出版物2017-

2020

  • New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems.

    Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita

    In this paper, we address high performance extreme‐scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular‐scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real‐space nonbonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal‐space nonbonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell.

  • CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.

    Seonghoon Kim, Hiraku Oshima, Han Zhang, Nathan R. Kern, Suyong Re, Jumin Lee, Benoît Roux, Yuji Sugita, Wei Jiang, Wonpil Im

    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.

  • Prediction of Protein–Ligand Binding Pose and Affinity Using the gREST+ FEP Method.

    Hiraku Oshima, Suyong Re, Yuji Sugita

    The accurate prediction of protein–ligand binding affinity is a central challenge in computational chemistry and in-silico drug discovery. The free energy perturbation (FEP) method based on molecular dynamics (MD) simulation provides reasonably accurate results only if a reliable structure is available via high-resolution X-ray crystallography. To overcome the limitation, we propose a sequential prediction protocol using generalized replica exchange with solute tempering (gREST) and FEP. At first, ligand binding poses are predicted using gREST, which weakens protein–ligand interactions at high temperatures to sample multiple binding poses. To avoid ligand dissociation at high temperatures, a flat-bottom restraint potential centered on the binding site is applied in the simulation. The binding affinity of the most reliable pose is then calculated using FEP. The protocol is applied to the bindings of ten ligands to FK506 binding proteins (FKBP), showing the excellent agreement between the calculated and experimental binding affinities. The present protocol, which is referred to as the gREST+FEP method, would help to predict the binding affinities without high-resolution structural information on the ligand-bound state.

  • Molecular Dynamics Simulation of Glycans.

    Suyong Re, Yoshiki Yamaguchi, Yuji Sugita

    Three-dimensional structural diversity (conformational diversity) of glycans is essential for their biological functions. Molecular dynamics (MD) simulations provide insight into the three-dimensional (3D-) structures of biomolecules in atomic resolution which are difficult to obtain by experiment. However, their highly complex and flexible structures make glycans difficult to simulate. This minireview summarizes recent challenges in MD simulations of glycans using enhanced sampling techniques. Using MD simulations, various 3D-structures are revealed at atomic resolution, not only for isolated glycans but also for glycoconjugates and glycan-bound complexes. The role of MD simulations is not limited for interpretation of experimental results. The simulations are used to predict experiments, leading the integrated computational and experimental studies on the structure-function relationship of glycans. We hope that this article will help prompt various integrated studies of glycans in the future.

  • Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis.

    Daisuke Fujinami, Hajime Motomura, Hiraku Oshima, Abdullah-Al Mahin, Khaled M. Elsayed, Takeshi Zendo, Yuji Sugita, Kenji Sonomoto, and Daisuke Kohda.
    J. Phys. Chem. Lett., 11, 1934–1939 (2020).

    Slow polypeptide conformational changes on time scales of >1 s are generally assumed to be highly cooperative two-state transitions, reflecting the high energy barrier. However, few experimental characterizations have tested the validity of this assumption. We performed residue-specific NMR thermodynamic analysis of the 27-residue lantibiotic peptide, nukacin ISK-1, to characterize the isomerization between two topological states on the second time scale. Unexpectedly, the thermal transition behaviors were distinct among peptide regions, indicating that the topological isomerization process is a mosaic of different degrees of cooperativity. The conformational change path between the two NMR structures was deduced by a targeted molecular dynamics simulation. The unique side-chain threading motions through the monosulfide rings are the structural basis of the high energy barrier, and the nonlocal interactions in the hydrophobic core are the structural basis of the cooperativity. Taken together, we provide an energetic description of the topological isomerization of nukacin ISK-1.

2019

  • Structural mechanisms underlying activity changes in an AMPA-type glutamate receptor induced by substitutions in its ligand-binding domain

    Masayoshi Sakakura, Yumi Ohkubo, Hiraku Oshima, Suyong Re, Masahiro Ito, Yuji Sugita, and Hideo Takahashi
    Structure, 27, 1698–1709 (2019)
    α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors produce postsynaptic current by transmitting an agonist-induced structural change in the ligand-binding domain (LBD) to the transmembrane channel. Receptors carrying T686S/A substitutions in their LBDs produce weaker glutamate-evoked currents than wild-type (WT) receptors. However, the substitutions induce little differences in the crystal structures of their LBDs. To understand the structural mechanism underlying reduced activities of these AMPAR variants, we analyzed the structural dynamics of WT, T686S, and T686A variants of LBD using nuclear magnetic resonance. The HD exchange studies of the LBDs showed that the kinetic step where the ligand-binding cleft closes was changed by the substitutions, and the substitution-induced population shift from cleft-closed to cleft-open structures is responsible for the reduced activities of the variants. The chemical shift analyses revealed another structural equilibrium between cleft-locked and cleft-partially-open conformations. The substitution-induced population shift in this equilibrium may be related to slower desensitization observed for these variants.
  • Replica-exchange umbrella sampling combined with Gaussian accelerated molecular dynamics for free-energy calculation of biomolecules

    Hiraku Oshima, Suyong Re, and Yuji Sugita
    J. Chem. Theory Comput., 15, 5199-5208 (2019) *selected as Supplementary Cover
    We have developed an enhanced conformational sampling method combining replica-exchange umbrella sampling (REUS) with Gaussian accelerated molecular dynamics (GaMD). REUS enhances the sampling along predefined reaction coordinates, while GaMD accelerates the conformational dynamics by adding a boost potential to the system energy. The method, which we call GaREUS (Gaussian accelerated replica-exchange umbrella sampling), enhances the sampling more efficiently than REUS or GaMD, while the computational resource for GaREUS is the same as that required for REUS. The two-step reweighting procedure using the multistate Bennett acceptance ratio method and the cumulant expansion for the exponential average is applied to the simulation trajectories for obtaining the unbiased free-energy landscapes. We apply GaREUS to the calculations of free-energy landscapes for three different cases: conformational equilibria of N-glycan, folding of chignolin, and conformational change of adenyl kinase. We show that GaREUS speeds up the convergences of free-energy calculations using the same amount of computational resources as REUS. The free-energy landscapes reweighted from the trajectories of GaREUS agree with previously reported ones. GaREUS is applicable to free-energy calculations of various biomolecular dynamics and functions with reasonable computational costs.
  • Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape

    Suyong Re, Hiraku Oshima, Kento Kasahara, Motoshi Kamiya, and Yuji Sugita
    Proc. Natl. Acad. Sci. USA, 116, 18404-18409 (2019)
    Modern drug discovery increasingly focuses on the drug-target binding kinetics which depend on drug (un)binding pathways. The conventional molecular dynamics simulation can observe only a few binding events even using the fastest supercomputer. Here, we develop 2D gREST/REUS simulation with enhanced flexibility of the ligand and the protein binding site. Simulation (43 μs) in total applied for an inhibitor binding to c-Src kinase covers 100 binding and un-binding events. On the statistically converged free-energy landscapes, we succeed in predicting the X-ray binding structure, including water positions. Furthermore, we characterize hidden semibound poses and transient encounter complexes on the free-energy landscapes. Regulatory residues distant from the catalytic core are responsible for the initial inhibitor uptake and regulation of subsequent bindings, which was unresolved by experiments. Stabilizing/blocking of either the semibound poses or the encounter complexes can be an effective strategy to optimize drug-target residence time.
  • De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

    Ai Niitsu, Suyong Re, Hiraku Oshima, Motoshi Kamiya, Yuji Sugita
    J. Chem. Inf. Model., 59, 3879-3888 (2019) *selected as Supplementary Cover
    Molecular recognition underpins all specific protein–ligand interactions and is essential for biomolecular functions. The prediction of canonical binding poses and distinguishing binders from nonbinders are much sought after goals. Here, we apply the generalized replica exchange with solute tempering method, gREST, combined with a flat-bottom potential to evaluate binder and nonbinder interactions with a T4 lysozyme Leu99Ala mutant. The buried hydrophobic cavity and possibility of coupled conformational changes in this protein make binding predictions difficult. The present gREST simulations, enabling enhanced flexibilities of the ligand and protein residues near the binding site, sample bindings in multiple poses, and correct portrayal of X-ray structures. The free-energy profiles of binders (benzene, ethylbenzene, and n-hexylbenzene) are distinct from those of nonbinders (phenol and benzaldehyde). Bindings of the two larger molecules seem to be associated with a structural change toward an excited conformation of the protein, which agrees with experimental findings. The protocol is generally applicable to various proteins having buried cavities with limited access for ligands with different shapes, sizes, and chemical properties.
  • Replica-Exchange Methods for Biomolecular Simulations

    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.
  • Molecular Dynamics Simulation of Glycans

    Suyong Re, Yoshiki Yamaguchi, Yuji Sugita
    Trends Glycosci. Glycotechnol., (2019) DOI:10.4052/tigg.1616.1.
    Three-dimensional structural diversity (conformational diversity) of glycans is essential for their biological functions. Mo- lecular dynamics (MD) simulations provide insight into the three-dimensional (3D-) structures of biomolecules in atomic resolution which are difficult to obtain by experiment. However, their highly complex and flexible structures make glycans difficult to simulate. This minireview summarizes recent challenges in MD simulations of glycans using enhanced sampling techniques. Using MD simulations, various 3D-structures are revealed at atomic resolution, not only for isolated glycans but also for glycoconjugates and glycan-bound complexes. The role of MD simulations is not limited for interpretation of experimental results. The simulations are used to predict experiments, leading the integrated computational and experimental studies on the structure-function relationship of glycans. We hope that this article will help prompt various integrated studies of glycans in the future.
  • Population Shift Mechanism for Partial Agonism of AMPA Receptor

    Hiraku Oshima, Suyong Re, Masayoshi Sakakura, Hideo Takahashi, Yuji Sugita
    Biophys. J., 116, 57-68 (2019).
    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.

2018

  • Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase

    Suyong Re, Shigehisa Watabe, Wataru Nishima, Eiro Muneyuki, Yoshiki Yamaguchi, Alexander D. MacKerell Jr. and Yuji Sugita
    Sci. Rep., 8, 1644 (2018).
    Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changes of biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us to separate carbohydrate isomers with subtle conformational differences, but the relationship between CCS and atomic structure remains elusive. Here, we characterize conformational ensembles of gasphase N-glycans under the electrospray ionization condition using molecular dynamics simulations with enhanced sampling. We show that the separation of CCSs between isomers reflects folding features of N-glycans, which are determined both by chemical compositions and protonation states. Providing a physicochemical basis of CCS for N-glycans helps not only to interpret IM-MS measurements but also to estimate CCSs of complex glycans.

2017

  • GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

    Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya and Yuji Sugita
    J. Comput. Chem., 38, 2193-2206 (2017).
    GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc..
  • Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.

    Michael Feig, Isseki Yu, Po-hung Wang, Grzegorz Nawrocki and Yuji Sugita
    J. Phys. Chem. B, 121, 8009-8025 (2017).
    The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments.
  • Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics.

    Raimondas Galvelis, Suyong Re, and Yuji Sugita
    J. Chem. Theory Comput., 13, 1934–1942 (2017).
    Molecular dynamics (MD) simulation of a N-glycan in solution is challenging because of high-energy barriers of the glycosidic linkages, functional group rotational barriers, and numerous intra- and intermolecular hydrogen bonds. In this study, we apply different enhanced conformational sampling approaches, namely, metadynamics (MTD), the replica-exchange MD (REMD), and the recently proposed replica state exchange MTD (RSE-MTD), to a N-glycan in solution and compare the conformational sampling efficiencies of the approaches. MTD helps to cross the high-energy barrier along the ω angle by utilizing a bias potential, but it cannot enhance sampling of the other degrees of freedom. REMD ensures moderate-energy barrier crossings by exchanging temperatures between replicas, while it hardly crosses the barriers along ω. In contrast, RSE-MTD succeeds to cross the high-energy barrier along ω as well as to enhance sampling of the other degrees of freedom. We tested two RSE-MTD schemes: in one scheme, 64 replicas were simulated with the bias potential along ω at different temperatures, while simulations of four replicas were performed with the bias potentials for different CVs at 300 K. In both schemes, one unbiased replica at 300 K was included to compute conformational properties of the glycan. The conformational sampling of the former is better than the other enhanced sampling methods, while the latter shows reasonable performance without spending large computational resources. The latter scheme is likely to be useful when a N-glycan-attached protein is simulated.