1
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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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2
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Hayward S. A Retrospective on the Development of Methods for the Analysis of Protein Conformational Ensembles. Protein J 2023:10.1007/s10930-023-10113-9. [PMID: 37072659 DOI: 10.1007/s10930-023-10113-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 04/20/2023]
Abstract
Analysing protein conformational ensembles whether from molecular dynamics (MD) simulation or other sources for functionally relevant conformational changes can be very challenging. In the nineteen nineties dimensional reduction methods were developed primarily for analysing MD trajectories to determine dominant motions with the aim of understanding their relationship to function. Coarse-graining methods were also developed so the conformational change between two structures could be described in terms of the relative motion of a small number of quasi-rigid regions rather than in terms of a large number of atoms. When these methods are combined, they can characterize the large-scale motions inherent in a conformational ensemble providing insight into possible functional mechanism. The dimensional reduction methods first applied to protein conformational ensembles were referred to as Quasi-Harmonic Analysis, Principal Component Analysis and Essential Dynamics Analysis. A retrospective on the origin of these methods is presented, the relationships between them explained, and more recent developments reviewed.
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Affiliation(s)
- Steven Hayward
- Laboratory for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich, UK.
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3
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Zhang Y, Zhong X, Su S, Huang G. Discovery of Novel Prebiotic Carbohydrates and Sugar Mimics of BlMsmE, a Solute-Binding Protein of the ABC Transporter from Bacillus licheniformis. J Phys Chem B 2020; 124:9996-10006. [DOI: 10.1021/acs.jpcb.0c05583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yubo Zhang
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Xianfeng Zhong
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Siyun Su
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Guidong Huang
- Department of Food Science, Foshan University, Foshan 528231, China
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4
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Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins. Curr Res Struct Biol 2020; 2:180-190. [PMID: 34235478 PMCID: PMC8244415 DOI: 10.1016/j.crstbi.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
Two mechanisms, induced fit (IF) and conformational selection (CS), have been proposed to explain ligand recognition coupled conformational changes. The histidine binding protein (HisJ) adopts the CS mechanism, in which a pre-equilibrium is established between the open and the closed states with the ligand binding to the closed state. Despite being structurally similar to HisJ, the maltose binding protein (MBP) adopts the IF mechanism, in which the ligand binds the open state and induces a transition to the closed state. To understand the molecular determinants of this difference, we performed molecular dynamics (MD) simulations of coarse-grained dual structure based models. We find that intra-protein contacts unique to the closed state are sufficient to promote the conformational transition in HisJ, indicating a CS-like mechanism. In contrast, additional ligand-mimicking contacts are required to “induce” the conformational transition in MBP suggesting an IF-like mechanism. In agreement with experiments, destabilizing modifications to two structural features, the spine helix (SH) and the balancing interface (BI), present in MBP but absent in HisJ, reduce the need for ligand-mimicking contacts indicating that SH and BI act as structural restraints that keep MBP in the open state. We introduce an SH like element into HisJ and observe that this can impede the conformational transition increasing the importance of ligand-mimicking contacts. Similarly, simultaneous mutations to BI and SH in MBP reduce the barrier to conformational transitions significantly and promote a CS-like mechanism. Together, our results show that structural restraints present in the protein structure can determine the mechanism of conformational transitions and even simple models that correctly capture such structural features can predict their positions. MD simulations of such models can thus be used, in conjunction with mutational experiments, to regulate protein ligand interactions, and modulate ligand binding affinities. MBP operates by induced fit, HisJ by the conformational selection mechanism. Dual structure based models (dSBMs) encode two structures of a protein. MD simulations of dSBMs can identify the mechanism of conformational transitions. Locks, absent in HisJ, hold MBP open with ligand contacts required for closing. Binding mechanisms can be modified by altering such structural locks.
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Key Words
- BI, Balancing interface
- CS, conformational selection
- CTD, C-terminal domain
- Conformational selection
- Dual structure based models
- FEP, free energy profile
- HisJ, histidine binding protein
- IF, induced fit
- Induced fit
- MBP, maltose binding protein
- MD simulations
- MD, molecular dynamics
- NTD, N-terminal domain
- PBP, periplasmic binding protein
- Periplasmic binding proteins
- SH, spine helix
- Structural restraints
- WT, wild-type
- dSBM, dual structure-based model
- sSBM, single structure-based model
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5
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Kondo HX, Kiribayashi R, Kuroda D, Kohda J, Kugimiya A, Nakano Y, Tsumoto K, Takano Y. Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16. Sci Rep 2019; 9:19840. [PMID: 31882602 PMCID: PMC6934664 DOI: 10.1038/s41598-019-56154-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/06/2019] [Indexed: 11/22/2022] Open
Abstract
PG16 is a broadly neutralizing antibody to the human immunodeficiency virus (HIV). A crystal structure of PG16 revealed that the unusually long 28-residue complementarity determining region (CDR) H3 forms a unique subdomain, referred to as a "hammerhead", that directly contacts the antigen. The hammerhead apparently governs the function of PG16 while a previous experimental assay showed that the mutation of TyrH100Q to Ala, which does not directly contact the antigen, decreased the neutralization ability of PG16. However, the molecular mechanism by which a remote mutation from the hammerhead or contact paratope affects the neutralization potency has remained unclear. Here, we performed molecular dynamics simulations of the wild-type and variants (TyrH100Q to Ala, and TyrH100Q to Phe) of PG16, to clarify the effects of these mutations on the dynamics of CDR-H3. Our simulations revealed that the structural rigidity of the CDR-H3 in PG16 is attributable to the hydrogen bond interaction between TyrH100Q and ProH99, as well as the steric support by TyrH100Q. The loss of both interactions increases the intrinsic fluctuations of the CDR-H3 in PG16, leading to a conformational transition of CDR-H3 toward an inactive state.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, Kitami, 090-8507, Japan.
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan.
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, Suita, 565-0874, Japan.
| | - Ryo Kiribayashi
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan
| | - Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
| | - Jiro Kohda
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan
| | - Akimitsu Kugimiya
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan
| | - Yasuhisa Nakano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan
| | - Kouhei Tsumoto
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan.
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6
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Abstract
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they face a distinct set of challenges compared with more familiar human-engineered macroscopic machines. Here we review central questions in their performance as free energy transducers, outline theoretical and modeling approaches to understand these questions, identify both physical limits on their operational characteristics and design principles for improving performance, and discuss emerging areas of research.
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Affiliation(s)
- Aidan I Brown
- Department of Physics , University of California, San Diego , La Jolla , California 92093 , United States
| | - David A Sivak
- Department of Physics , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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7
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Roccatano D, Hayward S. Free Energy Profile of Domain Movement in Ligand-Free Citrate Synthase. J Phys Chem B 2019; 123:1998-2004. [PMID: 30744380 DOI: 10.1021/acs.jpcb.8b12001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Citrate synthase plays a fundamental role in the metabolic cycle of the cell. Its catalytic mechanism is complex involving the binding of two substrates that cause a domain movement. In this paper, we used classical molecular dynamics simulations and umbrella-sampling simulations to determine the potential of mean force along a reaction coordinate for the domain movement in ligand-free citrate synthase from pig ( Sus scrofa). The results show that, at 293 K, the closed-domain conformation has a ∼4 kb T higher energy than the open-domain conformation. In a simple two-state model, this difference means that the enzyme spends 98% of the time in the open-domain conformation ready to receive the substrate, oxaloacetate, rather than the closed-domain conformation where the binding site would be inaccessible to the substrate. Given that experimental evidence indicates that the binding of oxaloacetate induces at least partial closure, this would imply an induced-fit mechanism which we argue is applicable to all enzymes with a functional domain movement for reasons of catalytic efficiency. A barrier of 4 kb T gives an estimation of the mean first passage time in the range 1-10 μs.
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Affiliation(s)
- Danilo Roccatano
- School of Mathematics and Physics , University of Lincoln , Brayford Pool, Lincoln LN6 7TS , United Kingdom
| | - Steven Hayward
- Computational Biology Laboratory, School of Computing Sciences , University of East Anglia , Norwich NR4 7TJ , United Kingdom
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8
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McCluskey K, Carlos Penedo J. An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters. Phys Chem Chem Phys 2018; 19:6921-6932. [PMID: 28225108 DOI: 10.1039/c6cp08798a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Riboswitches are short RNA motifs that sensitively and selectively bind cognate ligands to modulate gene expression. Like protein receptor-ligand pairs, their binding dynamics are traditionally categorized as following one of two paradigmatic mechanisms: conformational selection and induced fit. In conformational selection, ligand binding stabilizes a particular state already present in the receptor's dynamic ensemble. In induced fit, ligand-receptor interactions enable the system to overcome the energetic barrier into a previously inaccessible state. In this article, we question whether a polarized division of RNA binding mechanisms truly meets the conceptual needs of the field. We will review the history behind this classification of RNA-ligand interactions, and the way induced fit in particular has been rehabilitated by single-molecule studies of RNA aptamers. We will highlight several recent results from single-molecule experimental studies of riboswitches that reveal gaps or even contradictions between common definitions of the two terms, and we will conclude by proposing a more robust framework that considers the range of RNA behaviors unveiled in recent years as a reality to be described, rather than an increasingly unwieldy set of exceptions to the traditional models.
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Affiliation(s)
- K McCluskey
- Department of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK.
| | - J Carlos Penedo
- Department of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK. and Biomolecular Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9SS, UK.
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9
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Harada R, Shigeta Y. An assessment of optimal time scale of conformational resampling for parallel cascade selection molecular dynamics. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1362696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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10
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Harada R, Shigeta Y. Structural dissimilarity sampling with dynamically self-guiding selection. J Comput Chem 2017; 38:1921-1929. [DOI: 10.1002/jcc.24837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/26/2017] [Accepted: 05/02/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Ryuhei Harada
- Division of Life Science, Center for Computational Sciences, University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Yasuteru Shigeta
- Division of Life Science, Center for Computational Sciences, University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
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11
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Sakuraba S, Kono H. Spotting the difference in molecular dynamics simulations of biomolecules. J Chem Phys 2017; 145:074116. [PMID: 27544096 DOI: 10.1063/1.4961227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (LDA-ITER) to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the "difference" between two trajectories.
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Affiliation(s)
- Shun Sakuraba
- Molecular Modeling and Simulation Group, Quantum Beam Science Center, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kidugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kidugawa, Kyoto 619-0215, Japan
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12
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Lv D, Li C, Tan J, Zhang X, Wang C, Su J. Identification of functionally key residues in maltose transporter with an elastic network model-based thermodynamic method. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1234077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Dashuai Lv
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Chunhua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Jianjun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Xiaoyi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Cunxin Wang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Jiguo Su
- College of Science, Yanshan University, Qinhuangdao, China
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13
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Moree B, Connell K, Mortensen RB, Liu CT, Benkovic SJ, Salafsky J. Protein Conformational Changes Are Detected and Resolved Site Specifically by Second-Harmonic Generation. Biophys J 2016; 109:806-15. [PMID: 26287632 PMCID: PMC4547196 DOI: 10.1016/j.bpj.2015.07.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/29/2015] [Accepted: 07/02/2015] [Indexed: 12/21/2022] Open
Abstract
We present here a straightforward, broadly applicable technique for real-time detection and measurement of protein conformational changes in solution. This method is based on tethering proteins labeled with a second-harmonic generation (SHG) active dye to supported lipid bilayers. We demonstrate our method by measuring the conformational changes that occur upon ligand binding with three well-characterized proteins labeled at lysine residues: calmodulin (CaM), maltose-binding protein (MBP), and dihydrofolate reductase (DHFR). We also create a single-site cysteine mutant of DHFR engineered within the Met20 catalytic loop region and study the protein’s structural motion at this site. Using published x-ray crystal structures, we show that the changes in the SHG signals upon ligand binding are the result of structural motions that occur at the labeled sites between the apo and ligand-bound forms of the proteins, which are easily distinguished from each other. In addition, we demonstrate that different magnitudes of the SHG signal changes are due to different and specific ligand-induced conformational changes. Taken together, these data illustrate the potential of the SHG approach for detecting and measuring protein conformational changes for a wide range of biological applications.
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Affiliation(s)
- Ben Moree
- Biodesy, Inc., South San Francisco, California
| | | | | | - C Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania
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14
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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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15
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Huang W, Blinov N, Wishart DS, Kovalenko A. Role of water in ligand binding to maltose-binding protein: insight from a new docking protocol based on the 3D-RISM-KH molecular theory of solvation. J Chem Inf Model 2015; 55:317-28. [PMID: 25545470 DOI: 10.1021/ci500520q] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maltose-binding protein is a periplasmic binding protein responsible for transport of maltooligosaccarides through the periplasmic space of Gram-negative bacteria, as a part of the ABC transport system. The molecular mechanisms of the initial ligand binding and induced large scale motion of the protein's domains still remain elusive. In this study, we use a new docking protocol that combines a recently proposed explicit water placement algorithm based on the 3D-RISM-KH molecular theory of solvation and conventional docking software (AutoDock Vina) to explain the mechanisms of maltotriose binding to the apo-open state of a maltose-binding protein. We confirm the predictions of previous NMR spectroscopic experiments on binding modes of the ligand. We provide the molecular details on the binding mode that was not previously observed in the X-ray experiments. We show that this mode, which is defined by the fine balance between the protein-ligand direct interactions and solvation effects, can trigger the protein's domain motion resulting in the holo-closed structure of the maltose-binding protein with the maltotriose ligand in excellent agreement with the experimental data. We also discuss the role of water in blocking unfavorable binding sites and water-mediated interactions contributing to the stability of observable binding modes of maltotriose.
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Affiliation(s)
- WenJuan Huang
- Department of Mechanical Engineering, University of Alberta , Edmonton, AB T6G 2G8, Canada
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16
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Ermakova E, Kurbanov R. Effect of ligand binding on the dynamics of trypsin. Comparison of different approaches. J Mol Graph Model 2014; 49:99-109. [PMID: 24642055 DOI: 10.1016/j.jmgm.2014.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 11/17/2022]
Abstract
The intramolecular signal transduction induced by the binding of ligands to trypsin was investigated by molecular dynamics simulations. Ligand binding changes the residue-residue interaction energies and suppresses the mobility of loops that are in direct contact with the ligand. The reduced mobility of these loops results in the altered flexibility of the nearby loops and thereby transmits the information from ligand binding site to the remote sites. The analysis of the flexibility of all residues confirmed the coupling between loops L1 (185-188) and L2 (221-224) and the residues in the active center. The significance of S1 pocket residues for the signal transduction from the active center to the substrate-binding site was confirmed by the dynamical network and covariance matrix analyses. Gaussian network model and principal component analysis demonstrated that the active center residues had zero amplitude in the slowest fluctuations acting as hinges or anchors. Overall, our results provide a new insight into protein-ligand interactions and show how the allosteric signaling may occur.
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Affiliation(s)
- Elena Ermakova
- Kazan Institute of Biochemistry and Biophysics RAS, P.O. Box 30, Kazan 420111, Russia.
| | - Rauf Kurbanov
- Kazan Institute of Biochemistry and Biophysics RAS, P.O. Box 30, Kazan 420111, Russia
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17
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Daniels KG, Tonthat NK, McClure DR, Chang YC, Liu X, Schumacher MA, Fierke CA, Schmidler SC, Oas TG. Ligand concentration regulates the pathways of coupled protein folding and binding. J Am Chem Soc 2014; 136:822-5. [PMID: 24364358 DOI: 10.1021/ja4086726] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coupled ligand binding and conformational change plays a central role in biological regulation. Ligands often regulate protein function by modulating conformational dynamics, yet the order in which binding and conformational change occurs are often hotly debated. Here we show that the "conformational selection versus induced fit" distinction on which this debate is based is a false dichotomy because the mechanism depends on ligand concentration. Using the binding of pyrophosphate (PPi) to Bacillus subtilis RNase P protein as a model, we show that coupled reactions are best understood as a change in flux between competing pathways with distinct orders of binding and conformational change. The degree of partitioning through each pathway depends strongly on PPi concentration, with ligand binding redistributing the conformational ensemble toward the folded state by both increasing folding rates and decreasing unfolding rates. These results indicate that ligand binding induces marked and varied changes in protein conformational dynamics, and that the order of binding and conformational change is ligand concentration dependent.
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Affiliation(s)
- Kyle G Daniels
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
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18
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Lukman S, Verma CS, Fuentes G. Exploiting Protein Intrinsic Flexibility in Drug Design. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:245-69. [DOI: 10.1007/978-3-319-02970-2_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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19
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Wang J, Shao Q, Xu Z, Liu Y, Yang Z, Cossins BP, Jiang H, Chen K, Shi J, Zhu W. Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics. J Phys Chem B 2013; 118:134-43. [PMID: 24350625 DOI: 10.1021/jp4105129] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Large-scale conformational changes of proteins are usually associated with the binding of ligands. Because the conformational changes are often related to the biological functions of proteins, understanding the molecular mechanisms of these motions and the effects of ligand binding becomes very necessary. In the present study, we use the combination of normal-mode analysis and umbrella sampling molecular dynamics simulation to delineate the atomically detailed conformational transition pathways and the associated free-energy landscapes for three well-known protein systems, viz., adenylate kinase (AdK), calmodulin (CaM), and p38α kinase in the absence and presence of respective ligands. For each protein under study, the transient conformations along the conformational transition pathway and thermodynamic observables are in agreement with experimentally and computationally determined ones. The calculated free-energy profiles reveal that AdK and CaM are intrinsically flexible in structures without obvious energy barrier, and their ligand binding shifts the equilibrium from the ligand-free to ligand-bound conformation (population shift mechanism). In contrast, the ligand binding to p38α leads to a large change in free-energy barrier (ΔΔG ≈ 7 kcal/mol), promoting the transition from DFG-in to DFG-out conformation (induced fit mechanism). Moreover, the effect of the protonation of D168 on the conformational change of p38α is also studied, which reduces the free-energy difference between the two functional states of p38α and thus further facilitates the conformational interconversion. Therefore, the present study suggests that the detailed mechanism of ligand binding and the associated conformational transition is not uniform for all kinds of proteins but correlated to their respective biological functions.
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Affiliation(s)
- Jinan Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, 201203, China
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20
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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21
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22
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A single-molecule dissection of ligand binding to a protein with intrinsic dynamics. Nat Chem Biol 2013; 9:313-8. [DOI: 10.1038/nchembio.1213] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 02/21/2013] [Indexed: 01/12/2023]
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23
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Merstorf C, Maciejak O, Mathé J, Pastoriza-Gallego M, Thiebot B, Clément MJ, Pelta J, Auvray L, Curmi PA, Savarin P. Mapping the conformational stability of maltose binding protein at the residue scale using nuclear magnetic resonance hydrogen exchange experiments. Biochemistry 2012; 51:8919-30. [PMID: 23046344 DOI: 10.1021/bi3003605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Being able to differentiate local fluctuations from global folding-unfolding dynamics of a protein is of major interest for improving our understanding of structure-function determinants. The maltose binding protein (MBP), a protein that belongs to the maltose transport system, has a structure composed of two globular domains separated by a rigid-body "hinge bending". Here we determined, by using hydrogen exchange (HX) nuclear magnetic resonance experiments, the apparent stabilization free energies of 101 residues of MBP bound to β-cyclodextrin (MBP-βCD) under native conditions. We observed that the last helix of MBP (helix α14) has a lower protection factor than the rest of the protein. Further, HX experiments were performed using guanidine hydrochloride under subdenaturing conditions to discriminate between local fluctuations and global unfolding events and to determine the MBP-βCD energy landscape. The results show that helix α4 and a part of helices α5 and α6 are clearly grouped into a subdenaturing folding unit and represent a partially folded intermediate under native conditions. In addition, we observed that amide protons located in the hinge between the two globular domains share similar ΔG(gu)(app) and m values and should unfold simultaneously. These observations provide new points of view for improving our understanding of the thermodynamic stability and the mechanisms that drive folding-unfolding dynamics of proteins.
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Affiliation(s)
- Céline Merstorf
- Centre National de la Recherche Scientifique UMR 8587, Université Evry-Val d'Essonne et Cergy Pontoise, Laboratoire d'Analyse et de modélisation pour la Biologie et l'Environnement, Evry 91025, France
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24
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Matsunaga Y, Fujisaki H, Terada T, Furuta T, Moritsugu K, Kidera A. Minimum free energy path of ligand-induced transition in adenylate kinase. PLoS Comput Biol 2012; 8:e1002555. [PMID: 22685395 PMCID: PMC3369945 DOI: 10.1371/journal.pcbi.1002555] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 04/27/2012] [Indexed: 02/01/2023] Open
Abstract
Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme.
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25
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Wang Y, Tang C, Wang E, Wang J. Exploration of multi-state conformational dynamics and underlying global functional landscape of maltose binding protein. PLoS Comput Biol 2012; 8:e1002471. [PMID: 22532792 PMCID: PMC3330084 DOI: 10.1371/journal.pcbi.1002471] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/26/2012] [Indexed: 02/04/2023] Open
Abstract
An increasing number of biological machines have been revealed to have more than two macroscopic states. Quantifying the underlying multiple-basin functional landscape is essential for understanding their functions. However, the present models seem to be insufficient to describe such multiple-state systems. To meet this challenge, we have developed a coarse grained triple-basin structure-based model with implicit ligand. Based on our model, the constructed functional landscape is sufficiently sampled by the brute-force molecular dynamics simulation. We explored maltose-binding protein (MBP) which undergoes large-scale domain motion between open, apo-closed (partially closed) and holo-closed (fully closed) states responding to ligand binding. We revealed an underlying mechanism whereby major induced fit and minor population shift pathways co-exist by quantitative flux analysis. We found that the hinge regions play an important role in the functional dynamics as well as that increases in its flexibility promote population shifts. This finding provides a theoretical explanation of the mechanistic discrepancies in PBP protein family. We also found a functional “backtracking” behavior that favors conformational change. We further explored the underlying folding landscape in response to ligand binding. Consistent with earlier experimental findings, the presence of ligand increases the cooperativity and stability of MBP. This work provides the first study to explore the folding dynamics and functional dynamics under the same theoretical framework using our triple-basin functional model. A central goal of biology is to understand the function of the organism and its constituent parts at each of its scales of complexity. Function at the molecular level is often realized by changes in conformation. Unfortunately, experimental explorations of global motions critical for functional conformational changes are still challenging. In the present work, we developed a coarse grained triple-well structure-based model to explore the underlying functional landscape of maltose-binding protein (MBP). By quantitative flux analysis, we uncover the underlying mechanism by which the major induced fit and minor population shift pathways co-exist. Though we have previously lent credence to the assertion that dynamical equilibrium between open and minor closed conformations exist for all the free PBPs, the generality of this rule is still a matter of open debate. We found that the hinge flexibility is favorable to population shift mechanism. This finding provides a theoretical explanation of the mechanism discrepancies in PBP protein family. We also simulated the folding dynamics using this functional multi-basin model which successfully reproduced earlier protein melting experiment. This represents an exciting opportunity to characterize the interplay between folding and function, which is a long-standing question in the community. The theoretical approach employed in this study is general and can be applied to other systems.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Chun Tang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- * E-mail: (EW); (JW)
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- College of Physics, Jilin University, Changchun, Jilin, China
- Department of Chemistry, Physics and Applied Mathematics, State University of New York at Stony Brook, Stony Brook, New York, United States of America
- * E-mail: (EW); (JW)
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26
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Dietzen M, Zotenko E, Hildebrandt A, Lengauer T. On the applicability of elastic network normal modes in small-molecule docking. J Chem Inf Model 2012; 52:844-56. [PMID: 22320151 DOI: 10.1021/ci2004847] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Incorporating backbone flexibility into protein-ligand docking is still a challenging problem. In protein-protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein-ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a set of conformations that optimally reproduce its C(α) trace with respect to the underlying normal mode subspace. Using AutoDock, GOLD, and FlexX we then docked the original ligands into these conformations to assess how the docking performance depends on the number of modes used to reproduce the holo structure. The results of our study indicate that, even for such a best-case scenario, the use of normal mode analysis in small-molecule docking is restricted and that a general rule on how many modes to use does not seem to exist or at least is not easy to find.
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27
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Bucher D, Grant BJ, McCammon JA. Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry 2011; 50:10530-9. [PMID: 22050600 PMCID: PMC3226325 DOI: 10.1021/bi201481a] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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A full characterization of the thermodynamic forces underlying
ligand-associated conformational changes in proteins is essential
for understanding and manipulating diverse biological processes, including
transport, signaling, and enzymatic activity. Recent experiments on
the maltose binding protein (MBP) have provided valuable data about
the different conformational states implicated in the ligand recognition
process; however, a complete picture of the accessible pathways and
the associated changes in free energy remains elusive. Here we describe
results from advanced accelerated molecular dynamics (aMD) simulations,
coupled with adaptively biased force (ABF) and thermodynamic integration
(TI) free energy methods. The combination of approaches allows us
to track the ligand recognition process on the microsecond time scale
and provides a detailed characterization of the protein’s dynamic
and the relative energy of stable states. We find that an induced-fit
(IF) mechanism is most likely and that a mechanism involving both
a conformational selection (CS) step and an IF step is also possible.
The complete recognition process is best viewed as a “Pac Man”
type action where the ligand is initially localized to one domain
and naturally occurring hinge-bending vibrations in the protein are
able to assist the recognition process by increasing the chances of
a favorable encounter with side chains on the other domain, leading
to a population shift. This interpretation is consistent with experiments
and provides new insight into the complex recognition mechanism. The
methods employed here are able to describe IF and CS effects and provide
formally rigorous means of computing free energy changes. As such,
they are superior to conventional MD and flexible docking alone and
hold great promise for future development and applications to drug
discovery.
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Affiliation(s)
- Denis Bucher
- Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093, United States.
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