101
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Yagi K, Yamada K, Kobayashi C, Sugita Y. Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. J Chem Theory Comput 2019; 15:1924-1938. [PMID: 30730746 PMCID: PMC8864611 DOI: 10.1021/acs.jctc.8b01193] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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Quantum
mechanics/molecular mechanics (QM/MM) calculations are
applied for anharmonic vibrational analyses of biomolecules and solvated
molecules. The QM/MM method is implemented into a molecular dynamics
(MD) program, GENESIS, by interfacing with external electronic structure
programs. Following the geometry optimization and the harmonic normal-mode
analysis based on a partial Hessian, the anharmonic potential energy
surface (PES) is generated from QM/MM energies and gradients calculated
at grid points. The PES is used for vibrational self-consistent field
(VSCF) and post-VSCF calculations to compute the vibrational spectrum.
The method is first applied to a phosphate ion in solution. With both
the ion and neighboring water molecules taken as a QM region, IR spectra
of representative hydration structures are calculated by the second-order
vibrational quasi-degenerate perturbation theory (VQDPT2) at the level
of B3LYP/cc-pVTZ and TIP3P force field. A weight-average of IR spectra
over the structures reproduces the experimental spectrum with a mean
absolute deviation of 16 cm–1. Then, the method
is applied to an enzyme, P450 nitric oxide reductase (P450nor), with
the NO molecule bound to a ferric (FeIII) heme. Starting
from snapshot structures obtained from MD simulations of P450nor in
solution, QM/MM calculations have been carried out at the level of
B3LYP-D3/def2-SVP(D). The spin state of FeIII(NO) is likely
a closed-shell singlet state based on a ratio of N–O and Fe–NO
stretching frequencies (νN–O and νFe–NO) calculated for closed- and open-shell singlet
states. The calculated νN–O and νFe–NO overestimate the experimental ones by 120 and
75 cm–1, respectively. The electronic structure
and solvation of FeIII(NO) affect the structure around
the heme of P450nor leading to an increase in νN–O and νFe–NO.
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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
| | - Kenta Yamada
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 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, 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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102
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Sugita Y, Kamiya M, Oshima H, Re S. Replica-Exchange Methods for Biomolecular Simulations. Methods Mol Biol 2019; 2022:155-177. [PMID: 31396903 DOI: 10.1007/978-1-4939-9608-7_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this study, a replica-exchange method was developed to overcome conformational sampling difficulties in computer simulations of spin glass or other systems with rugged free-energy landscapes. This method was then applied to the protein-folding problem in combination with molecular dynamics (MD) simulation. Owing to its simplicity and sampling efficiency, the replica-exchange method has been applied to many other biological problems and has been continuously improved. The method has often been combined with other sampling techniques, such as umbrella sampling, free-energy perturbation, metadynamics, and Gaussian accelerated MD (GaMD). In this chapter, we first summarize the original replica-exchange molecular dynamics (REMD) method and discuss how new algorithms related to the original method are implemented to add new features. Heterogeneous and flexible structures of an N-glycan in a solution are simulated as an example of applications by REMD, replica exchange with solute tempering, and GaMD. The sampling efficiency of these methods on the N-glycan system and the convergence of the free-energy changes are compared. REMD simulation protocols and trajectory analysis using the GENESIS software are provided to facilitate the practical use of advanced simulation methods.
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Affiliation(s)
- Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan. .,Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan. .,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | - Motoshi Kamiya
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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103
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Jung J, Kobayashi C, Sugita Y. Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. J Chem Theory Comput 2018; 15:84-94. [PMID: 30468577 DOI: 10.1021/acs.jctc.8b00874] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In molecular dynamics (MD) simulations, an accurate evaluation of temperature is essential for controlling temperature as well as pressure in the isothermal-isobaric conditions. According to the Tolman's equipartition theorem, all motions of all particles should share a single temperature. However, conventional temperature estimation from kinetic energy does not include Hessian terms properly, and thereby, the equipartition theorem is not satisfied with a large time step. In this paper, we show how to evaluate temperature the most accurately without increasing computational cost. We define two kinds of kinetic energies, evaluated at full- and half-time steps that underestimate or overestimate temperature, respectively. A combination of these two kinetic energies provides an optimal instantaneous temperature up to the third order of the time step. The method is tested for a one-dimensional harmonic oscillator, pure water molecules, a Bovine pancreatic trypsin inhibitor (BPTI) protein in water molecules, and a hydrated 1,2-dispalmitoyl- sn-phosphatidylcholine (DPPC) lipid bilayer in water molecules. In all tests, the optimal temperature estimator fulfills the equipartition theorem better than existing methods and reproduces well the usual physical properties for time steps up to and including 5 fs.
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Affiliation(s)
- Jaewoon Jung
- 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
| | - Chigusa Kobayashi
- Computational Biophysics Research Team , RIKEN Center for Computational Science , 7-1-26 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 , 7-1-26 Minatojima-minamimachi , Chuo-ku, Kobe , Hyogo 650-0047 , Japan.,Laboratory for Biomolecular Function Simulation , RIKEN Center for Biosystems Dynamics Research , 6-7-1 Minatojima-minamimachi , Chuo-ku, Kobe , Hyogo 650-0047 , Japan
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104
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Population Shift Mechanism for Partial Agonism of AMPA Receptor. Biophys J 2018; 116:57-68. [PMID: 30573176 DOI: 10.1016/j.bpj.2018.11.3122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 12/13/2022] Open
Abstract
α-amino-3-hydroxy-5-methyl-4-isoaxazolepropionic acid (AMPA) ionotropic glutamate receptors mediate fast excitatory neurotransmission in the central nervous system, and their dysfunction is associated with neurological diseases. Glutamate binding to ligand-binding domains (LBDs) of AMPA receptors induces channel opening in the transmembrane domains of the receptors. The T686A mutation reduces glutamate efficacy so that the glutamate behaves as a partial agonist. The crystal structures of wild-type and mutant LBDs are very similar and cannot account for the observed behavior. To elucidate the molecular mechanism inducing partial agonism of the T686A mutant, we computed the free-energy landscapes governing GluA2 LBD closure using replica-exchange umbrella sampling simulations. A semiclosed state, not observed in crystal structures, appears in the mutant during simulation. In this state, the LBD cleft opens slightly because of breaking of interlobe hydrogen bonds, reducing the efficiency of channel opening. The energy difference between the LBD closed and semiclosed states is small, and transitions between the two states would occur by thermal fluctuations. Evidently, glutamate binding to the T686A mutant induces a population shift from a closed to a semiclosed state, explaining the partial agonism in the AMPA receptor.
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105
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Mori T, Kulik M, Miyashita O, Jung J, Tama F, Sugita Y. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning. Structure 2018; 27:161-174.e3. [PMID: 30344106 DOI: 10.1016/j.str.2018.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/22/2018] [Accepted: 09/18/2018] [Indexed: 01/21/2023]
Abstract
Flexible fitting is a powerful technique to build the 3D structures of biomolecules from cryoelectron microscopy (cryo-EM) density maps. One popular method is a cross-correlation coefficient-based approach, where the molecular dynamics (MD) simulation is carried out with the biasing potential that includes the cross-correlation coefficient between the experimental and simulated density maps. Here, we propose efficient parallelization schemes for the calculation of the cross-correlation coefficient to accelerate flexible fitting. Our schemes are tested for small, medium, and large biomolecules using CPU and hybrid CPU + GPU architectures. The scheme for the atomic decomposition MD is suitable for small proteins such as Ca2+-ATPase with the all-atom Go model, while that for the domain decomposition MD is better for larger systems such as ribosome with the all-atom Go or the all-atom explicit solvent models. Our methods allow flexible fitting for various biomolecules with reasonable computational cost. This approach also connects high-resolution structure refinements with investigation of protein structure-function relationship.
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Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Marta Kulik
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Florence Tama
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Physics, Graduate School of Science, and Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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106
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Fujisaki H, Moritsugu K, Matsunaga Y. Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions. Int J Mol Sci 2018; 19:E3177. [PMID: 30326661 PMCID: PMC6213965 DOI: 10.3390/ijms19103177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 01/07/2023] Open
Abstract
To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics need to be characterized, but its atomistic details are hard to obtain both experimentally and computationally. Here, we review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: one is the Onsager⁻Machlup action method, and the other is the weighted ensemble method. Some applications of the above methods to biomolecular systems are also discussed and illustrated.
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Grants
- JPMJPR1679 Japan Science and Technology Agency
- 16K00059 Ministry of Education, Culture, Sports, Science and Technology
- 17KT0101 Ministry of Education, Culture, Sports, Science and Technology
- 25840060 Ministry of Education, Culture, Sports, Science and Technology
- 15K18520 Ministry of Education, Culture, Sports, Science and Technology
- JP18am0101109 Japan Agency for Medical Research and Development
- 17gm0810012h0001 Japan Agency for Medical Research and Development
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Affiliation(s)
- Hiroshi Fujisaki
- Department of Physics, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-0023, Japan.
- AMED-CREST, Japan Agency for Medical Research and Development, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan.
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Yasuhiro Matsunaga
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
- JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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107
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Kamiya M, Sugita Y. Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations. J Chem Phys 2018; 149:072304. [PMID: 30134668 DOI: 10.1063/1.5016222] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Replica-exchange molecular dynamics (REMD) and their variants have been widely used in simulations of the biomolecular structure and dynamics. Replica exchange with solute tempering (REST) is one of the methods where temperature of a pre-defined solute molecule is exchanged between replicas, while solvent temperatures in all the replicas are kept constant. REST greatly reduces the number of replicas compared to the temperature REMD, while replicas at low temperatures are often trapped under their conditions, interfering with the conformational sampling. Here, we introduce a new scheme of REST, referred to as generalized REST (gREST), where the solute region is defined as a part of a molecule or a part of the potential energy terms, such as the dihedral-angle energy term or Lennard-Jones energy term. We applied this new method to folding simulations of a β-hairpin (16 residues) and a Trp-cage (20 residues) in explicit water. The protein dihedral-angle energy term is chosen as the solute region in the simulations. gREST reduces the number of replicas necessary for good random walks in the solute-temperature space and covers a wider conformational space compared to the conventional REST2. Considering the general applicability, gREST should become a promising tool for the simulations of protein folding, conformational dynamics, and an in silico drug design.
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Affiliation(s)
- Motoshi Kamiya
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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108
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Wang Y, Tian P, Boomsma W, Lindorff-Larsen K. Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias. J Phys Chem B 2018; 122:11174-11185. [DOI: 10.1021/acs.jpcb.8b06335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yong Wang
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Pengfei Tian
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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109
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Matsunaga Y, Sugita Y. Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories. J Chem Phys 2018; 148:241731. [DOI: 10.1063/1.5019750] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Y. Matsunaga
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Y. Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 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
- 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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110
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Matsunaga Y, Sugita Y. Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning. eLife 2018; 7:32668. [PMID: 29723137 PMCID: PMC5933924 DOI: 10.7554/elife.32668] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide time-series data, such as donor-acceptor distances, whereas the latter give atomistic information, although this information is often biased by model parameters. Here, we devise a machine-learning method to combine the complementary information from the two approaches and construct a consistent model of conformational dynamics. It is applied to the folding dynamics of the formin-binding protein WW domain. MD simulations over 400 μs led to an initial Markov state model (MSM), which was then "refined" using single-molecule Förster resonance energy transfer (FRET) data through hidden Markov modeling. The refined or data-assimilated MSM reproduces the FRET data and features hairpin one in the transition-state ensemble, consistent with mutation experiments. The folding pathway in the data-assimilated MSM suggests interplay between hydrophobic contacts and turn formation. Our method provides a general framework for investigating conformational transitions in other proteins.
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Affiliation(s)
- Yasuhiro Matsunaga
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.,JST PRESTO, Kawaguchi, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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111
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Jung J, Kobayashi C, Sugita Y. Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. J Chem Phys 2018; 148:164109. [DOI: 10.1063/1.5008438] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jaewoon Jung
- 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 640-0047, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, 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, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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112
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A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue. Sci Rep 2018; 8:6336. [PMID: 29679079 PMCID: PMC5910437 DOI: 10.1038/s41598-018-24775-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 04/05/2018] [Indexed: 12/16/2022] Open
Abstract
Since 2015, widespread Zika virus outbreaks in Central and South America have caused increases in microcephaly cases, and this acute problem requires urgent attention. We employed molecular dynamics and Gaussian accelerated molecular dynamics techniques to investigate the structure of Zika NS5 protein with S-adenosyl-L-homocysteine (SAH) and an RNA analogue, namely 7-methylguanosine 5'-triphosphate (m7GTP). For the binding motif of Zika virus NS5 protein and SAH, we suggest that the four Zika NS5 substructures (residue orders: 101-112, 54-86, 127-136 and 146-161) and the residues (Ser56, Gly81, Arg84, Trp87, Thr104, Gly106, Gly107, His110, Asp146, Ile147, and Gly148) might be responsible for the selectivity of the new Zika virus drugs. For the binding motif of Zika NS5 protein and m7GTP, we suggest that the three Zika NS5 substructures (residue orders: 11-31, 146-161 and 207-218) and the residues (Asn17, Phe24, Lys28, Lys29, Ser150, Arg213, and Ser215) might be responsible for the selectivity of the new Zika virus drugs.
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113
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Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chem Sci 2018; 9:956-972. [PMID: 29732110 PMCID: PMC5909332 DOI: 10.1039/c7sc04531j] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/24/2017] [Indexed: 12/23/2022] Open
Abstract
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
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Affiliation(s)
- Louis Lagardère
- Sorbonne Université , Institut des Sciences du Calcul et des Données , Paris , France
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Luc-Henri Jolly
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
| | - Filippo Lipparini
- Universita di Pisa , Dipartimento di Chimica e Chimica Industriale , Pisa , Italy
| | - Félix Aviat
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Benjamin Stamm
- MATHCCES , Department of Mathematics , RWTH Aachen University , Aachen , Germany
| | - Zhifeng F Jing
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Matthew Harger
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76202 , USA
| | - Michael J Schnieders
- The University of Iowa , Department of Biomedical Engineering , Iowa City , IA , USA
| | - Nohad Gresh
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Yvon Maday
- Sorbonne Université , Laboratoire Jacques-Louis Lions , UMR 7598 , CNRS , Paris , France
- Institut Universitaire de France , Paris , France
- Brown University , Division of Applied Maths , Providence , RI , USA
| | - Pengyu Y Ren
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Jay W Ponder
- Washington University in Saint Louis , Department of Chemistry , Saint Louis , MI , USA
| | - Jean-Philip Piquemal
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
- Institut Universitaire de France , Paris , France
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114
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Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:237-258. [PMID: 30617833 DOI: 10.1007/978-981-13-2200-6_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Small-angle X-ray scattering (SAXS) is an efficient experimental tool to measure the overall shape of macromolecular structures in solution. However, due to the low resolution of SAXS data, high-resolution data obtained from X-ray crystallography or NMR and computational methods such as molecular dynamics (MD) simulations are complementary to SAXS data for understanding protein functions based on their structures at atomic resolution. Because MD simulations provide a physicochemically proper structural ensemble for flexible proteins in solution and a precise description of solvent effects, the hybrid analysis of SAXS and MD simulations is a promising method to estimate reasonable solution structures and structural ensembles in solution. Here, we review typical and useful in silico methods for modeling three dimensional protein structures, calculating theoretical SAXS profiles, and analyzing ensemble structures consistent with experimental SAXS profiles. We also review two examples of the hybrid analysis, termed MD-SAXS method in which MD simulations are carried out without any knowledge of experimental SAXS data, and the experimental SAXS data are used only to assess the consistency of the solution model from MD simulations with those observed in experiments. One example is an investigation of the intrinsic dynamics of EcoO109I using the computational method to obtain a theoretical profile from the trajectory of an MD simulation. The other example is a structural investigation of the vitamin D receptor ligand-binding domain using snapshots generated by MD simulations and assessment of the snapshots by experimental SAXS data.
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115
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Ekimoto T, Ikeguchi M. Multiscale molecular dynamics simulations of rotary motor proteins. Biophys Rev 2017; 10:605-615. [PMID: 29204882 DOI: 10.1007/s12551-017-0373-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/23/2017] [Indexed: 12/16/2022] Open
Abstract
Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.
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Affiliation(s)
- Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 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.
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