51
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Khuntawee W, Rungrotmongkol T, Wolschann P, Pongsawasdi P, Kungwan N, Okumura H, Hannongbua S. Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations. Carbohydr Polym 2016; 141:99-105. [DOI: 10.1016/j.carbpol.2015.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 09/04/2015] [Accepted: 10/08/2015] [Indexed: 11/27/2022]
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52
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Fukuda I, Moritsugu K. Coupled Nosé-Hoover equations of motion to implement a fluctuating heat-bath temperature. Phys Rev E 2016; 93:033306. [PMID: 27078483 DOI: 10.1103/physreve.93.033306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Indexed: 11/07/2022]
Abstract
The Nosé-Hoover (NH) equation provides a universal and powerful computer simulation protocol to realize an equilibrium canonical temperature for a target physical system. Here we demonstrate a general formalism to couple such NH equations. We provide a coupled NH equation that is constructed by coupling the NH equation of a target physical system and the NH equation of a temperature system. Thus, in contrast to the conventional single NH equation, the heat-bath temperature is a dynamical variable. The temperature fluctuations are not ad hoc, but instead are generated by the newly defined temperature system, and the statistical distribution of the temperature is completely described with an arbitrarily given probability function. The current equations of motion thus describe the physical system that develops with a predistributed fluctuating temperature, which allows enhanced sampling of the physical system. Since the total system is governed by a prescribed distribution, the equilibrium of the physical system is also reconstructed by reweighting. We have formulated a scheme for specifically setting the distribution of the dynamical inverse temperature and demonstrate the statistical relationship between the dynamical and physical temperatures. The statistical features, dynamical properties, and sampling abilities of the current method are demonstrated via the distributions, trajectories, dynamical correlations, and free energy landscapes for both a model system and a biomolecular system. These results indicated that the current coupled NH scheme works well.
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Affiliation(s)
- Ikuo Fukuda
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
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53
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Itoh SG, Okumura H. Replica-permutation method to enhance sampling efficiency. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2014.923576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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54
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Sirovetz BJ, Schafer NP, Wolynes PG. Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature–Pressure Plane. J Phys Chem B 2015; 119:11416-27. [DOI: 10.1021/acs.jpcb.5b03828] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Brian J. Sirovetz
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
- Department
of Chemistry, Rice University, Space Science 201, Houston, Texas 77251, United States
| | - Nicholas P. Schafer
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
| | - Peter G. Wolynes
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
- Department
of Chemistry, Rice University, Space Science 201, Houston, Texas 77251, United States
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55
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Inagaki K, Satoh T, Itoh SG, Okumura H, Kato K. Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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56
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Moritsugu K, Terada T, Kidera A. Multiscale enhanced sampling driven by multiple coarse-grained models. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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57
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Mori Y, Okumura H. Molecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.938071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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58
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Mori Y, Okumura H. Molecular dynamics of the structural changes of helical peptides induced by pressure. Proteins 2014; 82:2970-81. [DOI: 10.1002/prot.24654] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/24/2014] [Accepted: 07/15/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Yoshiharu Mori
- Department of Theoretical and Computational Molecular Science; Institute for Molecular Science; Okazaki Aichi 444-8585 Japan
| | - Hisashi Okumura
- Department of Theoretical and Computational Molecular Science; Institute for Molecular Science; Okazaki Aichi 444-8585 Japan
- Research Center for Computational Science; Institute for Molecular Science; Okazaki Aichi 444-8585 Japan
- Department of Structural Molecular Science; The Graduate University for Advanced Studies; Okazaki Aichi 444-8585 Japan
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59
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Okumura H, Itoh SG. Amyloid fibril disruption by ultrasonic cavitation: nonequilibrium molecular dynamics simulations. J Am Chem Soc 2014; 136:10549-52. [PMID: 24987794 DOI: 10.1021/ja502749f] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the disruption of amyloid fibrils of Alzheimer's amyloid-β peptides by ultrasonic cavitation. For this purpose, we performed nonequilibrium all-atom molecular dynamics simulations with sinusoidal pressure and visualized the process with movies. When the pressure is negative, a bubble is formed, usually at hydrophobic residues in the transmembrane region. Most β-strands maintain their secondary structures in the bubble. When the pressure becomes positive, the bubble collapses, and water molecules crash against the hydrophilic residues in the nontransmembrane region to disrupt the amyloid. Shorter amyloids require longer sonication times for disruption because they do not have enough hydrophobic residues to serve as a nucleus to form a bubble. These results agree with experiments in which monodispersed amyloid fibrils were obtained by ultrasonication.
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Affiliation(s)
- Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science , Okazaki, Aichi 444-8585, Japan
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60
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Dias CL, Chan HS. Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding. J Phys Chem B 2014; 118:7488-7509. [DOI: 10.1021/jp501935f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cristiano L. Dias
- Department
of Physics, New Jersey Institute of Technology, University Heights, Tiernan Hall, Room 463, Newark, New Jersey 07102, United States
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
| | - Hue Sun Chan
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
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61
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Abedi Karjiban R, Lim WZ, Basri M, Abdul Rahman MB. Molecular Dynamics of Thermoenzymes at High Temperature and Pressure: A Review. Protein J 2014; 33:369-76. [DOI: 10.1007/s10930-014-9568-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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62
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Chiang HL, Chen CJ, Okumura H, Hu CK. Transformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations. J Comput Chem 2014; 35:1430-7. [PMID: 24831733 DOI: 10.1002/jcc.23633] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 04/11/2014] [Accepted: 04/18/2014] [Indexed: 12/25/2022]
Abstract
Aggregation of polyglutamine peptides with β-sheet structures is related to some important neurodegenerative diseases such as Huntington's disease. However, it is not clear how polyglutamine peptides form the β-sheets and aggregate. To understand this problem, we performed all-atom replica-exchange molecular dynamics simulations of one and two polyglutamine peptides with 10 glutamine residues in explicit water molecules. Our results show that two polyglutamine peptides mainly formed helix or coil structures when they are separated, as in the system with one-polyglutamine peptide. As the interpeptide distance decreases, the intrapeptide β-sheet structure sometimes appear as an intermediate state, and finally the interpeptide β-sheets are formed. We also find that the polyglutamine dimer tends to form the antiparallel β-sheet conformations rather than the parallel β-sheet, which is consistent with previous experiments and a coarse-grained molecular dynamics simulation.
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Affiliation(s)
- Hsin-Lin Chiang
- Department of Physics, National Tsing Hua University, Hsinchu, 30013, Taiwan; Institute of Physics, Academia Sinica, Taipei, 11529, Taiwan
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63
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Piana S, Klepeis JL, Shaw DE. Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. Curr Opin Struct Biol 2014; 24:98-105. [DOI: 10.1016/j.sbi.2013.12.006] [Citation(s) in RCA: 294] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 01/15/2023]
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64
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Meng B, Ashbaugh HS. Pressure reentrant assembly: direct simulation of volumes of micellization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14743-14747. [PMID: 23930981 DOI: 10.1021/la402798f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Surfactants exhibit maxima in their critical micelle concentrations upon application of hydrostatic pressure, which is attributable to changes in their volumes of micellization from positive to negative values with increasing pressure. We present a direct molecular simulation analysis of the volumes of micellization of an anionic, cationic, and nonionic surfactant in aqueous solution at pressures up to 2500 bar. Excellent agreement with experiment is observed. A Kirkwood-Buff theory analysis based on proximal solvent distributions permits the breakdown of the volumes of micellization into constituent surfactant headgroup and tailgroup contributions. Although the micellization volume crossover is analogous to the transfer of an alkane from water to its pure liquid, significant differences are observed, including lower compressibilities of micelle volumes compared to that of the alkane liquid, negative partial compressibilites for anionic sulfated surfactant monomers, and large nonionic ethoxy headgroup contributions to the micellization volume.
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Affiliation(s)
- Bin Meng
- Department of Chemical and Biomolecular Engineering, Tulane University , New Orleans, Louisiana 70118, United States
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65
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Chen X, Zhu S, Wang S, Yang D, Zhang J. Molecular dynamics study on the stability of wild-type and the R220K mutant of human prion protein. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.824572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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66
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Molecular dynamics simulation of temperature induced unfolding of animal prion protein. J Mol Model 2013; 19:4433-41. [DOI: 10.1007/s00894-013-1955-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/22/2013] [Indexed: 01/22/2023]
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67
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Okumura H, Itoh SG. Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation. Phys Chem Chem Phys 2013; 15:13852-61. [PMID: 23839056 DOI: 10.1039/c3cp44443k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the transformation between the α-helix and β-hairpin structures of an 18-residue design peptide, whose sequence is INYWLAHAKAGYIVHWTA. This peptide has both α-helix and β-hairpin structures in aqueous solution. For this purpose, we proposed the helix-strand replica-exchange method. This is one of the Hamiltonian replica-exchange methods in which we exchange parameters for umbrella potentials to enhance the α-helix or β-strand structure formation. We performed an all-atom helix-strand replica-exchange molecular dynamics (MD) simulation of this peptide in explicit water solvent with five replicas. Because the suitable umbrella potential was applied, the helix-strand replica-exchange MD simulation reproduced conformations closer to experimental conformations than a temperature replica-exchange MD simulation when the same numbers of the replicas were used, while the temperature replica-exchange MD simulation does not require bias along any specific order parameter. We calculated its free-energy landscape and revealed the transformation pathways between the α-helix and β-hairpin structures and the folding pathways from an extended structure. Although the fractions of the α-helix and β-hairpin structures are less than those obtained by the experiment, the free-energy difference between the two structures is calculated to be almost zero, which agrees with the experimental results.
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Affiliation(s)
- Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi, Japan.
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68
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Mori Y, Okumura H. Pressure-Induced Helical Structure of a Peptide Studied by Simulated Tempering Molecular Dynamics Simulations. J Phys Chem Lett 2013; 4:2079-2083. [PMID: 26283256 DOI: 10.1021/jz400769w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It is known experimentally that an AK16 peptide forms more α-helix structures with increasing pressure while proteins unfold in general. In order to understand this abnormality, molecular dynamics (MD) simulations with the simulated tempering method for the isobaric-isothermal ensemble were performed in a wide pressure range from 1.0 × 10(-4) GPa to 1.4 GPa. From the results of the simulations, it is found that the fraction of the folded state decreases once and increases after that with increasing pressure. The partial molar volume change from the folded state to unfolded state increases monotonically from a negative value to a positive value with pressure. The behavior under high pressure conditions is consistent with the experimental results. The radius of gyration of highly helical structures decreases with increasing pressure, which indicates that the helix structure shrinks with pressure. This is the reason why the fraction of the folded state increases as pressure increases.
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Affiliation(s)
- Yoshiharu Mori
- †Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
| | - Hisashi Okumura
- ‡Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- §Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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69
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Morishita T, Itoh SG, Okumura H, Mikami M. On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics. J Comput Chem 2013; 34:1375-84. [PMID: 23460528 DOI: 10.1002/jcc.23267] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/10/2013] [Accepted: 02/07/2013] [Indexed: 11/11/2022]
Abstract
Mean-force dynamics (MFD), which is a fictitious dynamics for a set of collective variables on a potential of mean-force, is a powerful algorithm to efficiently explore free-energy landscapes. Recently, we have introduced logarithmic MFD (LogMFD) (Morishita et al., Phys. Rev. E 2012, 85, 066702) which overcomes difficulties encounterd in free-energy calculations using standard approaches such as thermodynamic integration. Here, we present a guide to implementing LogMFD calculations paying attention to the practical issues in choosing the parameters in LogMFD. A primary focus is given to the effect of the parameters on the accuracy of the reconstructed free-energy profiles. A recipe for reducing the errors due to energy dissipation is presented. We also demonstrate that multidimensional free-energy landscapes can be reconstructed on-the-fly using LogMFD, which cannot be accomplished using any other free-energy calculation techniques.
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Affiliation(s)
- Tetsuya Morishita
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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70
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Itoh SG, Okumura H. Replica-Permutation Method with the Suwa-Todo Algorithm beyond the Replica-Exchange Method. J Chem Theory Comput 2012; 9:570-81. [PMID: 26589055 DOI: 10.1021/ct3007919] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM). In RPM, not only exchanges between two replicas but also permutations among more than two replicas are performed. Furthermore, instead of the Metropolis algorithm, the Suwa-Todo algorithm is employed for replica-permutation trials to minimize its rejection ratio. We applied RPM to particles in a double-well potential energy, Met-enkephalin in a vacuum, and a C-peptide analog of ribonuclease A in explicit water. For comparison purposes, replica-exchange molecular dynamics simulations were also performed. As a result, RPM sampled not only the temperature space but also the conformational space more efficiently than REM for all systems. From our simulations of C-peptide, we obtained the α-helix structure with salt bridges between Gly2 and Arg10, which is known in experiments. Calculating its free-energy landscape, the folding pathway was revealed from an extended structure to the α-helix structure with the salt bridges. We found that the folding pathway consists of the two steps: The first step is the "salt-bridge formation step," and the second step is the "α-helix formation step."
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Affiliation(s)
- Satoru G Itoh
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan.,Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Hisashi Okumura
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan.,Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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71
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Itoh SG, Okumura H. Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules. J Comput Chem 2012. [PMID: 23197415 DOI: 10.1002/jcc.23167] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We propose a new type of the Hamiltonian replica-exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM (CREM). In this method, electrostatic charge parameters in the Coulomb interactions are exchanged among replicas while temperatures are exchanged in the usual REM. By varying the atom charges, the CREM overcomes free-energy barriers and realizes more efficient sampling in the conformational space than the REM. Furthermore, this method requires only a smaller number of replicas because only the atom charges of solute molecules are used as exchanged parameters. We performed Coulomb replica-exchange MD simulations of an alanine dipeptide in explicit water solvent and compared the results with those of the conventional canonical, replica exchange, and van der Waals REMs. Two force fields of AMBER parm99 and AMBER parm99SB were used. As a result, the CREM sampled all local-minimum free-energy states more frequently than the other methods for both force fields. Moreover, the Coulomb, van der Waals, and usual REMs were applied to a fragment of an amyloid-β peptide (Aβ) in explicit water solvent to compare the sampling efficiency of these methods for a larger system. The CREM sampled structures of the Aβ fragment more efficiently than the other methods. We obtained β-helix, α-helix, 3(10)-helix, β-hairpin, and β-sheet structures as stable structures and deduced pathways of conformational transitions among these structures from a free-energy landscape.
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Affiliation(s)
- Satoru G Itoh
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan.
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