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Borges-Araújo L, Pereira GP, Valério M, Souza PCT. Assessing the Martini 3 protein model: A review of its path and potential. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141014. [PMID: 38670324 DOI: 10.1016/j.bbapap.2024.141014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Coarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the organization of protein macro-complexes, and even the interaction of proteins with other molecules. The Martini force field is one of the most widely used CG models for bio-molecular simulations, partly because of the enormous success of its protein model. With the recent release of a new and improved version of the Martini force field - Martini 3 - a new iteration of its protein model was also made available. The Martini 3 protein force field is an evolution of its Martini 2 counterpart, aimed at improving many of the shortcomings that had been previously identified. In this mini-review, we first provide a general overview of the model and then focus on the successful advances made in the short time since its release, many of which would not have been possible before. Furthermore, we discuss reported limitations, potential directions for model improvement and comment on what the likely future development and application avenues are.
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Affiliation(s)
- Luís Borges-Araújo
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Gilberto P Pereira
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Mariana Valério
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Paulo C T Souza
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France.
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2
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Jung J, Yagi K, Tan C, Oshima H, Mori T, Yu I, Matsunaga Y, Kobayashi C, Ito S, Ugarte La Torre D, Sugita Y. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. J Phys Chem B 2024; 128:6028-6048. [PMID: 38876465 PMCID: PMC11215777 DOI: 10.1021/acs.jpcb.4c02096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/16/2024]
Abstract
GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational dynamics of a single biomolecule, as well as molecular interactions in large biomolecular assemblies and between multiple biomolecules in cellular environments. To achieve the latter purpose, the earlier versions of GENESIS emphasized high performance in atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale MD simulations that include atomistic, coarse-grained, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. They demonstrate high performance and are integrated with enhanced conformational sampling algorithms and free-energy calculations without using external programs except for the QM programs. In this article, we review new functions, molecular models, and other essential features in GENESIS version 2.1 and discuss ongoing developments for future releases.
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Affiliation(s)
- Jaewoon Jung
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Cheng Tan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Graduate
School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Takaharu Mori
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department
of Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Isseki Yu
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department
of Bioinformatics, Maebashi Institute of
Technology, Maebashi, Gunma 371-0816, Japan
| | - Yasuhiro Matsunaga
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Graduate
School of Science and Engineering, Saitama
University, Saitama 338-8570, Japan
| | - Chigusa Kobayashi
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Shingo Ito
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Diego Ugarte La Torre
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
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3
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Mora-Gamboa MPC, Ferrucho-Calle MC, Ardila-Leal LD, Rojas-Ojeda LM, Galindo JF, Poutou-Piñales RA, Pedroza-Rodríguez AM, Quevedo-Hidalgo BE. Statistical Improvement of rGILCC 1 and rPOXA 1B Laccases Activity Assay Conditions Supported by Molecular Dynamics. Molecules 2023; 28:7263. [PMID: 37959683 PMCID: PMC10648076 DOI: 10.3390/molecules28217263] [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: 09/06/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Laccases (E.C. 1.10.3.2) are glycoproteins widely distributed in nature. Their structural conformation includes three copper sites in their catalytic center, which are responsible for facilitating substrate oxidation, leading to the generation of H2O instead of H2O2. The measurement of laccase activity (UL-1) results may vary depending on the type of laccase, buffer, redox mediators, and substrates employed. The aim was to select the best conditions for rGILCC 1 and rPOXA 1B laccases activity assay. After sequential statistical assays, the molecular dynamics proved to support this process, and we aimed to accumulate valuable insights into the potential application of these enzymes for the degradation of novel substrates with negative environmental implications. Citrate buffer treatment T2 (CB T2) (pH 3.0 ± 0.2; λ420nm, 2 mM ABTS) had the most favorable results, with 7.315 ± 0.131 UL-1 for rGILCC 1 and 5291.665 ± 45.83 UL-1 for rPOXA 1B. The use of citrate buffer increased the enzyme affinity for ABTS since lower Km values occurred for both enzymes (1.49 × 10-2 mM for rGILCC 1 and 3.72 × 10-2 mM for rPOXA 1B) compared to those obtained in acetate buffer (5.36 × 10-2 mM for rGILCC 1 and 1.72 mM for rPOXA 1B). The molecular dynamics of GILCC 1-ABTS and POXA 1B-ABTS showed stable behavior, with root mean square deviation (RMSD) values not exceeding 2.0 Å. Enzyme activities (rGILCC 1 and rPOXA 1B) and 3D model-ABTS interactions (GILCC 1-ABTS and POXA 1B-ABTS) were under the strong influence of pH, wavelength, ions, and ABTS concentration, supported by computational studies identifying the stabilizing residues and interactions. Integration of the experimental and computational approaches yielded a comprehensive understanding of enzyme-substrate interactions, offering potential applications in environmental substrate treatments.
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Affiliation(s)
- María P. C. Mora-Gamboa
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - María C. Ferrucho-Calle
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - Leidy D. Ardila-Leal
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
- Laboratorio de Biotecnología Vegetal, Grupo de Investigación en Asuntos Ambientales y Desarrollo Sostenible (MINDALA), Departamento de Ciencias Agrarias y del Ambiente, Universidad Francisco de Paula Santander, Ocaña 546552, Colombia
| | - Lina M. Rojas-Ojeda
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Johan F. Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Raúl A. Poutou-Piñales
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - Aura M. Pedroza-Rodríguez
- Laboratorio de Microbiología Ambiental y Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Balkys E. Quevedo-Hidalgo
- Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
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4
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Jung J, Kobayashi C, Sugita Y. Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. J Comput Chem 2023. [PMID: 37141320 DOI: 10.1002/jcc.27124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Generalized replica exchange with solute tempering (gREST) is one of the enhanced sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike the replica-exchange molecular dynamics (REMD) method, solvent temperatures are the same in all replicas, while solute temperatures are different and are exchanged frequently between replicas for exploring various solute structures. Here, we apply the gREST scheme to large biological systems containing over one million atoms using a large number of processors in a supercomputer. First, communication time on a multi-dimensional torus network is reduced by matching each replica to MPI processors optimally. This is applicable not only to gREST but also to other multi-copy algorithms. Second, energy evaluations, which are necessary for the multistate bennet acceptance ratio (MBAR) method for free energy estimations, are performed on-the-fly during the gREST simulations. Using these two advanced schemes, we observed 57.72 ns/day performance in 128-replica gREST calculations with 1.5 million atoms system using 16,384 nodes in Fugaku. These schemes implemented in the latest version of GENESIS software could open new possibilities to answer unresolved questions on large biomolecular complex systems with slow conformational dynamics.
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Affiliation(s)
- Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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5
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An J, Guan J, Nie Y. Semi-Rational Design of L-Isoleucine Dioxygenase Generated Its Activity for Aromatic Amino Acid Hydroxylation. Molecules 2023; 28:molecules28093750. [PMID: 37175159 PMCID: PMC10180240 DOI: 10.3390/molecules28093750] [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: 03/11/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Fe (II)-and 2-ketoglutarate-dependent dioxygenases (Fe (II)/α-KG DOs) have been applied to catalyze hydroxylation of amino acids. However, the Fe (II)/α-KG DOs that have been developed and characterized are not sufficient. L-isoleucine dioxygenase (IDO) is an Fe (II)/α-KG DO that specifically catalyzes the formation of 4-hydroxyisoleucine (4-HIL) from L-isoleucine (L-Ile) and exhibits a substrate specificity toward L-aliphatic amino acids. To expand the substrate spectrum of IDO toward aromatic amino acids, in this study, we analyzed the regularity of the substrate spectrum of IDO using molecular dynamics (MD) simulation and found that the distance between Fe2+, C2 of α-KG and amino acid chain's C4 may be critical for regulating the substrate specificity of the enzyme. The mutation sites (Y143, S153 and R227) were also subjected to single point saturation mutations based on polarity pockets and residue free energy contributions. It was found that Y143D, Y143I and S153A mutants exhibited catalytic L-phenylalanine activity, while Y143I, S153A, S153Q and S153Y exhibited catalytic L-homophenylalanine activity. Consequently, this study extended the substrate spectrum of IDO with aromatic amino acids and enhanced its application property.
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Affiliation(s)
- Jianhong An
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- International Joint Research Laboratory for Brewing Microbiology and Applied Enzymology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- Eye Hospital, Wenzhou Medical University, 270 Xueyuan Road, Wenzhou 325000, China
| | - Jiaojiao Guan
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- International Joint Research Laboratory for Brewing Microbiology and Applied Enzymology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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6
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Salaria P, Akshinthala P, Kapavarapu R, M AR. Identification of novel C-15 fluoro isosteviol derivatives for GABA-AT inhibition by in silico investigations. J Mol Model 2023; 29:76. [PMID: 36826597 DOI: 10.1007/s00894-023-05479-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/17/2023] [Indexed: 02/25/2023]
Abstract
CONTEXT The treatment of epilepsy is associated with the inhibition of γ-aminobutyric acid-aminotransferase (GABA-AT), which suppresses the concentration of a key neurotransmitter GABA. Isosteviol, a natural bioactive molecule, has been reported to possess an anticonvulsant property. In this work, we first reported a series of C-15 fluoro isosteviol analogs which are bearing different functional groups at C-16 to investigate the interactions with GABA-AT by applying molecular docking and molecular dynamic simulation approach. The results revealed that all fluoro isosteviol analogs displayed a greater binding affinity than references vigabatrin, an FDA-approved GABA-AT inactivator, and CPP-115, which has Orphan Drug Designation status, and positioned at the same binding site as references. Furthermore, molecular dynamic (MD) simulation studies on minimum (A1), maximum (E1) binding energy score of fluoro isosteviol analogs, and isosteviol (G1) revealed their stable complex formation in terms of RMSD, RMSF, RG, and hydrogen bond formation. All analogs were found to have drug-like nature, non-toxic, >80% absorption, and the majority tend to penetrate brain-blood-barrier (BBB). The investigations found in this study can help in the development of isosteviol derivatives as drugs for the treatment of epilepsy. METHODS The two-dimensional (2D) ligand structures were drawn using ChembioDraw Ultra 14.0. Molecular docking with Autodock4 and molecular dynamic simulation with GROMACS version 2020.1 were performed. The CHARMM27 all-atom force field was applied for writing the topology. Biovia Discovery Studio DS2021 was used for viewing and analyzing the protein-ligand complexes. The data generated from molecular dynamic simulation trajectories were plotted using the Origin® 8 software. The Open Babel software was utilized for extracting SMILEs files of all the fluoro isosteviol analogs. The drug-likeness and ADMET of the molecules were evaluated by SwissADME and ADMETlab 2.0 web tools.
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Affiliation(s)
- Punam Salaria
- School of Sciences (Chemistry), National Institute of Technology Andhra Pradesh, Tadepalligudem, Andhra Pradesh, India
| | - Parameswari Akshinthala
- Department of Science and Humanities, MLR Institute of Technology, Dundigal, Hyderabad, Telangana, India
| | - Ravikumar Kapavarapu
- Department of Pharmaceutical Chemistry and Photochemistry, Nirmala College of Pharmacy, Mangalagiri, Andhra Pradesh, India
| | - Amarendar Reddy M
- School of Sciences (Chemistry), National Institute of Technology Andhra Pradesh, Tadepalligudem, Andhra Pradesh, India.
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Wang Z, Zheng L, Wang S, Lin M, Wang Z, Kong AWK, Mu Y, Wei Y, Li W. A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function. Brief Bioinform 2023; 24:6887112. [PMID: 36502369 DOI: 10.1093/bib/bbac520] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 10/31/2022] [Indexed: 12/14/2022] Open
Abstract
The recently reported machine learning- or deep learning-based scoring functions (SFs) have shown exciting performance in predicting protein-ligand binding affinities with fruitful application prospects. However, the differentiation between highly similar ligand conformations, including the native binding pose (the global energy minimum state), remains challenging that could greatly enhance the docking. In this work, we propose a fully differentiable, end-to-end framework for ligand pose optimization based on a hybrid SF called DeepRMSD+Vina combined with a multi-layer perceptron (DeepRMSD) and the traditional AutoDock Vina SF. The DeepRMSD+Vina, which combines (1) the root mean square deviation (RMSD) of the docking pose with respect to the native pose and (2) the AutoDock Vina score, is fully differentiable; thus is capable of optimizing the ligand binding pose to the energy-lowest conformation. Evaluated by the CASF-2016 docking power dataset, the DeepRMSD+Vina reaches a success rate of 94.4%, which outperforms most reported SFs to date. We evaluated the ligand conformation optimization framework in practical molecular docking scenarios (redocking and cross-docking tasks), revealing the high potentialities of this framework in drug design and discovery. Structural analysis shows that this framework has the ability to identify key physical interactions in protein-ligand binding, such as hydrogen-bonding. Our work provides a paradigm for optimizing ligand conformations based on deep learning algorithms. The DeepRMSD+Vina model and the optimization framework are available at GitHub repository https://github.com/zchwang/DeepRMSD-Vina_Optimization.
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Affiliation(s)
- Zechen Wang
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Liangzhen Zheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Mingzhi Lin
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Zhihao Wang
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Adams Wai-Kin Kong
- Rolls-Royce Corporate Lab, Nanyang Technological University, Singapore 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yanjie Wei
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, Shandong 250100, China
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8
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Matsunaga Y, Kamiya M, Oshima H, Jung J, Ito S, Sugita Y. Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation. Biophys Rev 2022; 14:1503-1512. [PMID: 36659993 PMCID: PMC9842838 DOI: 10.1007/s12551-022-01030-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Multistate Bennett acceptance ratio (MBAR) works as a method to analyze molecular dynamics (MD) simulation data after the simulations have been finished. It is widely used to estimate free-energy changes between different states and averaged properties at the states of interest. MBAR allows us to treat a wide range of states from those at different temperature/pressure to those with different model parameters. Due to the broad applicability, the MBAR equations are rather difficult to apply for free-energy calculations using different types of MD simulations including enhanced conformational sampling methods and free-energy perturbation. In this review, we first summarize the basic theory of the MBAR equations and categorize the representative usages into the following four: (i) perturbation, (ii) scaling, (iii) accumulation, and (iv) full potential energy. For each, we explain how to prepare input data using MD simulation trajectories for solving the MBAR equations. MBAR is also useful to estimate reliable free-energy differences using MD trajectories based on a semi-empirical quantum mechanics/molecular mechanics (QM/MM) model and ab initio QM/MM energy calculations on the MD snapshots. We also explain how to use the MBAR software in the GENESIS package, which we call mbar_analysis, for the four representative cases. The proposed estimations of free-energy changes and thermodynamic averages are effective and useful for various biomolecular systems.
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Affiliation(s)
- Yasuhiro Matsunaga
- grid.263023.60000 0001 0703 3735Graduate School of Science and Engineering, Saitama University, Saitama, Saitama 338-8570 Japan
| | - Motoshi Kamiya
- grid.467196.b0000 0001 2285 6123Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585 Japan
| | - Hiraku Oshima
- grid.508743.dLaboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047 Japan
| | - Jaewoon Jung
- grid.474693.bComputational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047 Japan
| | - Shingo Ito
- grid.7597.c0000000094465255Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
| | - Yuji Sugita
- grid.508743.dLaboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047 Japan ,grid.474693.bComputational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047 Japan ,grid.7597.c0000000094465255Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
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9
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Fu H, Zhou Y, Jing X, Shao X, Cai W. Meta-Analysis Reveals That Absolute Binding Free-Energy Calculations Approach Chemical Accuracy. J Med Chem 2022; 65:12970-12978. [PMID: 36179112 DOI: 10.1021/acs.jmedchem.2c00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Systematic and quantitative analysis of the reliability of formally exact methods that in silico calculate absolute protein-ligand binding free energies remains lacking. Here, we provide, for the first time, evidence-based information on the reliability of these methods by statistically studying 853 cases from 34 different research groups through meta-analysis. The results show that formally exact methods approach chemical accuracy (error = 1.58 kcal/mol), even if people are challenging difficult tasks such as blind drug screening in recent years. The geometrical-pathway-based methods prove to possess a better convergence ability than the alchemical ones, while the latter have a larger application range. We also reveal the importance of always using the latest force fields to guarantee reliability and discuss the pros and cons of turning to an implicit solvent model in absolute binding free-energy calculations. Moreover, based on the meta-analysis, an evidence-based guideline for in silico binding free-energy calculations is provided.
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Affiliation(s)
- Haohao Fu
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin300192, China
| | - Yan Zhou
- School of Medicine, Nankai University, Tianjin300071, China.,Department of Ultrasound, Tianjin Third Central Hospital, Tianjin300170, China
| | - Xiang Jing
- Department of Ultrasound, Tianjin Third Central Hospital, Tianjin300170, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin300192, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin300192, China
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10
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Osaki K, Ekimoto T, Yamane T, Ikeguchi M. 3D-RISM-AI: A Machine Learning Approach to Predict Protein-Ligand Binding Affinity Using 3D-RISM. J Phys Chem B 2022; 126:6148-6158. [PMID: 35969673 PMCID: PMC9421647 DOI: 10.1021/acs.jpcb.2c03384] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/27/2022] [Indexed: 11/30/2022]
Abstract
Hydration free energy (HFE) is a key factor in improving protein-ligand binding free energy (BFE) prediction accuracy. The HFE itself can be calculated using the three-dimensional reference interaction model (3D-RISM); however, the BFE predictions solely evaluated using 3D-RISM are not correlated to the experimental BFE for abundant protein-ligand pairs. In this study, to predict the BFE for multiple sets of protein-ligand pairs, we propose a machine learning approach incorporating the HFEs obtained using 3D-RISM, termed 3D-RISM-AI. In the learning process, structural metrics, intra-/intermolecular energies, and HFEs obtained via 3D-RISM of ∼4000 complexes in the PDBbind database (ver. 2018) were used. The BFEs predicted using 3D-RISM-AI were well correlated to the experimental data (Pearson's correlation coefficient of 0.80 and root-mean-square error of 1.91 kcal/mol). As important factors for the prediction, the difference in the solvent accessible surface area between the bound and unbound structures and the hydration properties of the ligands were detected during the learning process.
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Affiliation(s)
- Kazu Osaki
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Toru Ekimoto
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsutomu Yamane
- Center
for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Center
for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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11
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Oshima H, Sugita Y. Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions. J Chem Inf Model 2022; 62:2846-2856. [PMID: 35639709 DOI: 10.1021/acs.jcim.1c01532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The free-energy perturbation (FEP) method predicts relative and absolute free-energy changes of biomolecules in solvation and binding with other molecules. FEP is, therefore, one of the most essential tools in in silico drug design. In conventional FEP, to smoothly connect two thermodynamic states, the potential energy is modified as a linear combination of the end-state potential energies by introducing scaling factors. When the particle mesh Ewald is used for electrostatic calculations, conventional FEP requires two reciprocal-space calculations per time step, which largely decreases the computational performance. To overcome this problem, we propose a new FEP scheme by introducing a modified Hamiltonian instead of interpolation of the end-state potential energies. The scheme introduces nonuniform scaling into the electrostatic potential as used in Replica Exchange with Solute Tempering 2 (REST2) and does not require additional reciprocal-space calculations. We tested this modified Hamiltonian in FEP calculations in several biomolecular systems. In all cases, the calculated free-energy changes with the current scheme are in good agreement with those from conventional FEP. The modified Hamiltonian in FEP greatly improves the computational performance, which is particularly marked for large biomolecular systems whose reciprocal-space calculations are the major bottleneck of total computational time.
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Affiliation(s)
- Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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12
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Shinobu A, Re S, Sugita Y. Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics. Front Mol Biosci 2022; 9:878830. [PMID: 35573746 PMCID: PMC9099257 DOI: 10.3389/fmolb.2022.878830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular dynamics (MD) simulations are increasingly used to study various biological processes such as protein folding, conformational changes, and ligand binding. These processes generally involve slow dynamics that occur on the millisecond or longer timescale, which are difficult to simulate by conventional atomistic MD. Recently, we applied a two-dimensional (2D) replica-exchange MD (REMD) method, which combines the generalized replica exchange with solute tempering (gREST) with the replica-exchange umbrella sampling (REUS) in kinase-inhibitor binding simulations, and successfully observed multiple ligand binding/unbinding events. To efficiently apply the gREST/REUS method to other kinase-inhibitor systems, we establish modified, practical protocols with non-trivial simulation parameter tuning. The current gREST/REUS simulation protocols are tested for three kinase-inhibitor systems: c-Src kinase with PP1, c-Src kinase with Dasatinib, and c-Abl kinase with Imatinib. We optimized the definition of kinase-ligand distance as a collective variable (CV), the solute temperatures in gREST, and replica distributions and umbrella forces in the REUS simulations. Also, the initial structures of each replica in the 2D replica space were prepared carefully by pulling each ligand from and toward the protein binding sites for keeping stable kinase conformations. These optimizations were carried out individually in multiple short MD simulations. The current gREST/REUS simulation protocol ensures good random walks in 2D replica spaces, which are required for enhanced sampling of inhibitor dynamics around a target kinase.
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Affiliation(s)
- Ai Shinobu
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Suyong Re
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Ibaraki, Japan
| | - Yuji Sugita
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- *Correspondence: Yuji Sugita,
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13
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Taguchi M, Oyama R, Kaneso M, Hayashi S. Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease. J Chem Inf Model 2022; 62:1328-1344. [PMID: 35212226 DOI: 10.1021/acs.jcim.1c01193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A human immunodeficiency virus-1 (HIV-1) protease is a homodimeric aspartic protease essential for the replication of HIV. The HIV-1 protease is a target protein in drug discovery for antiretroviral therapy, and various inhibitor molecules of transition state analogues have been developed. However, serious drug-resistant mutants have emerged. For understanding the molecular mechanism of the drug resistance, an accurate examination of the impacts of the mutations on ligand binding and enzymatic activity is necessary. Here, we present a molecular simulation study on the ligand binding of indinavir, a potent transition state analogue inhibitor, to the wild-type protein and a V82T/I84V drug-resistant mutant of the HIV-1 protease. We employed a hybrid ab initio quantum mechanical/molecular mechanical (QM/MM) free-energy optimization technique which combines a highly accurate QM description of the ligand molecule and its interaction with statistically ample conformational sampling of the MM protein environment by long-time molecular dynamics simulations. Through the free-energy calculations of protonation states of catalytic groups at the binding pocket and of the ligand-binding affinity changes upon the mutations, we successfully reproduced the experimentally observed significant reduction of the binding affinity upon the drug-resistant mutations and elucidated the underlying molecular mechanism. The present study opens the way for understanding the molecular mechanism of drug resistance through the direct quantitative comparison of ligand binding and enzymatic reaction with the same accuracy.
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Affiliation(s)
- Masahiko Taguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| | - Ryo Oyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Kaneso
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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14
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King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery. Front Mol Biosci 2021; 8:712085. [PMID: 34458321 PMCID: PMC8387144 DOI: 10.3389/fmolb.2021.712085] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 01/11/2023] Open
Abstract
The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
- Department of Materials Science and Engineering, University of California, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
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15
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Lin Z, Zou J, Liu S, Peng C, Li Z, Wan X, Fang D, Yin J, Gobbo G, Chen Y, Ma J, Wen S, Zhang P, Yang M. A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Predictions: New Opportunities and Challenges for Drug Discovery. J Chem Inf Model 2021; 61:2720-2732. [PMID: 34086476 DOI: 10.1021/acs.jcim.0c01329] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Free energy perturbation (FEP) has become widely used in drug discovery programs for binding affinity prediction between candidate compounds and their biological targets. However, limitations of FEP applications also exist, including, but not limited to, high cost, long waiting time, limited scalability, and breadth of application scenarios. To overcome these problems, we have developed XFEP, a scalable cloud computing platform for both relative and absolute free energy predictions using optimized simulation protocols. XFEP enables large-scale FEP calculations in a more efficient, scalable, and affordable way, for example, the evaluation of 5000 compounds can be performed in 1 week using 50-100 GPUs with a computing cost roughly equivalent to the cost for the synthesis of only one new compound. By combining these capabilities with artificial intelligence techniques for goal-directed molecule generation and evaluation, new opportunities can be explored for FEP applications in the drug discovery stages of hit identification, hit-to-lead, and lead optimization based not only on structure exploitation within the given chemical series but also including evaluation and comparison of completely unrelated molecules during structure exploration in a larger chemical space. XFEP provides the basis for scalable FEP applications to become more widely used in drug discovery projects and to speed up the drug discovery process from hit identification to preclinical candidate compound nomination.
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Affiliation(s)
- Zhixiong Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Junjie Zou
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Shuai Liu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China.,XtalPi Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Chunwang Peng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Zhipeng Li
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Xiao Wan
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Dong Fang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Jian Yin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Gianpaolo Gobbo
- XtalPi Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Yongpan Chen
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Jian Ma
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Shuhao Wen
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China.,XtalPi Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Peiyu Zhang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Mingjun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
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16
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Yagi K, Ito S, Sugita Y. Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations. J Phys Chem B 2021; 125:4701-4713. [PMID: 33914537 PMCID: PMC10986901 DOI: 10.1021/acs.jpcb.1c01862] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding molecular mechanisms of enzymatic reactions is of vital importance in biochemistry and biophysics. Here, we introduce new functions of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in the GENESIS program to compute the minimum-energy pathways (MEPs) and free-energy profiles of enzymatic reactions. For this purpose, an interface in GENESIS is developed to utilize a highly parallel electronic structure program, QSimulate-QM (https://qsimulate.com), calling it as a shared library from GENESIS. Second, algorithms to search the MEP are implemented, combining the string method (E et al. J. Chem. Phys. 2007, 126, 164103) with the energy minimization of the buffer MM region. The method implemented in GENESIS is applied to an enzyme, triosephosphate isomerase, which converts dihyroxyacetone phosphate to glyceraldehyde 3-phosphate in four proton-transfer processes. QM/MM-molecular dynamics simulations show performances of greater than 1 ns/day with the density functional tight binding (DFTB), and 10-30 ps/day with the hybrid density functional theory, B3LYP-D3. These performances allow us to compute not only MEP but also the potential of mean force (PMF) of the enzymatic reactions using the QM/MM calculations. The barrier height obtained as 13 kcal mol-1 with B3LYP-D3 in the QM/MM calculation is in agreement with the experimental results. The impact of conformational sampling in PMF calculations and the level of electronic structure calculations (DFTB vs B3LYP-D3) suggests reliable computational protocols for enzymatic reactions without high computational costs.
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Affiliation(s)
- Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shingo Ito
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, 7-1-26 minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, 1-6-5 minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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17
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Ren W, Dokainish HM, Shinobu A, Oshima H, Sugita Y. Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations. J Phys Chem B 2021; 125:2898-2909. [PMID: 33728914 PMCID: PMC10954230 DOI: 10.1021/acs.jpcb.0c11600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conformational changes of proteins upon ligand binding are usually explained in terms of several mechanisms including the induced fit, conformational selection, or their mixtures. Due to the slow time scales, conventional molecular dynamics (cMD) simulations based on the atomistic models cannot easily simulate the open-to-closed conformational transition in proteins. In our previous study, we have developed an enhanced sampling scheme (generalized replica exchange with solute tempering selected surface charged residues: gREST_SSCR) for multidomain proteins and applied it to ligand-mediated conformational changes in the G134R mutant of ribose-binding protein (RBPG134R) in solution. The free-energy landscape (FEL) of RBPG134R in the presence of a ribose at the binding site included the open and closed states and two intermediates, open-like and closed-like forms. Only the open and open-like forms existed in the FEL without a ribose. In the current study, the coupling between the conformational changes and ligand binding is further investigated using coarse-grained MD, multiple atomistic cMD, and free-energy calculations. The ribose is easily dissociated from the binding site of wild-type RBP and RBPG134R in the cMD simulations starting from the open and open-like forms. In contrast, it is stable at the binding site in the simulations from the closed and closed-like forms. The free-energy calculations provide the binding affinities of different structures, supporting the results of cMD simulations. Importantly, cMD simulations from the closed-like structures reveal transitions toward the closed one in the presence of a bound ribose. On the basis of the computational results, we propose a molecular mechanism in which conformational selection and induced fit happen in the first and second halves of the open-to-closed transition in RBP, respectively.
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Affiliation(s)
- Weitong Ren
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hisham M. Dokainish
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ai Shinobu
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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18
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Armacost KA, Riniker S, Cournia Z. Exploring Novel Directions in Free Energy Calculations. J Chem Inf Model 2020; 60:5283-5286. [PMID: 33222441 DOI: 10.1021/acs.jcim.0c01266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kira A Armacost
- Computational and Structural Chemistry, MRL, Merck & Co., Inc. West Point, Pennsylvania 19486, United States
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Zoe Cournia
- Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 11527 Athens, Greece
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19
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Kim S, Oshima H, Zhang H, Kern NR, Re S, Lee J, Roux B, Sugita Y, Jiang W, Im W. CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations. J Chem Theory Comput 2020; 16:7207-7218. [PMID: 33112150 DOI: 10.1021/acs.jctc.0c00884] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Alchemical free energy simulations have long been utilized to predict free energy changes for binding affinity and solubility of small molecules. However, while the theoretical foundation of these methods is well established, seamlessly handling many of the practical aspects regarding the preparation of the different thermodynamic end states of complex molecular systems and the numerous processing scripts often remains a burden for successful applications. In this work, we present CHARMM-GUI Free Energy Calculator (http://www.charmm-gui.org/input/fec) that provides various alchemical free energy perturbation molecular dynamics (FEP/MD) systems with input and post-processing scripts for NAMD and GENESIS. Four submodules are available: Absolute Ligand Binder (for absolute ligand binding FEP/MD), Relative Ligand Binder (for relative ligand binding FEP/MD), Absolute Ligand Solvator (for absolute ligand solvation FEP/MD), and Relative Ligand Solvator (for relative ligand solvation FEP/MD). Each module is designed to build multiple systems of a set of selected ligands at once for high-throughput FEP/MD simulations. The capability of Free Energy Calculator is illustrated by absolute and relative solvation FEP/MD of a set of ligands and absolute and relative binding FEP/MD of a set of ligands for T4-lysozyme in solution and the adenosine A2A receptor in a membrane. The calculated free energy values are overall consistent with the experimental and published free energy results (within ∼1 kcal/mol). We hope that Free Energy Calculator is useful to carry out high-throughput FEP/MD simulations in the field of biomolecular sciences and drug discovery.
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Affiliation(s)
- Seonghoon Kim
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.,School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Han Zhang
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Nathan R Kern
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Jumin Lee
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe 650-0047, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Wei Jiang
- Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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