1
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Fatima S, Mehrafrooz B, Boggs DG, Ali N, Singh S, Thielges MC, Bridwell-Rabb J, Aksimentiev A, Olshansky L. Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein. Biochemistry 2024; 63:2040-2050. [PMID: 39088332 DOI: 10.1021/acs.biochem.4c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
Hydrogen-bonding (H-bonding) interactions in metalloprotein active sites can critically regulate enzyme function. Changes in the protein structure triggered by interplay with substrates, products, and partner proteins are often translated to the metallocofactor by way of specific changes in H-bond networks connected to the active site. However, the complexities of metalloprotein architecture and mechanism often preclude our ability to define the precise molecular interactions giving rise to these intricate regulatory pathways. To address this shortcoming, we have developed conformationally switchable artificial metalloproteins (swArMs) in which allosteric Gln-binding triggers protein conformational changes that impact the microenvironment surrounding an installed metallocofactor. Herein, we report a combined structural, spectroscopic, and computational approach to enhance the conformation-dependent changes in H-bond interactions surrounding the metallocofactor site of a swArM. Structure-informed molecular dynamics simulations were employed to predict point mutations that could enhance active site H-bond interactions preferentially in the Gln-bound holo-conformation of the swArM. Testing our predictions via the unique infrared spectral signals associated with the metallocofactor site, we have identified three key residues capable of imparting conformational control over the metallocofactor microenvironment. The resultant swArMs not only model biologically relevant structural regulation but also provide an enhanced Gln-responsive biological probe to be leveraged in future biosensing applications.
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Affiliation(s)
- Saman Fatima
- Department of Chemistry, Center for Biophysics and Quantitative Biology, Materials Research Laboratory, and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Behzad Mehrafrooz
- Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, and Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - David G Boggs
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Noor Ali
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Swapnil Singh
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Aleksei Aksimentiev
- Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, and Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lisa Olshansky
- Department of Chemistry, Center for Biophysics and Quantitative Biology, Materials Research Laboratory, and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
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2
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Yang S, Song C. Switching Go̅ -Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions. J Chem Theory Comput 2024; 20:2618-2629. [PMID: 38447049 DOI: 10.1021/acs.jctc.3c01222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Proteins are dynamic biomolecules that can transform between different conformational states when exerting physiological functions, which is difficult to simulate using all-atom methods. Coarse-grained (CG) Go̅-like models are widely used to investigate large-scale conformational transitions, which usually adopt implicit solvent models and therefore cannot explicitly capture the interaction between proteins and surrounding molecules, such as water and lipid molecules. Here, we present a new method, named Switching Go̅-Martini, to simulate large-scale protein conformational transitions between different states, based on the switching Go̅ method and the CG Martini 3 force field. The method is straightforward and efficient, as demonstrated by the benchmarking applications for multiple protein systems, including glutamine binding protein (GlnBP), adenylate kinase (AdK), and β2-adrenergic receptor (β2AR). Moreover, by employing the Switching Go̅-Martini method, we can not only unveil the conformational transition from the E2Pi-PL state to E1 state of the type 4 P-type ATPase (P4-ATPase) flippase ATP8A1-CDC50 but also provide insights into the intricate details of lipid transport.
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Affiliation(s)
- Song Yang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chen Song
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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3
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Manalastas-Cantos K, Adoni KR, Pfeifer M, Märtens B, Grünewald K, Thalassinos K, Topf M. Modeling Flexible Protein Structure With AlphaFold2 and Crosslinking Mass Spectrometry. Mol Cell Proteomics 2024; 23:100724. [PMID: 38266916 PMCID: PMC10884514 DOI: 10.1016/j.mcpro.2024.100724] [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: 09/13/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024] Open
Abstract
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2 and conformer selection using XL-MS data. For conformer selection, we developed two scores-the monolink probability score (MP) and the crosslink probability score (XLP)-both of which are based on residue depth from the protein surface. We benchmarked MP and XLP on a large dataset of decoy protein structures and showed that our scores outperform previously developed scores. We then tested our methodology on three proteins having an open and closed conformation in the Protein Data Bank: Complement component 3 (C3), luciferase, and glutamine-binding periplasmic protein, first generating ensembles using AF2, which were then screened for the open and closed conformations using experimental XL-MS data. In five out of six cases, the most accurate model within the AF2 ensembles-or a conformation within 1 Å of this model-was identified using crosslinks, as assessed through the XLP score. In the remaining case, only the monolinks (assessed through the MP score) successfully identified the open conformation of glutamine-binding periplasmic protein, and these results were further improved by including the "occupancy" of the monolinks. This serves as a compelling proof-of-concept for the effectiveness of monolinks. In contrast, the AF2 assessment score was only able to identify the most accurate conformation in two out of six cases. Our results highlight the complementarity of AF2 with experimental methods like XL-MS, with the MP and XLP scores providing reliable metrics to assess the quality of the predicted models. The MP and XLP scoring functions mentioned above are available at https://gitlab.com/topf-lab/xlms-tools.
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Affiliation(s)
- Karen Manalastas-Cantos
- Center for Data and Computing in Natural Sciences, Universität Hamburg, Hamburg, Germany; Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Kish R Adoni
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Matthias Pfeifer
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany
| | - Birgit Märtens
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany
| | - Kay Grünewald
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Maya Topf
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany.
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4
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 PMCID: PMC11324865 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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5
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Shi Q, Liu L, Duan H, Jiang Y, Luo W, Sun G, Ge Y, Liang L, Liu W, Shi H, Hu J. Revealing Allosteric Mechanism of Amino Acid Binding Proteins from Open to Closed State. Molecules 2023; 28:7139. [PMID: 37894619 PMCID: PMC10609312 DOI: 10.3390/molecules28207139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/14/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Amino acid binding proteins (AABPs) undergo significant conformational closure in the periplasmic space of Gram-negative bacteria, tightly binding specific amino acid substrates and then initiating transmembrane transport of nutrients. Nevertheless, the possible closure mechanisms after substrate binding, especially long-range signaling, remain unknown. Taking three typical AABPs-glutamine binding protein (GlnBP), histidine binding protein (HisJ) and lysine/arginine/ornithine binding protein (LAOBP) in Escherichia coli (E. coli)-as research subjects, a series of theoretical studies including sequence alignment, Gaussian network model (GNM), anisotropic network model (ANM), conventional molecular dynamics (cMD) and neural relational inference molecular dynamics (NRI-MD) simulations were carried out. Sequence alignment showed that GlnBP, HisJ and LAOBP have high structural similarity. According to the results of the GNM and ANM, AABPs' Index Finger and Thumb domains exhibit closed motion tendencies that contribute to substrate capture and stable binding. Based on cMD trajectories, the Index Finger domain, especially the I-Loop region, exhibits high molecular flexibility, with residues 11 and 117 both being potentially key residues for receptor-ligand recognition and initiation of receptor allostery. Finally, the signaling pathway of AABPs' conformational closure was revealed by NRI-MD training and trajectory reconstruction. This work not only provides a complete picture of AABPs' recognition mechanism and possible conformational closure, but also aids subsequent structure-based design of small-molecule oncology drugs.
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Affiliation(s)
- Quanshan Shi
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Ling Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Huaichuan Duan
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China;
| | - Yu Jiang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Wenqin Luo
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Guangzhou Sun
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Yutong Ge
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Hubing Shi
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China;
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
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6
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Oh J, Durai P, Kannan P, Park J, Yeon YJ, Lee WK, Park K, Seo MH. Domain-wise dissection of thermal stability enhancement in multidomain proteins. Int J Biol Macromol 2023; 237:124141. [PMID: 36958447 DOI: 10.1016/j.ijbiomac.2023.124141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023]
Abstract
Stability is critical for the proper functioning of all proteins. Optimization of protein thermostability is a key step in the development of industrial enzymes and biologics. Herein, we demonstrate that multidomain proteins can be stabilized significantly using domain-based engineering followed by the recombination of the optimized domains. Domain-level analysis of designed protein variants with similar structures but different thermal profiles showed that the independent enhancement of the thermostability of a constituent domain improves the overall stability of the whole multidomain protein. The crystal structure and AlphaFold-predicted model of the designed proteins via domain-recombination provided a molecular explanation for domain-based stepwise stabilization. Our study suggests that domain-based modular engineering can minimize the sequence space for calculations in computational design and experimental errors, thereby offering useful guidance for multidomain protein engineering.
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Affiliation(s)
- Jisung Oh
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Prasannavenkatesh Durai
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea
| | - Priyadharshini Kannan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea
| | - Jaehui Park
- College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Won-Kyu Lee
- New Drug Development Center, Osong Medical Innovation Foundation, Chungbuk 28160, South Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea.
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea.
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7
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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8
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Fatima S, Boggs DG, Ali N, Thompson PJ, Thielges MC, Bridwell-Rabb J, Olshansky L. Engineering a Conformationally Switchable Artificial Metalloprotein. J Am Chem Soc 2022; 144:21606-21616. [DOI: 10.1021/jacs.2c08885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Saman Fatima
- Department of Chemistry, University of Illinois Urbana−Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States
| | - David G. Boggs
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan48109, United States
| | - Noor Ali
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Peter J. Thompson
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana−Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan48109, United States
| | - Lisa Olshansky
- Department of Chemistry, University of Illinois Urbana−Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana−Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States
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9
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Avery C, Patterson J, Grear T, Frater T, Jacobs DJ. Protein Function Analysis through Machine Learning. Biomolecules 2022; 12:1246. [PMID: 36139085 PMCID: PMC9496392 DOI: 10.3390/biom12091246] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein-ligand binding, including allosteric effects, protein-protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.
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Affiliation(s)
- Chris Avery
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - John Patterson
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Tyler Grear
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Theodore Frater
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Donald J. Jacobs
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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10
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Sala D, Del Alamo D, Mchaourab HS, Meiler J. Modeling of protein conformational changes with Rosetta guided by limited experimental data. Structure 2022; 30:1157-1168.e3. [PMID: 35597243 PMCID: PMC9357069 DOI: 10.1016/j.str.2022.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/08/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022]
Abstract
Conformational changes are an essential component of functional cycles of many proteins, but their characterization often requires an integrative structural biology approach. Here, we introduce and benchmark ConfChangeMover (CCM), a new method built into the widely used macromolecular modeling suite Rosetta that is tailored to model conformational changes in proteins using sparse experimental data. CCM can rotate and translate secondary structural elements and modify their backbone dihedral angles in regions of interest. We benchmarked CCM on soluble and membrane proteins with simulated Cα-Cα distance restraints and sparse experimental double electron-electron resonance (DEER) restraints, respectively. In both benchmarks, CCM outperformed state-of-the-art Rosetta methods, showing that it can model a diverse array of conformational changes. In addition, the Rosetta framework allows a wide variety of experimental data to be integrated with CCM, thus extending its capability beyond DEER restraints. This method will contribute to the biophysical characterization of protein dynamics.
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Affiliation(s)
- Davide Sala
- Institute for Drug Discovery, Leipzig University, Leipzig, Saxony 04103, Germany
| | - Diego Del Alamo
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Jens Meiler
- Institute for Drug Discovery, Leipzig University, Leipzig, Saxony 04103, Germany; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.
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11
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Chen Q, Li F, Zuo X, Chen J, Qin P, Wang C, Xu J, Yang D, Xing B, Liu Y, Jia P, Li L, Yang C, Yu D. Reversible domain closure modulates GlnBP ligand binding affinity. PLoS One 2022; 17:e0263102. [PMID: 35446849 PMCID: PMC9022810 DOI: 10.1371/journal.pone.0263102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Glutamine binding protein (GlnBP) is an Escherichia Coli periplasmic binding protein, which binds and carries glutamine to the inner membrane ATP-binding cassette (ABC) transporter. GlnBP binds the ligand with affinity around 0.1μM measured by isothermal titration calorimetry (ITC) and ligand binding stabilizes protein structure shown by its increase in thermodynamic stability. However, the molecular determinant of GlnBP ligand binding is not known. Electrostatic and hydrophobic interaction between GlnBP and glutamine are critical factors. We propose that the freedome of closure movement is also vital for ligand binding. In order to approve this hypothesis, we generate a series of mutants with different linker length that has different magnitude of domain closure. Mutants show different ligand binding affinity, which indicates that the propensity of domain closure determines the ligand binding affinity. Ligand binding triggers gradual ensemble conformational change. Structural changes upon ligand binding are monitored by combination of small angle x-ray scattering (SAXS) and NMR spectroscopy. Detailed structure characterization of GlnBP contributes to a better understanding of ligand binding and provides the structural basis for biosensor design.
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Affiliation(s)
- Qun Chen
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province, China
| | - Fang Li
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Argonne, IL, United States of America
| | - Jin Chen
- Institute of Chinese medical sciences, University of Macau, Macau, China
| | - Peiwu Qin
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province, China
| | - Chuhui Wang
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province, China
| | - Jin Xu
- Shenzhen Aier Eye Hospital, Futian District, Guangdong Province, China
| | - Danyu Yang
- Shenzhen Aier Eye Hospital, Futian District, Guangdong Province, China
| | - Baogang Xing
- University of Science and Technology Hospital, Shenzhen, Guangdong Province, China
| | - Ying Liu
- Food Inspection & Quarantine Center, Shenzhen Custom, Shenzhen, Guangdong, China
| | - Peng Jia
- Food Inspection & Quarantine Center, Shenzhen Custom, Shenzhen, Guangdong, China
| | - Linling Li
- Shenzhen Maternity and Child Healthcare Hospital, Affiliated to Southern Medical University, Shenzhen, Guangdong, China
| | - Chengming Yang
- University of Science and Technology Hospital, Shenzhen, Guangdong Province, China
- * E-mail: (DY); (CY)
| | - Dongmei Yu
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, Shandong Province, China
- * E-mail: (DY); (CY)
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12
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Wu S, Zhang W, Li W, Huang W, Kong Q, Chen Z, Wei W, Yan S. Dissecting the Protein Dynamics Coupled Ligand Binding with Kinetic Models and Single-Molecule FRET. Biochemistry 2022; 61:433-445. [PMID: 35226469 DOI: 10.1021/acs.biochem.1c00771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein-ligand interactions are crucial to many biological processes. Ligand binding and dissociation are the basic steps that allow proteins to function. Protein conformational dynamics have been shown to play important roles in ligand binding and dissociation. However, it is challenging to determine the ligand binding kinetics of dynamic proteins. Here, we undertook comprehensive single-molecule FRET (smFRET) measurements and kinetic model analysis to characterize the conformational dynamics coupled ligand binding of glutamine-binding protein (GlnBP). We showed that hinge and T118A mutations of GlnBP affect its conformational dynamics as well as the ligand binding affinity. Based on smFRET measurements, the kinetic model of ligand-GlnBP interactions was constructed. Using experimentally measured parameters, we solved the rate equations of the model and obtained the undetectable parameters of the model which allowed us to understand the ligand binding kinetics fully. Our results demonstrate that modulation of the conformational dynamics of GlnBP affects the ligand binding and dissociation rates. This study provides insights into the binding kinetics of ligands, which are related to the protein function itself.
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Affiliation(s)
- Shaowen Wu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Wenyang Zhang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Wenyan Li
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Qian Kong
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Zhongjian Chen
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Wenkang Wei
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
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13
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Abstract
Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria with the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviors in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to the modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information processing via c-di-GMP signal transduction not only is fundamental to bacterial survival in dynamic environments but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.
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14
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Kuznetsova A, Masrati G, Vigonsky E, Livnat-Levanon N, Rose J, Grupper M, Baloum A, Yang JG, Rees DC, Ben-Tal N, Lewinson O. Titratable transmembrane residues and a hydrophobic plug are essential for manganese import via the Bacillus anthracis ABC transporter MntBC-A. J Biol Chem 2021; 297:101087. [PMID: 34416234 PMCID: PMC8487065 DOI: 10.1016/j.jbc.2021.101087] [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: 02/09/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/07/2022] Open
Abstract
All extant life forms require trace transition metals (e.g., Fe2/3+, Cu1/2+, and Mn2+) to survive. However, as these are environmentally scarce, organisms have evolved sophisticated metal uptake machineries. In bacteria, high-affinity import of transition metals is predominantly mediated by ABC transporters. During bacterial infection, sequestration of metal by the host further limits the availability of these ions, and accordingly, bacterial ABC transporters (importers) of metals are key virulence determinants. However, the structure–function relationships of these metal transporters have not been fully elucidated. Here, we used metal-sensitivity assays, advanced structural modeling, and enzymatic assays to study the ABC transporter MntBC-A, a virulence determinant of the bacterial human pathogen Bacillus anthracis. We find that despite its broad metal-recognition profile, MntBC-A imports only manganese, whereas zinc can function as a high-affinity inhibitor of MntBC-A. Computational analysis shows that the transmembrane metal permeation pathway is lined with six titratable residues that can coordinate the positively charged metal, and mutagenesis studies show that they are essential for manganese transport. Modeling suggests that access to these titratable residues is blocked by a ladder of hydrophobic residues, and ATP-driven conformational changes open and close this hydrophobic seal to permit metal binding and release. The conservation of this arrangement of titratable and hydrophobic residues among ABC transporters of transition metals suggests a common mechanism. These findings advance our understanding of transmembrane metal recognition and permeation and may aid the design and development of novel antibacterial agents.
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Affiliation(s)
- Anastasiya Kuznetsova
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elena Vigonsky
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Nurit Livnat-Levanon
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Jessica Rose
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Moti Grupper
- Infectious Disease Unit, Rambam Health Care Campus, Haifa, Israel
| | - Adan Baloum
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Janet G Yang
- Department of Chemistry, University of San Francisco, San Francisco, California, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oded Lewinson
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel.
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15
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Linthwaite VL, Cann MJ. A methodology for carbamate post-translational modification discovery and its application in Escherichia coli. Interface Focus 2021; 11:20200028. [PMID: 33633830 DOI: 10.1098/rsfs.2020.0028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 11/12/2022] Open
Abstract
Carbon dioxide can influence cell phenotypes through the modulation of signalling pathways. CO2 regulates cellular processes as diverse as metabolism, cellular homeostasis, chemosensing and pathogenesis. This diversity of regulated processes suggests a broadly conserved mechanism for CO2 interactions with diverse cellular targets. CO2 is generally unreactive but can interact with neutral amines on protein under normal intracellular conditions to form a carbamate post-translational modification (PTM). We have previously demonstrated the presence of this PTM in a subset of protein produced by the model plant species Arabidopsis thaliana. Here, we describe a detailed methodology for identifying new carbamate PTMs in an extracted soluble proteome under biologically relevant conditions. We apply this methodology to the soluble proteome of the model prokaryote Escherichia coli and identify new carbamate PTMs. The application of this methodology, therefore, supports the hypothesis that the carbamate PTM is both more widespread in biology than previously suspected and may represent a broadly relevant mechanism for CO2-protein interactions.
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Affiliation(s)
| | - Martin J Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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16
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Takaba K, Tran DP, Kitao A. Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins. J Chem Phys 2021; 152:225101. [PMID: 32534517 DOI: 10.1063/5.0004654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We propose edge expansion parallel cascade selection molecular dynamics (eePaCS-MD) as an efficient adaptive conformational sampling method to investigate the large-amplitude motions of proteins without prior knowledge of the conformational transitions. In this method, multiple independent MD simulations are iteratively conducted from initial structures randomly selected from the vertices of a multi-dimensional principal component subspace. This subspace is defined by an ensemble of protein conformations sampled during previous cycles of eePaCS-MD. The edges and vertices of the conformational subspace are determined by solving the "convex hull problem." The sampling efficiency of eePaCS-MD is achieved by intensively repeating MD simulations from the vertex structures, which increases the probability of rare event occurrence to explore new large-amplitude collective motions. The conformational sampling efficiency of eePaCS-MD was assessed by investigating the open-close transitions of glutamine binding protein, maltose/maltodextrin binding protein, and adenylate kinase and comparing the results to those obtained using related methods. In all cases, the open-close transitions were simulated in ∼10 ns of simulation time or less, offering 1-3 orders of magnitude shorter simulation time compared to conventional MD. Furthermore, we show that the combination of eePaCS-MD and accelerated MD can further enhance conformational sampling efficiency, which reduced the total computational cost of observing the open-close transitions by at most 36%.
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Affiliation(s)
- Kenichiro Takaba
- Pharmaceutical Research Center, Laboratory for Medicinal Chemistry, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Duy Phuoc Tran
- School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
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17
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Zhang Y, Cao Z, Zhang JZ, Xia F. Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions. J Chem Theory Comput 2020; 16:6678-6689. [PMID: 32926616 DOI: 10.1021/acs.jctc.0c00551] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The double-well model is usually used to describe the conformational transition between two states of a protein. Since conformational changes usually occur within a relatively large time scale, coarse-grained models are often used to accelerate the dynamic process due to their inexpensive computational cost. In this work, we develop a double-well ultra-coarse-grained (DW-UCG) model to describe the conformational transitions of the adenylate kinase, glutamine-binding protein, and lactoferrin. The coarse-grained simulation results show that the DW-UCG model of adenylate kinase captures the crucial intermediate states in the LID-closing and NMP-closing pathways, reflecting the key secondary structural changes in the conformational transition. A comparison of the different DW-UCG models of adenylate kinase indicates that an appropriate choice of bead resolution could generate the free energy landscape that is comparable to that from the residue-based model. The coarse-grained simulations for the glutamine-binding protein and lactoferrin also demonstrate that the DW-UCG model is valid in reproducing the correct two-state behavior for their functional study, which indicates the potential application of the DW-UCG model in investigating the mechanism of conformational changes of large proteins.
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Affiliation(s)
- Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University, Xiamen 361005, China.,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University, Xiamen 361005, China
| | - John Zenghui Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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18
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Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities. Commun Biol 2020; 3:419. [PMID: 32747735 PMCID: PMC7400645 DOI: 10.1038/s42003-020-01149-z] [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: 03/09/2020] [Accepted: 07/14/2020] [Indexed: 11/08/2022] Open
Abstract
Protein dynamics plays key roles in ligand binding. However, the microscopic description of conformational dynamics-coupled ligand binding remains a challenge. In this study, we integrate molecular dynamics simulations, Markov state model (MSM) analysis and experimental methods to characterize the conformational dynamics of ligand-bound glutamine binding protein (GlnBP). We show that ligand-bound GlnBP has high conformational flexibility and additional metastable binding sites, presenting a more complex energy landscape than the scenario in the absence of ligand. The diverse conformations of GlnBP demonstrate different binding affinities and entail complex transition kinetics, implicating a concerted ligand binding mechanism. Single molecule fluorescence resonance energy transfer measurements and mutagenesis experiments are performed to validate our MSM-derived structure ensemble as well as the binding mechanism. Collectively, our study provides deeper insights into the protein dynamics-coupled ligand binding, revealing an intricate regulatory network underlying the apparent binding affinity. Zhang, Wu, Feng et al. show that ligand-bound glutamine binding protein assumes multiple metastable binding sites, presenting a more dynamic energy landscape than its ligand-free form. This study provides insights into the ligand-binding mechanisms coupled with protein dynamics that underly the apparent binding affinity.
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19
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Ciftci D, Huysmans GHM, Wang X, He C, Terry D, Zhou Z, Fitzgerald G, Blanchard SC, Boudker O. Single-molecule transport kinetics of a glutamate transporter homolog shows static disorder. SCIENCE ADVANCES 2020; 6:eaaz1949. [PMID: 32523985 PMCID: PMC7259943 DOI: 10.1126/sciadv.aaz1949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Kinetic properties of membrane transporters are typically poorly defined because high-resolution functional assays analogous to single-channel recordings are lacking. Here, we measure single-molecule transport kinetics of a glutamate transporter homolog from Pyrococcus horikoshii, GltPh, using fluorescently labeled periplasmic amino acid binding protein as a fluorescence resonance energy transfer-based sensor. We show that individual transporters can function at rates varying by at least two orders of magnitude that persist for multiple turnovers. A gain-of-function mutant shows increased population of the fast-acting transporters, leading to a 10-fold increase in the mean transport rate. These findings, which are broadly consistent with earlier single-molecule measurements of GltPh conformational dynamics, suggest that GltPh transport is defined by kinetically distinct populations that exhibit long-lasting "molecular memory."
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Affiliation(s)
- Didar Ciftci
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Tri-Institutional Training Program in Chemical Biology, New York, NY 10065, USA
| | - Gerard H. M. Huysmans
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Xiaoyu Wang
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Changhao He
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Daniel Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Gabriel Fitzgerald
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Tri-Institutional Training Program in Chemical Biology, New York, NY 10065, USA
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Tri-Institutional Training Program in Chemical Biology, New York, NY 10065, USA
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, 10065, USA
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20
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Sabrialabed S, Yang JG, Yariv E, Ben-Tal N, Lewinson O. Substrate recognition and ATPase activity of the E. coli cysteine/cystine ABC transporter YecSC-FliY. J Biol Chem 2020; 295:5245-5256. [PMID: 32144203 PMCID: PMC7170509 DOI: 10.1074/jbc.ra119.012063] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/03/2020] [Indexed: 12/20/2022] Open
Abstract
Sulfur is essential for biological processes such as amino acid biogenesis, iron-sulfur cluster formation, and redox homeostasis. To acquire sulfur-containing compounds from the environment, bacteria have evolved high-affinity uptake systems, predominant among which is the ABC transporter family. Theses membrane-embedded enzymes use the energy of ATP hydrolysis for transmembrane transport of a wide range of biomolecules against concentration gradients. Three distinct bacterial ABC import systems of sulfur-containing compounds have been identified, but the molecular details of their transport mechanism remain poorly characterized. Here we provide results from a biochemical analysis of the purified Escherichia coli YecSC-FliY cysteine/cystine import system. We found that the substrate-binding protein FliY binds l-cystine, l-cysteine, and d-cysteine with micromolar affinities. However, binding of the l- and d-enantiomers induced different conformational changes of FliY, where the l- enantiomer-substrate-binding protein complex interacted more efficiently with the YecSC transporter. YecSC had low basal ATPase activity that was moderately stimulated by apo FliY, more strongly by d-cysteine-bound FliY, and maximally by l-cysteine- or l-cystine-bound FliY. However, at high FliY concentrations, YecSC reached maximal ATPase rates independent of the presence or nature of the substrate. These results suggest that FliY exists in a conformational equilibrium between an open, unliganded form that does not bind to the YecSC transporter and closed, unliganded and closed, liganded forms that bind this transporter with variable affinities but equally stimulate its ATPase activity. These findings differ from previous observations for similar ABC transporters, highlighting the extent of mechanistic diversity in this large protein family.
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Affiliation(s)
- Siwar Sabrialabed
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Janet G Yang
- Department of Chemistry, University of San Francisco, San Francisco, California 94117
| | - Elon Yariv
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6139001, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6139001, Israel
| | - Oded Lewinson
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
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21
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Kooshapur H, Ma J, Tjandra N, Bermejo GA. NMR Analysis of Apo Glutamine‐Binding Protein Exposes Challenges in the Study of Interdomain Dynamics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hamed Kooshapur
- Laboratory of Structural BiophysicsBiochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of Health Bethesda MD 20892 USA
| | - Junhe Ma
- Laboratory of Structural BiophysicsBiochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of Health Bethesda MD 20892 USA
- Present address: Ashland Specialty Ingredients 500 Hercules Rd. Wilmington DE 19808 USA
| | - Nico Tjandra
- Laboratory of Structural BiophysicsBiochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of Health Bethesda MD 20892 USA
| | - Guillermo A. Bermejo
- Office of Intramural ResearchCenter for Information TechnologyNational Institutes of Health Bethesda MD 20892 USA
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22
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Kooshapur H, Ma J, Tjandra N, Bermejo GA. NMR Analysis of Apo Glutamine-Binding Protein Exposes Challenges in the Study of Interdomain Dynamics. Angew Chem Int Ed Engl 2019; 58:16899-16902. [PMID: 31515908 DOI: 10.1002/anie.201911015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Indexed: 02/06/2023]
Abstract
Glutamine-binding protein (GlnBP) displays an apo, "open" and a holo, "closed" crystal form, mutually related by a rigid-body reorientation of its domains. A fundamental question about such large-scale conformational transitions, whether the closed state exists in the absence of ligand, is controversial in the case of GlnBP. NMR observations have indicated no evidence of the closed form, whereas experimentally validated computations have suggested a remarkable ca. 40 % population. Herein, a paramagnetic NMR strategy designed to detect the putative apo-closed species shows that a major population of the latter is highly improbable. Further, NMR residual dipolar couplings collected under three anisotropic conditions do not reveal differential domain alignment and establish that the average solution conformation is satisfied by the apo-open crystal structure. Our results indicate that the computational prediction of large-scale interdomain motions is not trivial and may lead to erroneous conclusions without proper experimental validation.
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Affiliation(s)
- Hamed Kooshapur
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Junhe Ma
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Present address: Ashland Specialty Ingredients, 500 Hercules Rd., Wilmington, DE, 19808, USA
| | - Nico Tjandra
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guillermo A Bermejo
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD, 20892, USA
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23
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Radka CD, Labiuk SL, DeLucas LJ, Aller SG. Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms. Acta Crystallogr D Struct Biol 2019; 75:831-840. [PMID: 31478906 PMCID: PMC6719664 DOI: 10.1107/s2059798319010866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/02/2019] [Indexed: 12/23/2022] Open
Abstract
In the structural biology of bacterial substrate-binding proteins (SBPs), a growing number of comparisons between substrate-bound and substrate-free forms of metal atom-binding (cluster A-I) SBPs have revealed minimal structural differences between forms. These observations contrast with SBPs that bind substrates such as amino acids or nucleic acids and may undergo >60° rigid-body rotations. Substrate transfer in these SBPs is described by a Venus flytrap model, although this model may not apply to all SBPs. In this report, structures are presented of substrate-free (apo) and reconstituted substrate-bound (holo) YfeA, a polyspecific cluster A-I SBP from Yersinia pestis. It is demonstrated that an apo cluster A-I SBP can be purified by fractionation when co-expressed with its cognate transporter, adding an alternative strategy to the mutagenesis or biochemical treatment used to generate other apo cluster A-I SBPs. The apo YfeA structure contains 111 disordered protein atoms in a mobile helix located in the flexible carboxy-terminal lobe. Metal binding triggers a 15-fold reduction in the solvent-accessible surface area of the metal-binding site and reordering of the 111 protein atoms in the mobile helix. The flexible lobe undergoes a 13.6° rigid-body rotation that is driven by a spring-hammer metal-binding mechanism. This asymmetric rigid-body rotation may be unique to metal atom-binding SBPs (i.e. clusters A-I, A-II and D-IV).
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Affiliation(s)
- Christopher D. Radka
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shaunivan L. Labiuk
- Canadian Macromolecular Crystallography Facility, Canadian Light Source, Saskatoon, SK S7N 2V3, Canada
| | - Lawrence J. DeLucas
- Division of Human Exploration and Spaceflight, Aerospace Corporation, El Segundo, CA 90245, USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology, Birmingham, AL 35294, USA
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24
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Matthews N, Kitao A, Laycock S, Hayward S. Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. J Chem Inf Model 2019; 59:2900-2912. [DOI: 10.1021/acs.jcim.9b00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nick Matthews
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, M6-13, Meguro, Tokyo 152-8550, Japan
| | - Stephen Laycock
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Steven Hayward
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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25
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Rahman MM, Machuca MA, Roujeinikova A. Preliminary X-ray crystallographic studies on the Helicobacter pylori ABC transporter glutamine-binding protein GlnH. Drug Discov Ther 2019; 13:52-58. [DOI: 10.5582/ddt.2019.01008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mohammad M. Rahman
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
| | - Mayra A. Machuca
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
- Department of Biochemistry and Molecular Biology, Monash University
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26
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Balasco N, Smaldone G, Ruggiero A, De Simone A, Vitagliano L. Local structural motifs in proteins: Detection and characterization of fragments inserted in helices. Int J Biol Macromol 2018; 118:1924-1930. [PMID: 30017977 DOI: 10.1016/j.ijbiomac.2018.07.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 11/26/2022]
Abstract
The global/local fold of protein structures is stabilized by a variety of specific interactions. A primary role in this context is played by hydrogen bonds. In order to identify novel motifs in proteins, we searched Protein Data Bank structures looking for backbone H-bonds formed by NH groups of two (or more) consecutive residues with consecutive CO groups of distant residues in the sequence. The present analysis unravels the occurrence of recurrent structural motifs that, to the best of our knowledge, had not been characterized in literature. Indeed, these H-bonding patterns are found (i) in a specific parallel β-sheet capping, (ii) in linking of β-hairpins to α-helices, and (iii) in α-helix insertions. Interestingly, structural analyses of these motifs indicate that Gly residues frequently occupy prominent positions. The formation of these motifs is likely favored by the limited propensity of Gly to be embodied in helices/sheets. Of particular interest is the motif corresponding to insertions in helices that was detected in 1% of analyzed structures. Inserted fragments may assume different structures and aminoacid compositions and usually display diversified evolutionary conservation. Since inserted regions are physically separated from the rest of the protein structure, they represent hot spots for ad-hoc protein functionalization.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy.
| | | | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College South Kensington Campus, London SW7 2AZ, UK
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy.
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27
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Ukai H, Araki Y, Kira S, Oikawa Y, May AI, Noda T. Gtr/Ego-independent TORC1 activation is achieved through a glutamine-sensitive interaction with Pib2 on the vacuolar membrane. PLoS Genet 2018; 14:e1007334. [PMID: 29698392 PMCID: PMC5919408 DOI: 10.1371/journal.pgen.1007334] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 03/15/2018] [Indexed: 12/18/2022] Open
Abstract
TORC1 is a central regulator of cell growth in response to amino acids. The role of the evolutionarily conserved Gtr/Rag pathway in the regulation of TORC1 is well-established. Recent genetic studies suggest that an additional regulatory pathway, depending on the activity of Pib2, plays a role in TORC1 activation independently of the Gtr/Rag pathway. However, the interplay between the Pib2 pathway and the Gtr/Rag pathway remains unclear. In this study, we show that Pib2 and Gtr/Ego form distinct complexes with TORC1 in a mutually exclusive manner, implying dedicated functional relationships between TORC1 and Pib2 or Gtr/Rag in response to specific amino acids. Furthermore, simultaneous depletion of Pib2 and the Gtr/Ego system abolishes TORC1 activity and completely compromises the vacuolar localization of TORC1. Thus, the amino acid-dependent activation of TORC1 is achieved through the Pib2 and Gtr/Ego pathways alone. Finally, we show that glutamine induces a dose-dependent increase in Pib2-TORC1 complex formation, and that glutamine binds directly to the Pib2 complex. These data provide strong preliminary evidence for Pib2 functioning as a putative glutamine sensor in the regulation of TORC1. TORC1 is a central regulator of cell growth in response to amino acids. The evolutionarily conserved Gtr/Rag pathway is a well-established TORC1 regulatory pathway. In this study, we show that two molecular machineries, Pib2 and Gtr/Ego, form distinct complexes with TORC1 in a mutually exclusive manner, implying an exclusive functional relationship between TORC1 and Pib2 or Gtr/Rag in response to various amino acids. We also show that the amino acid-dependent activation of TORC1 is achieved through the Pib2 and Gtr/Ego pathways by anchoring them to the vacuolar membrane. Finally, we show that glutamine binds directly to the Pib2 complex and that glutamine enhances Pib2-TORC1 complex formation. Collectively we provide evidence supporting a role for Pib2 as an element of a putative glutamine sensor.
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Affiliation(s)
- Hirofumi Ukai
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Yasuhiro Araki
- Graduate School of Dentistry, Osaka University, Osaka, Japan
- * E-mail: (TN); (YA)
| | - Shintaro Kira
- Graduate School of Dentistry, Osaka University, Osaka, Japan
| | - Yu Oikawa
- Research Center of Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Alexander I. May
- Research Center of Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Takeshi Noda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Graduate School of Dentistry, Osaka University, Osaka, Japan
- * E-mail: (TN); (YA)
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28
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An P, Lewandowski TM, Erbay TG, Liu P, Lin Q. Sterically Shielded, Stabilized Nitrile Imine for Rapid Bioorthogonal Protein Labeling in Live Cells. J Am Chem Soc 2018; 140:4860-4868. [PMID: 29565582 DOI: 10.1021/jacs.8b00126] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In pursuit of fast bioorthogonal reactions, reactive moieties have been increasingly employed for selective labeling of biomolecules in living systems, posing a challenge in attaining reactivity without sacrificing selectivity. To address this challenge, here we report a bioinspired strategy in which molecular shape controls the selectivity of a transient, highly reactive nitrile imine dipole. By tuning the shape of structural pendants attached to the ortho position of the N-aryl ring of diaryltetrazoles-precursors of nitrile imines, we discovered a sterically shielded nitrile imine that favors the 1,3-dipolar cycloaddition over the competing nucleophilic addition. The photogenerated nitrile imine exhibits an extraordinarily long half-life of 102 s in aqueous medium, owing to its unique molecular shape that hinders the approach of a nucleophile as shown by DFT calculations. The utility of this sterically shielded nitrile imine in rapid (∼1 min) bioorthogonal labeling of glucagon receptor in live mammalian cells was demonstrated.
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Affiliation(s)
- Peng An
- Department of Chemistry , State University of New York at Buffalo , Buffalo , New York 14260-3000 , United States
| | - Tracey M Lewandowski
- Department of Chemistry , State University of New York at Buffalo , Buffalo , New York 14260-3000 , United States
| | - Tuğçe G Erbay
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Peng Liu
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Qing Lin
- Department of Chemistry , State University of New York at Buffalo , Buffalo , New York 14260-3000 , United States
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29
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Lv D, Gong W, Zhang Y, Liu Y, Li C. A coarse-grained method to predict the open-to-closed behavior of glutamine binding protein. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Ding YH, Gong Z, Dong X, Liu K, Liu Z, Liu C, He SM, Dong MQ, Tang C. Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links. J Biol Chem 2017; 292:1187-1196. [PMID: 27994050 PMCID: PMC5270465 DOI: 10.1074/jbc.m116.761841] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/25/2016] [Indexed: 11/06/2022] Open
Abstract
Chemical cross-linking coupled with mass spectroscopy (CXMS) provides proximity information for the cross-linked residues and is used increasingly for modeling protein structures. However, experimentally identified cross-links are sometimes incompatible with the known structure of a protein, as the distance calculated between the cross-linked residues far exceeds the maximum length of the cross-linker. The discrepancies may persist even after eliminating potentially false cross-links and excluding intermolecular ones. Thus the "over-length" cross-links may arise from alternative excited-state conformation of the protein. Here we present a method and associated software DynaXL for visualizing the ensemble structures of multidomain proteins based on intramolecular cross-links identified by mass spectrometry with high confidence. Representing the cross-linkers and cross-linking reactions explicitly, we show that the protein excited-state structure can be modeled with as few as two over-length cross-links. We demonstrate the generality of our method with three systems: calmodulin, enzyme I, and glutamine-binding protein, and we show that these proteins alternate between different conformations for interacting with other proteins and ligands. Taken together, the over-length chemical cross-links contain valuable information about protein dynamics, and our findings here illustrate the relationship between dynamic domain movement and protein function.
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Affiliation(s)
- Yue-He Ding
- the National Institute of Biological Sciences, Beijing 102206
| | - Zhou Gong
- From the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071
| | - Xu Dong
- From the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071
| | - Kan Liu
- From the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071
| | - Zhu Liu
- the Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, and
| | - Chao Liu
- the Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, CAS, Beijing 100190, China
| | - Si-Min He
- the Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, CAS, Beijing 100190, China
| | - Meng-Qiu Dong
- the National Institute of Biological Sciences, Beijing 102206,
| | - Chun Tang
- From the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071,
- the Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, and
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31
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Moritsugu K, Terada T, Kidera A. Free-Energy Landscape of Protein–Ligand Interactions Coupled with Protein Structural Changes. J Phys Chem B 2017; 121:731-740. [DOI: 10.1021/acs.jpcb.6b11696] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kei Moritsugu
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehirocho, Tsurumi, Yokohama 230-0045, Japan
| | - Tohru Terada
- Graduate
School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Akinori Kidera
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehirocho, Tsurumi, Yokohama 230-0045, Japan
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32
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Lewinson O, Livnat-Levanon N. Mechanism of Action of ABC Importers: Conservation, Divergence, and Physiological Adaptations. J Mol Biol 2017; 429:606-619. [PMID: 28104364 DOI: 10.1016/j.jmb.2017.01.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 01/08/2023]
Abstract
The past decade has seen a remarkable surge in structural characterization of ATP binding cassette (ABC) transporters, which have spurred a more focused functional analysis of these elaborate molecular machines. As a result, it has become increasingly apparent that there is a substantial degree of mechanistic variation between ABC transporters that function as importers, which correlates with their physiological roles. Here, we summarize recent advances in ABC importers' structure-function studies and provide an explanation as to the origin of the different mechanisms of action.
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Affiliation(s)
- Oded Lewinson
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, 31096 Haifa, Israel.
| | - Nurit Livnat-Levanon
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, 31096 Haifa, Israel
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33
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Hu P, Zhang Z, Shen F, Yu X, Li M, Ni H, Li L. Poly-γ-glutamic acid coupled Pseudomonas putida cells surface-displaying metallothioneins: composited copper(ii) biosorption and inducible flocculation in aqueous solution. RSC Adv 2017. [DOI: 10.1039/c7ra01546a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Schematic illustration of the preparation, biosorption, and induced flocculation of the biocomposite MB546-PGA.
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Affiliation(s)
- Penggao Hu
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Zhongna Zhang
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Fei Shen
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Xun Yu
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Hong Ni
- College of Life Sciences
- Hubei University
- Wuhan 430062
- China
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
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34
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Lv D, Wang C, Li C, Tan J, Zhang X. An efficient perturbation method to predict the functionally key sites of glutamine binding protein. Comput Biol Chem 2016; 67:62-68. [PMID: 28061385 DOI: 10.1016/j.compbiolchem.2016.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/09/2016] [Accepted: 12/15/2016] [Indexed: 12/16/2022]
Abstract
Glutamine-Binding Protein (GlnBP) of Escherichia coli, an important member of the periplasmic binding protein family, is responsible for the first step in the active transport of glutamine across the cytoplasmic membrane. In this work, the functionally key regulation sites of GlnBP were identified by utilizing a perturbation method proposed by our group, in which the residues whose perturbations markedly change the binding free energy between GlnBP and glutamine are considered to be functionally key residues. The results show that besides the substrate binding sites, some other residues distant from the binding pocket, including the ones in the hinge regions between the two domains, the front- and back- door channels and the exposed region, are important for the function of glutamine binding and transport. The predicted results are well consistent with the theoretical and experimental data, which indicates that our method is an effective approach to identify the key residues important for both ligand binding and long-range allosteric signal transmission. This work can provide some insights into the function performance of GlnBP and the physical mechanism of its allosteric regulation.
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Affiliation(s)
- Dashuai Lv
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Cunxin Wang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Jianjun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Xiaoyi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
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35
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Mitchell JA, Whitfield JH, Zhang WH, Henneberger C, Janovjak H, O’Mara ML, Jackson CJ. Rangefinder: A Semisynthetic FRET Sensor Design Algorithm. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua A. Mitchell
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Jason H. Whitfield
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - William H. Zhang
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Christian Henneberger
- Institute
of Neurology, University College London, London, WC1E 6BT, United Kingdom
- German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
- Institute
of Cellular Neurosciences, University of Bonn, 53113 Bonn, Germany
| | - Harald Janovjak
- Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Megan L. O’Mara
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
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36
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Feng Y, Zhang L, Wu S, Liu Z, Gao X, Zhang X, Liu M, Liu J, Huang X, Wang W. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yitao Feng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Lu Zhang
- Department of Chemistry; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
| | - Shaowen Wu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Zhijun Liu
- National Center for Protein Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; Shanghai China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Thuwal 23955 Saudi Arabia
| | - Xu Zhang
- Key Laboratory of Magnetic and Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; Centre for Magnetic Resonance; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan China
| | - Maili Liu
- Key Laboratory of Magnetic and Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; Centre for Magnetic Resonance; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan China
| | - Jianwei Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Xuhui Huang
- Department of Chemistry; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
- Division of Biomedical Engineering; Center of Systems Biology and Human Health; Institute for Advance Study and School of Science; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
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37
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Feng Y, Zhang L, Wu S, Liu Z, Gao X, Zhang X, Liu M, Liu J, Huang X, Wang W. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis. Angew Chem Int Ed Engl 2016; 55:13990-13994. [PMID: 27730716 DOI: 10.1002/anie.201606613] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/28/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Yitao Feng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Lu Zhang
- Department of Chemistry; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
| | - Shaowen Wu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Zhijun Liu
- National Center for Protein Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; Shanghai China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Thuwal 23955 Saudi Arabia
| | - Xu Zhang
- Key Laboratory of Magnetic and Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; Centre for Magnetic Resonance; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan China
| | - Maili Liu
- Key Laboratory of Magnetic and Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; Centre for Magnetic Resonance; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan China
| | - Jianwei Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Xuhui Huang
- Department of Chemistry; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
- Division of Biomedical Engineering; Center of Systems Biology and Human Health; Institute for Advance Study and School of Science; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
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38
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Harada R, Takano Y, Shigeta Y. TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins. J Chem Theory Comput 2016; 12:2436-45. [DOI: 10.1021/acs.jctc.6b00082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ryuhei Harada
- Department
of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- Computational
Engineering Applications Unit, RIKEN, Advanced Center for Computing and Communication, 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Yu Takano
- Department
of Biomedical Information Sciences, Hiroshima City University, 3-4-1
Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Yasuteru Shigeta
- Department
of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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39
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Harada R, Takano Y, Baba T, Shigeta Y. Simple, yet powerful methodologies for conformational sampling of proteins. Phys Chem Chem Phys 2016; 17:6155-73. [PMID: 25659594 DOI: 10.1039/c4cp05262e] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Several biological functions, such as molecular recognition, enzyme catalysis, signal transduction, allosteric regulation, and protein folding, are strongly related to conformational transitions of proteins. These conformational transitions are generally induced as slow dynamics upon collective motions, including biologically relevant large-amplitude fluctuations of proteins. Although molecular dynamics (MD) simulation has become a powerful tool for extracting conformational transitions of proteins, it might still be difficult to reach time scales of the biological functions because the accessible time scales of MD simulations are far from biological time scales, even if straightforward conventional MD (CMD) simulations using massively parallel computers are employed. Thus, it is desirable to develop efficient methods to achieve canonical ensembles with low computational costs. From this perspective, we review several enhanced conformational sampling techniques of biomolecules developed by us. In our methods, multiple independent short-time MD simulations are employed instead of single straightforward long-time CMD simulations. Our basic strategy is as follows: (i) selection of initial seeds (initial structures) for the conformational sampling in restarting MD simulations. Here, the seeds should be selected as candidates with high potential to transit. (ii) Resampling from the selected seeds by initializing velocities in restarting short-time MD simulations. A cycle of these simple protocols might drastically promote the conformational transitions of biomolecules. (iii) Once reactive trajectories extracted from the cycles of short-time MD simulations are obtained, a free energy profile is evaluated by means of umbrella sampling (US) techniques with the weighted histogram analysis method (WHAM) as a post-processing technique. For the selection of the initial seeds, we proposed four different choices: (1) Parallel CaScade molecular dynamics (PaCS-MD), (2) Fluctuation Flooding Method (FFM), (3) Outlier FLOODing (OFLOOD) method, and (4) TaBoo SeArch (TBSA) method. We demonstrate applications of our methods to several biological systems, such as domain motions of proteins with large-amplitude fluctuations, conformational transitions upon ligand binding, and protein folding/refolding to native structures of proteins. Finally, we show the conformational sampling efficiencies of our methods compared with those by CMD simulations and other previously developed enhanced conformational sampling methods.
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Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan.
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40
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Harada R, Nakamura T, Shigeta Y. Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution. J Comput Chem 2015; 37:724-38. [DOI: 10.1002/jcc.24255] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/06/2015] [Accepted: 10/29/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Ryuhei Harada
- Department of Physics Graduate School of Pure and Applied Sciences; University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8571 Japan
- Division of Life Sciences; Center for Computational Sciences, University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8571 Japan
- Computational Engineering Application Unit, RIKEN Advanced Center for Computing and Communication; 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | | | - Yasuteru Shigeta
- Department of Physics Graduate School of Pure and Applied Sciences; University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8571 Japan
- Division of Life Sciences; Center for Computational Sciences, University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8571 Japan
- JST, CREST; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
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41
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Andersen OJ, Grouleff J, Needham P, Walker RC, Jensen F. Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins. J Phys Chem B 2015; 119:14594-603. [PMID: 26482713 DOI: 10.1021/acs.jpcb.5b07816] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Current enhanced sampling molecular dynamics methods for studying large conformational changes in proteins suffer from certain limitations. These include, among others, the need for user defined collective variables, the prerequisite of both start and end point structures of the conformational change, and the need for a priori knowledge of the amount by which to boost specific parts of the potential. In this paper, a framework is proposed for a molecular dynamics method for studying ligand-induced conformational changes, in which the nonbonded interactions between the ligand and the protein are used to calculate a biasing force. The method requires only a single input structure, and does not entail the use of collective variables. We provide a proof-of-concept for accelerating conformational changes in three simple test molecules, as well as promising results for two proteins known to undergo domain closure upon ligand binding. For the ribose-binding protein, backbone root-mean-square deviations as low as 0.75 Å compared to the crystal structure of the closed conformation are obtained within 50 ns simulations, whereas no domain closures are observed in unbiased simulations. A skewed closed structure is obtained for the glutamine-binding protein at high bias values, indicating that specific protein-ligand interactions might suppress important protein-protein interactions.
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Affiliation(s)
- Ole Juul Andersen
- Department of Chemistry, Aarhus University , Aarhus, Denmark.,Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark
| | - Julie Grouleff
- Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Perri Needham
- San Diego Supercomputer Center , 10100 Hopkins Drive, La Jolla, California 92093-0505, United States
| | - Ross C Walker
- San Diego Supercomputer Center , 10100 Hopkins Drive, La Jolla, California 92093-0505, United States.,Department of Chemistry and Biochemistry, UC San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Frank Jensen
- Department of Chemistry, Aarhus University , Aarhus, Denmark
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42
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Jin X, Awale M, Zasso M, Kostro D, Patiny L, Reymond JL. PDB-Explorer: a web-based interactive map of the protein data bank in shape space. BMC Bioinformatics 2015; 16:339. [PMID: 26493835 PMCID: PMC4619230 DOI: 10.1186/s12859-015-0776-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/14/2015] [Indexed: 11/17/2022] Open
Abstract
Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB. ᅟ ᅟMaps of PDB in 3DP-space color-coded by heavy atom count and shape. ![]()
Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0776-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Jin
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland.
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland.
| | - Michaël Zasso
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland.
| | - Daniel Kostro
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland.
| | - Luc Patiny
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland.
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland.
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43
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Harada R, Kitao A. Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins. J Chem Theory Comput 2015; 11:5493-502. [PMID: 26574337 DOI: 10.1021/acs.jctc.5b00723] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is proposed as an efficient conformational sampling method to enhance the conformational transitions of proteins, which is an extension of the original targeted PaCS-MD (t-PaCS-MD). The original PaCS-MD comprises cycles of (i) selection of initial structures for multiple independent MD simulations toward a predetermined target and (ii) conformational sampling by the independent MDs. In nt-PaCS-MD, structures that significantly deviate from an average are regarded as candidates that have high potential to address other metastable states and are chosen as the initial structures in the selection. To select significantly deviated structures, we examine the root-mean-square deviation (RMSD) of snapshots generated from the average structure based on Gram-Schmidt orthogonalization. nt-PaCS-MD was applied to the folding of the mini-protein chignolin in implicit solvent and to the open-closed conformational transitions of T4 lysozyme (T4L) and glutamine binding protein (QBP) in explicit solvent. We show that nt-PaCS-MD can reach chignolin's native state and can also cause the open-closed transition of T4L and QBP on a nanosecond time scale, which are very efficient in terms of conformational sampling and comparable to that with t-PaCS-MD.
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Affiliation(s)
| | - Akio Kitao
- Institute of Molecular and Cellular Bioscience, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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44
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Abstract
This review considers the pathways for the degradation of amino acids and a few related compounds (agmatine, putrescine, ornithine, and aminobutyrate), along with their functions and regulation. Nitrogen limitation and an acidic environment are two physiological cues that regulate expression of several amino acid catabolic genes. The review considers Escherichia coli, Salmonella enterica serovar Typhimurium, and Klebsiella species. The latter is included because the pathways in Klebsiella species have often been thoroughly characterized and also because of interesting differences in pathway regulation. These organisms can essentially degrade all the protein amino acids, except for the three branched-chain amino acids. E. coli, Salmonella enterica serovar Typhimurium, and Klebsiella aerogenes can assimilate nitrogen from D- and L-alanine, arginine, asparagine, aspartate, glutamate, glutamine, glycine, proline, and D- and L-serine. There are species differences in the utilization of agmatine, citrulline, cysteine, histidine, the aromatic amino acids, and polyamines (putrescine and spermidine). Regardless of the pathway of glutamate synthesis, nitrogen source catabolism must generate ammonia for glutamine synthesis. Loss of glutamate synthase (glutamineoxoglutarate amidotransferase, or GOGAT) prevents utilization of many organic nitrogen sources. Mutations that create or increase a requirement for ammonia also prevent utilization of most organic nitrogen sources.
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45
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Maruyama Y, Itoh T, Kaneko A, Nishitani Y, Mikami B, Hashimoto W, Murata K. Structure of a Bacterial ABC Transporter Involved in the Import of an Acidic Polysaccharide Alginate. Structure 2015; 23:1643-1654. [PMID: 26235029 DOI: 10.1016/j.str.2015.06.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/05/2015] [Accepted: 06/24/2015] [Indexed: 12/15/2022]
Abstract
The acidic polysaccharide alginate represents a promising marine biomass for the microbial production of biofuels, although the molecular and structural characteristics of alginate transporters remain to be clarified. In Sphingomonas sp. A1, the ATP-binding cassette transporter AlgM1M2SS is responsible for the import of alginate across the cytoplasmic membrane. Here, we present the substrate-transport characteristics and quaternary structure of AlgM1M2SS. The addition of poly- or oligoalginate enhanced the ATPase activity of reconstituted AlgM1M2SS coupled with one of the periplasmic solute-binding proteins, AlgQ1 or AlgQ2. External fluorescence-labeled oligoalginates were specifically imported into AlgM1M2SS-containing proteoliposomes in the presence of AlgQ2, ATP, and Mg(2+). The crystal structure of AlgQ2-bound AlgM1M2SS adopts an inward-facing conformation. The interaction between AlgQ2 and AlgM1M2SS induces the formation of an alginate-binding tunnel-like structure accessible to the solvent. The translocation route inside the transmembrane domains contains charged residues suitable for the import of acidic saccharides.
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Affiliation(s)
- Yukie Maruyama
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takafumi Itoh
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Ai Kaneko
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Yu Nishitani
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Wataru Hashimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
| | - Kousaku Murata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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46
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Farabella I, Vasishtan D, Joseph AP, Pandurangan AP, Sahota H, Topf M. TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits. J Appl Crystallogr 2015; 48:1314-1323. [PMID: 26306092 PMCID: PMC4520291 DOI: 10.1107/s1600576715010092] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 05/24/2015] [Indexed: 12/21/2022] Open
Abstract
TEMPy is an object-oriented Python library that provides the means to validate density fits in electron microscopy reconstructions. This article highlights several features of particular interest for this purpose and includes some customized examples. Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.
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Affiliation(s)
- Irene Farabella
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet street, London WC1E 7HX, UK
| | - Daven Vasishtan
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford OX3 7BN, UK
| | - Agnel Praveen Joseph
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell , Didcot, Oxon OX11 0QX, UK
| | - Arun Prasad Pandurangan
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet street, London WC1E 7HX, UK
| | - Harpal Sahota
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet street, London WC1E 7HX, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet street, London WC1E 7HX, UK
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47
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Dawe GB, Aurousseau MR, Daniels BA, Bowie D. Retour aux sources: defining the structural basis of glutamate receptor activation. J Physiol 2015; 593:97-110. [PMID: 25556791 PMCID: PMC4293057 DOI: 10.1113/jphysiol.2014.277921] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/05/2014] [Indexed: 01/12/2023] Open
Abstract
Ionotropic glutamate receptors (iGluRs) are the major excitatory neurotransmitter receptor in the vertebrate CNS and, as a result, their activation properties lie at the heart of much of the neuronal network activity observed in the developing and adult brain. iGluRs have also been implicated in many nervous system disorders associated with postnatal development (e.g. autism, schizophrenia), cerebral insult (e.g. stroke, epilepsy), and disorders of the ageing brain (e.g. Alzheimer's disease, Parkinsonism). In view of this, an emphasis has been placed on understanding how iGluRs activate and desensitize in functional and structural terms. Early structural models of iGluRs suggested that the strength of the agonist response was primarily governed by the degree of closure induced in the ligand-binding domain (LBD). However, recent studies have suggested a more nuanced role for the LBD with current evidence identifying the iGluR LBD interface as a "hotspot" regulating agonist behaviour. Such ideas remain to be consolidated with recently solved structures of full-length iGluRs to account for the global changes that underlie channel activation and desensitization.
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Affiliation(s)
- G Brent Dawe
- Integrated Program in Neuroscience, McGill UniversityMontréal, Québec, Canada
- Department of Pharmacology and Therapeutics, McGill UniversityMontréal, Québec, Canada
| | - Mark R Aurousseau
- Graduate Program in Pharmacology, McGill UniversityMontréal, Québec, Canada
- Department of Pharmacology and Therapeutics, McGill UniversityMontréal, Québec, Canada
| | - Bryan A Daniels
- Department of Pharmacology and Therapeutics, McGill UniversityMontréal, Québec, Canada
| | - Derek Bowie
- Department of Pharmacology and Therapeutics, McGill UniversityMontréal, Québec, Canada
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48
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Lai Z, Zhang K, Wang J. Exploring multi-dimensional coordinate-dependent diffusion dynamics on the energy landscape of protein conformation change. Phys Chem Chem Phys 2014; 16:6486-95. [PMID: 24605364 DOI: 10.1039/c3cp54476a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We explore the multi-dimensional diffusion dynamics of protein conformational change. We found in general that the diffusion is anisotropic and inhomogeneous. The directional and positional dependence of diffusion have significant impacts on the protein conformational kinetics: the dominant kinetic path of conformational change is shifted from the naively expected steepest decent gradient paths. The kinetic transition state is shifted away from the transition state. The effective kinetic free energy barrier height, determining the kinetic rate of the conformational change, is shifted away from the one estimated from the thermodynamic free energy barrier. The shift of the transition state in position and value will modify the phi value analysis for identification of hot residues and interactions responsible for conformational dynamics. Ongoing and future experiments can test the predictions of the model.
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Affiliation(s)
- Zaizhi Lai
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, USA.
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49
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Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci U S A 2013; 110:20533-8. [PMID: 24297889 DOI: 10.1073/pnas.1315625110] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A long-standing problem in molecular biology is the determination of a complete functional conformational landscape of proteins. This includes not only proteins' native structures, but also all their respective functional states, including functionally important intermediates. Here, we reveal a signature of functionally important states in several protein families, using direct coupling analysis, which detects residue pair coevolution of protein sequence composition. This signature is exploited in a protein structure-based model to uncover conformational diversity, including hidden functional configurations. We uncovered, with high resolution (mean ~1.9 Å rmsd for nonapo structures), different functional structural states for medium to large proteins (200-450 aa) belonging to several distinct families. The combination of direct coupling analysis and the structure-based model also predicts several intermediates or hidden states that are of functional importance. This enhanced sampling is broadly applicable and has direct implications in protein structure determination and the design of ligands or drugs to trap intermediate states.
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50
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van Heeswijk WC, Westerhoff HV, Boogerd FC. Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 2013; 77:628-95. [PMID: 24296575 PMCID: PMC3973380 DOI: 10.1128/mmbr.00025-13] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.
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