Abstract
Cryo-electron-microscopy (cryo-EM) structures of flaviviruses reveal significant variation in epitope occupancy across different monoclonal antibodies that have largely been attributed to epitope-level differences in conformation or accessibility that affect antibody binding. The consequences of these variations for macroscopic properties such as antibody binding and neutralization are the results of the law of mass action-a stochastic process of innumerable binding and unbinding events between antibodies and the multiple binding sites on the flavivirus in equilibrium-that cannot be directly imputed from structure alone. We carried out coarse-grained spatial stochastic binding simulations for nine flavivirus antibodies with epitopes defined by cryo-EM or x-ray crystallography to assess the role of epitope spatial arrangement on antibody-binding stoichiometry, occupancy, and neutralization. In our simulations, all epitopes were equally competent for binding, representing the upper limit of binding stoichiometry that results from epitope spatial arrangement alone. Surprisingly, our simulations closely reproduced the relative occupancy and binding stoichiometry observed in cryo-EM, without having to account for differences in epitope accessibility or conformation, suggesting that epitope spatial arrangement alone may be sufficient to explain differences in binding occupancy and stoichiometry between antibodies. Furthermore, we found that there was significant heterogeneity in binding configurations even at saturating antibody concentrations, and that bivalent antibody binding may be more common than previously thought. Finally, we propose a structure-based explanation for the stoichiometric threshold model of neutralization.
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Affiliation(s)
- Daniel R Ripoll
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland
| | - Ilja Khavrutskii
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland
| | - Anders Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland
| | - Sidhartha Chaudhury
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland.
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34
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Frank AT, Law SM, Ahlstrom LS, Brooks CL. Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models. J Chem Theory Comput 2016; 11:325-31. [PMID: 25620895 PMCID: PMC4295808 DOI: 10.1021/ct5009125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Indexed: 12/18/2022]
Abstract
![]()
Given
the demonstrated utility of coarse-grained modeling and simulations
approaches in studying protein structure and dynamics, developing
methods that allow experimental observables to be directly recovered from coarse-grained models is of great importance. In
this work, we develop one such method that enables protein backbone
chemical shifts (1HN, 1Hα, 13Cα, 13C, 13Cβ, and 15N) to be predicted from Cα coordinates. We show that our Cα-based
method, LARMORCα, predicts backbone chemical shifts
with comparable accuracy to some all-atom approaches. More importantly,
we demonstrate that LARMORCα predicted chemical shifts
are able to resolve native structure from decoy pools that contain
both native and non-native models, and so it is sensitive to protein
structure. As an application, we use LARMORCα to
characterize the transient state of the fast-folding protein gpW using
recently published NMR relaxation dispersion derived backbone chemical
shifts. The model we obtain is consistent with the previously proposed
model based on independent analysis of the chemical shift dispersion
pattern of the transient state. We anticipate that LARMORCα will find utility as a tool that enables important protein conformational
substates to be identified by “parsing” trajectories
and ensembles generated using coarse-grained modeling and simulations.
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Affiliation(s)
- Aaron T Frank
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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35
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Nowroozi A, Shahlaei M. A coupling of homology modeling with multiple molecular dynamics simulation for identifying representative conformation of GPCR structures: a case study on human bombesin receptor subtype-3. J Biomol Struct Dyn 2016; 35:250-272. [DOI: 10.1080/07391102.2016.1140593] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Amin Nowroozi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
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36
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Li J, Cheng J. A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling. Sci Rep 2016; 6:25687. [PMID: 27161489 PMCID: PMC4861977 DOI: 10.1038/srep25687] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/21/2016] [Indexed: 12/04/2022] Open
Abstract
Generating tertiary structural models for a target protein from the known structure of its homologous template proteins and their pairwise sequence alignment is a key step in protein comparative modeling. Here, we developed a new stochastic point cloud sampling method, called MTMG, for multi-template protein model generation. The method first superposes the backbones of template structures, and the Cα atoms of the superposed templates form a point cloud for each position of a target protein, which are represented by a three-dimensional multivariate normal distribution. MTMG stochastically resamples the positions for Cα atoms of the residues whose positions are uncertain from the distribution, and accepts or rejects new position according to a simulated annealing protocol, which effectively removes atomic clashes commonly encountered in multi-template comparative modeling. We benchmarked MTMG on 1,033 sequence alignments generated for CASP9, CASP10 and CASP11 targets, respectively. Using multiple templates with MTMG improves the GDT-TS score and TM-score of structural models by 2.96–6.37% and 2.42–5.19% on the three datasets over using single templates. MTMG’s performance was comparable to Modeller in terms of GDT-TS score, TM-score, and GDT-HA score, while the average RMSD was improved by a new sampling approach. The MTMG software is freely available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/mtmg.html.
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Affiliation(s)
- Jilong Li
- Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Jianlin Cheng
- Department of Computer Science, University of Missouri, Columbia, MO 65211, USA.,Informatics Institute, University of Missouri, Columbia, MO 65211, USA
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37
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Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M, Chuang GY, DeKosky BJ, Doria-Rose NA, Druz A, Ernandes MJ, Georgiev IS, Jarosinski MC, Joyce MG, Lemmin TM, Leung S, Louder MK, McDaniel JR, Narpala S, Pancera M, Stuckey J, Wu X, Yang Y, Zhang B, Zhou T, Mullikin JC, Baxa U, Georgiou G, McDermott AB, Bonsignori M, Haynes BF, Moore PL, Morris L, Lee KK, Shapiro L, Mascola JR, Kwong PD. Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design. Nat Struct Mol Biol 2016; 23:81-90. [PMID: 26689967 PMCID: PMC4833398 DOI: 10.1038/nsmb.3144] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022]
Abstract
Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor. These V1V2-directed bNAbs used strand-strand interactions between a protruding antibody loop and a V1V2 strand but differed in their N-glycan recognition. Ontogeny analysis indicated that protruding loops develop early, and glycan interactions mature over time. Altogether, the multidonor information suggested that V1V2-directed bNAbs form an 'extended class', for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. The ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class.
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Affiliation(s)
- Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Cinque Soto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Max M. Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington
| | - Robert T. Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Michael Chambers
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Brandon J. DeKosky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Michael J. Ernandes
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ivelin S. Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Marissa C. Jarosinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - M. Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Thomas M. Lemmin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Sherman Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Mark K. Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jonathan R. McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jonathan Stuckey
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - James C. Mullikin
- NIH Intramural Sequenicng Center (NISC), National Human Geonome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ulrich Baxa
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Mattia Bonsignori
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Barton F. Haynes
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Penny L. Moore
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, South Africa
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, South Africa
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
- Department of Biochemistry & Molecular Biophysics and Department of Systems Biology, Columbia University, New York
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW. Protein docking using case-based reasoning. Proteins 2015; 81:2150-8. [PMID: 24123156 DOI: 10.1002/prot.24433] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein docking algorithms aim to calculate the three-dimensional (3D) structure of a protein complex starting from its unbound components. Although ab initio docking algorithms are improving, there is a growing need to use homology modeling techniques to exploit the rapidly increasing volumes of structural information that now exist. However, most current homology modeling approaches involve finding a pair of complete single-chain structures in a homologous protein complex to use as a 3D template, despite the fact that protein complexes are often formed from one or more domain-domain interactions (DDIs). To model 3D protein complexes by domain-domain homology, we have developed a case-based reasoning approach called KBDOCK which systematically identifies and reuses domain family binding sites from our database of nonredundant DDIs. When tested on 54 protein complexes from the Protein Docking Benchmark, our approach provides a near-perfect way to model single-domain protein complexes when full-homology templates are available, and it extends our ability to model more difficult cases when only partial or incomplete templates exist. These promising early results highlight the need for a new and diverse docking benchmark set, specifically designed to assess homology docking approaches.
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Affiliation(s)
- Anisah W Ghoorah
- Department of Obstetrics and Gynaecology, University of Tuebingen, Tuebingen, Germany
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Chaudhury S, Ripoll DR, Wallqvist A. Structure-based pKa prediction provides a thermodynamic basis for the role of histidines in pH-induced conformational transitions in dengue virus. Biochem Biophys Rep 2015; 4:375-385. [PMID: 29124227 PMCID: PMC5669449 DOI: 10.1016/j.bbrep.2015.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/21/2022] Open
Abstract
pH-induced conformational changes in dengue virus (DENV) are critical to its ability to infect host cells. The envelope protein heterodimers that make up the viral envelope shift from a dimer to a trimer conformation at low-pH during membrane fusion. Previous studies have suggested that the ionization of histidine residues at low-pH is central to this pH-induced conformational change. We sought out to use molecular modeling with structure-based pKa prediction to provide a quantitative basis for the role of histidines in pH-induced conformational changes and identify which histidine residues were primarily responsible for this transition. We combined existing crystallographic and cryo-electron microscopy data to construct templates of the dimer and trimer conformations for the mature and immature virus. We then generated homology models for the four DENV serotypes and carried out structure-based pKa prediction using Rosetta. Our results showed that the pKa values of a subset of conserved histidines in DENV successfully capture the thermodynamics necessary to drive pH-induced conformational changes during fusion. Here, we identified the structural determinants underlying these pKa values and compare our findings with previous experimental results. Structure-based pKa prediction for histidines in dengue virus was carried out. Conserved histidine residues drive pH-dependent conformation changes. The mature dimer form of the envelop protein is destabilized at low-pH.
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Affiliation(s)
- Sidhartha Chaudhury
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, United States
| | - Daniel R Ripoll
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, United States
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, United States
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Meier A, Söding J. Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling. PLoS Comput Biol 2015; 11:e1004343. [PMID: 26496371 PMCID: PMC4619893 DOI: 10.1371/journal.pcbi.1004343] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/19/2015] [Indexed: 11/22/2022] Open
Abstract
Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure. Its great importance for biological research is owed to its speed, simplicity, reliability and wide applicability, covering more than half of the residues in protein sequence space. Although multiple templates have been shown to generally increase model quality over single templates, the information from multiple templates has so far been combined using empirically motivated, heuristic approaches. We present here a rigorous statistical framework for multi-template homology modeling. First, we find that the query proteins’ atomic distance restraints can be accurately described by two-component Gaussian mixtures. This insight allowed us to apply the standard laws of probability theory to combine restraints from multiple templates. Second, we derive theoretically optimal weights to correct for the redundancy among related templates. Third, a heuristic template selection strategy is proposed. We improve the average GDT-ha model quality score by 11% over single template modeling and by 6.5% over a conventional multi-template approach on a set of 1000 query proteins. Robustness with respect to wrong constraints is likewise improved. We have integrated our multi-template modeling approach with the popular MODELLER homology modeling software in our free HHpred server http://toolkit.tuebingen.mpg.de/hhpred and also offer open source software for running MODELLER with the new restraints at https://bitbucket.org/soedinglab/hh-suite. Since a protein’s function is largely determined by its structure, predicting a protein’s structure from its amino acid sequence can be very useful to understand its molecular functions and its role in biological pathways. By far the most widely used computational approach for protein structure prediction relies on detecting a homologous relationship with a protein of known structure and using this protein as a template to model the structure of the query protein on it. The basic concepts of this homology modelling approach have not changed during the last 20 years. In this study we extend the probabilistic formulation of homology modelling to the consistent treatment of multiple templates. Our new theoretical approach allowed us to improve the quality of homology models by 11% over a baseline single-template approach and by 6.5% over a multi-template approach.
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Affiliation(s)
- Armin Meier
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Gene Center, Ludwig-Maximilians-Universität München Munich, Munich, Germany
| | - Johannes Söding
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Gene Center, Ludwig-Maximilians-Universität München Munich, Munich, Germany
- * E-mail:
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Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM. A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity. Nucleic Acids Res 2015; 43:9147-57. [PMID: 26384429 PMCID: PMC4627083 DOI: 10.1093/nar/gkv919] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/05/2015] [Indexed: 12/28/2022] Open
Abstract
Development of an accurate protein–DNA recognition code that can predict DNA specificity from protein sequence is a central problem in biology. C2H2 zinc fingers constitute by far the largest family of DNA binding domains and their binding specificity has been studied intensively. However, despite decades of research, accurate prediction of DNA specificity remains elusive. A major obstacle is thought to be the inability of current methods to account for the influence of neighbouring domains. Here we show that this problem can be addressed using a structural approach: we build structural models for all C2H2-ZF–DNA complexes with known binding motifs and find six distinct binding modes. Each mode changes the orientation of specificity residues with respect to the DNA, thereby modulating base preference. Most importantly, the structural analysis shows that residues at the domain interface strongly and predictably influence the binding mode, and hence specificity. Accounting for predicted binding mode significantly improves prediction accuracy of predicted motifs. This new insight into the fundamental behaviour of C2H2-ZFs has implications for both improving the prediction of natural zinc finger-binding sites, and for prioritizing further experiments to complete the code. It also provides a new design feature for zinc finger engineering.
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Affiliation(s)
- Michael Garton
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Hamed S Najafabadi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Frank W Schmitges
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Ernest Radovani
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada
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42
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Probing the conformation of FhaC with small-angle neutron scattering and molecular modeling. Biophys J 2015; 107:185-96. [PMID: 24988353 DOI: 10.1016/j.bpj.2014.05.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 04/20/2014] [Accepted: 05/05/2014] [Indexed: 11/22/2022] Open
Abstract
Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120-160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins.
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Petukh M, Kucukkal TG, Alexov E. On human disease-causing amino acid variants: statistical study of sequence and structural patterns. Hum Mutat 2015; 36:524-534. [PMID: 25689729 DOI: 10.1002/humu.22770] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/09/2015] [Indexed: 12/28/2022]
Abstract
Statistical analysis was carried out on large set of naturally occurring human amino acid variations, and it was demonstrated that there is a preference for some amino acid substitutions to be associated with diseases. At an amino acid sequence level, it was shown that the disease-causing variants frequently involve drastic changes in amino acid physicochemical properties of proteins such as charge, hydrophobicity, and geometry. Structural analysis of variants involved in diseases and being frequently observed in human population showed similar trends: disease-causing variants tend to cause more changes in hydrogen bond network and salt bridges as compared with harmless amino acid mutations. Analysis of thermodynamics data reported in the literature, both experimental and computational, indicated that disease-causing variants tend to destabilize proteins and their interactions, which prompted us to investigate the effects of amino acid mutations on large databases of experimentally measured energy changes in unrelated proteins. Although the experimental datasets were linked neither to diseases nor exclusory to human proteins, the observed trends were the same: amino acid mutations tend to destabilize proteins and their interactions. Having in mind that structural and thermodynamics properties are interrelated, it is pointed out that any large change in any of them is anticipated to cause a disease.
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Affiliation(s)
- Marharyta Petukh
- Department of Physics, Clemson University, Clemson, SC 29642, USA
| | - Tugba G Kucukkal
- Department of Physics, Clemson University, Clemson, SC 29642, USA
| | - Emil Alexov
- Department of Physics, Clemson University, Clemson, SC 29642, USA
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Lhota J, Hauptman R, Hart T, Ng C, Xie L. A new method to improve network topological similarity search: applied to fold recognition. Bioinformatics 2015; 31:2106-14. [PMID: 25717198 DOI: 10.1093/bioinformatics/btv125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/21/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework-Enrichment of Network Topological Similarity (ENTS)-to improve the performance of large scale similarity searches in bioinformatics. RESULTS We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network. AVAILABILITY AND IMPLEMENTATION Source code freely available upon request CONTACT : lxie@iscb.org.
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Affiliation(s)
- John Lhota
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
| | - Ruth Hauptman
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
| | - Thomas Hart
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
| | - Clara Ng
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
| | - Lei Xie
- Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A. Hunter College High School, New York, NY 10128, U.S.A., Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, U.S.A., Department of Biological Sciences, Hunter College, The City University of New York New York, NY 10065, U.S.A. and The Graduate Center, The City University of New York, New York, NY 10016, U.S.A
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Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol 2015; 33:555-62. [PMID: 25690854 DOI: 10.1038/nbt.3128] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 12/15/2014] [Indexed: 12/11/2022]
Abstract
Cys2-His2 zinc finger (C2H2-ZF) proteins represent the largest class of putative human transcription factors. However, for most C2H2-ZF proteins it is unknown whether they even bind DNA or, if they do, to which sequences. Here, by combining data from a modified bacterial one-hybrid system with protein-binding microarray and chromatin immunoprecipitation analyses, we show that natural C2H2-ZFs encoded in the human genome bind DNA both in vitro and in vivo, and we infer the DNA recognition code using DNA-binding data for thousands of natural C2H2-ZF domains. In vivo binding data are generally consistent with our recognition code and indicate that C2H2-ZF proteins recognize more motifs than all other human transcription factors combined. We provide direct evidence that most KRAB-containing C2H2-ZF proteins bind specific endogenous retroelements (EREs), ranging from currently active to ancient families. The majority of C2H2-ZF proteins, including KRAB proteins, also show widespread binding to regulatory regions, indicating that the human genome contains an extensive and largely unstudied adaptive C2H2-ZF regulatory network that targets a diverse range of genes and pathways.
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Affiliation(s)
- Hamed S Najafabadi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Sanie Mnaimneh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Frank W Schmitges
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Michael Garton
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Kathy N Lam
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Mihai Albu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Matthew T Weirauch
- 1] Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA. [2] Canadian Institutes for Advanced Research, Toronto, Ontario, Canada
| | - Ernest Radovani
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Philip M Kim
- 1] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Jack Greenblatt
- 1] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brendan J Frey
- 1] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [2] Canadian Institutes for Advanced Research, Toronto, Ontario, Canada. [3] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada. [4] Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Timothy R Hughes
- 1] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. [3] Canadian Institutes for Advanced Research, Toronto, Ontario, Canada
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Rosales-Hernández MC, Correa-Basurto J. The importance of employing computational resources for the automation of drug discovery. Expert Opin Drug Discov 2015; 10:213-9. [DOI: 10.1517/17460441.2015.1005071] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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47
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Trötschel C, Follmann M, Nettekoven JA, Mohrbach T, Forrest LR, Burkovski A, Marin K, Krämer R. Methionine uptake in Corynebacterium glutamicum by MetQNI and by MetPS, a novel methionine and alanine importer of the NSS neurotransmitter transporter family. Biochemistry 2015; 47:12698-709. [PMID: 18991398 DOI: 10.1021/bi801206t] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The soil bacterium Corynebacterium glutamicum is a model organism in amino acid biotechnology. Here we present the identification of two different L-methionine uptake systems including the first characterization of a bacterial secondary methionine carrier. The primary carrier MetQNI is a high affinity ABC-type transporter specific for l-methionine. Its expression is under the control of the transcription factor McbR, the global regulator of sulfur metabolism in C. glutamicum. Besides MetQNI, a novel secondary methionine uptake system of the NSS (neurotransmitter:sodium symporter) family was identified and named MetP. The MetP system is characterized by a lower affinity for methionine and uses Na(+) ions for energetic coupling. It is also the main alanine transporter in C. glutamicum and is expressed constitutively. These observations are consistent with models of methionine, alanine, and leucine bound to MetP, derived from the X-ray crystal structure of the LeuT transporter from Aquifex aeolicus. Complementation studies show that MetP consists of two components, a large subunit with 12 predicted transmembrane segments and, surprisingly, an additional subunit with one predicted transmembrane segment only. Thus, this new member of the NSS transporter family adds a novel feature to this class of carriers, namely, the functional dependence on an additional small subunit.
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Affiliation(s)
- Christian Trötschel
- Institute of Biochemistry, University of Koln, 50674 Koln, Germany, and Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
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48
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Nishi H, Demir E, Panchenko AR. Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites. J Mol Biol 2014; 427:511-20. [PMID: 25451034 DOI: 10.1016/j.jmb.2014.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 10/30/2014] [Accepted: 11/01/2014] [Indexed: 10/24/2022]
Abstract
Cellular fate depends on the spatiotemporal separation and integration of signaling processes that can be provided by phosphorylation events. In this study, we identify the crucial points in signaling crosstalk that can be triggered by discrete phosphorylation events on a single target protein. We integrated the data on individual human phosphosites with the evidence on their corresponding kinases, the functional consequences of phosphorylation on activity of the target protein and corresponding pathways. Our results show that there is a substantial fraction of phosphosites that can play critical roles in crosstalk between alternative and redundant pathways and regulatory outcome of phosphorylation can be linked to a type of phosphorylated residue. These regulatory phosphosites can serve as hubs in the signal flow and their functional roles are directly connected to their specific properties. Namely, phosphosites with similar regulatory functions are phosphorylated by the same kinases and participate in regulation of similar biochemical pathways. Such sites are more likely to cluster in sequence and space unlike sites with antagonistic outcomes of their phosphorylation on a target protein. In addition, we found that in silico phosphorylation of sites with similar functional consequences has comparable outcomes on a target protein stability. An important role of phosphorylation sites in biological crosstalk is evident from the analysis of their evolutionary conservation.
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Affiliation(s)
- Hafumi Nishi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emek Demir
- Computational Biology Center, Memorial Sloan Kettering Research Center, New York, NY 10065, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA.
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Structural and energetic determinants of adhesive binding specificity in type I cadherins. Proc Natl Acad Sci U S A 2014; 111:E4175-84. [PMID: 25253890 DOI: 10.1073/pnas.1416737111] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Type I cadherin cell-adhesion proteins are similar in sequence and structure and yet are different enough to mediate highly specific cell-cell recognition phenomena. It has previously been shown that small differences in the homophilic and heterophilic binding affinities of different type I family members can account for the differential cell-sorting behavior. Here we use a combination of X-ray crystallography, analytical ultracentrifugation, surface plasmon resonance and double electron-electron resonance (DEER) electron paramagnetic resonance spectroscopy to identify the molecular determinants of type I cadherin dimerization affinities. Small changes in sequence are found to produce subtle structural and dynamical changes that impact relative affinities, in part via electrostatic and hydrophobic interactions, and in part through entropic effects because of increased conformational heterogeneity in the bound states as revealed by DEER distance mapping in the dimers. These findings highlight the remarkable ability of evolution to exploit a wide range of molecular properties to produce closely related members of the same protein family that have affinity differences finely tuned to mediate their biological roles.
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50
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Characterization of biochemical properties of Bacillus subtilis RecQ helicase. J Bacteriol 2014; 196:4216-28. [PMID: 25246477 DOI: 10.1128/jb.06367-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RecQ family helicases function as safeguards of the genome. Unlike Escherichia coli, the Gram-positive Bacillus subtilis bacterium possesses two RecQ-like homologues, RecQ[Bs] and RecS, which are required for the repair of DNA double-strand breaks. RecQ[Bs] also binds to the forked DNA to ensure a smooth progression of the cell cycle. Here we present the first biochemical analysis of recombinant RecQ[Bs]. RecQ[Bs] binds weakly to single-stranded DNA (ssDNA) and blunt-ended double-stranded DNA (dsDNA) but strongly to forked dsDNA. The protein exhibits a DNA-stimulated ATPase activity and ATP- and Mg(2+)-dependent DNA helicase activity with a 3' → 5' polarity. Molecular modeling shows that RecQ[Bs] shares high sequence and structure similarity with E. coli RecQ. Surprisingly, RecQ[Bs] resembles the truncated Saccharomyces cerevisiae Sgs1 and human RecQ helicases more than RecQ[Ec] with regard to its enzymatic activities. Specifically, RecQ[Bs] unwinds forked dsDNA and DNA duplexes with a 3'-overhang but is inactive on blunt-ended dsDNA and 5'-overhung duplexes. Interestingly, RecQ[Bs] unwinds blunt-ended DNA with structural features, including nicks, gaps, 5'-flaps, Kappa joints, synthetic replication forks, and Holliday junctions. We discuss these findings in the context of RecQ[Bs]'s possible functions in preserving genomic stability.
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