Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution

Ayori Mitsutake, Masabiro Kinoshita, Yuko Okamoto, Fumio Hirata

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

This article reports the first attempt to combine the replica-exchange Monte Carlo method and the reference interaction site model (RISM) theory for simulating a peptide molecule in aqueous solution. The energy function is the sum of the conformational energy and the solvation free energy. The solvation free energy for a fixed conformation of the peptide molecule is calculated using the RISM theory. The replica-exchange method is modified so that the dependence of the energy function on the temperature can be incorporated. The effectiveness of the combined approach is demonstrated for Met-enkephalin in water. It is argued that the number of replicas required for a peptide molecule immersed in water is drastically reduced by employing the combined approach. Solvation properties and free energy surfaces of Met-enkephalin in water are discussed.

Original languageEnglish
Pages (from-to)19002-19012
Number of pages11
JournalJournal of Physical Chemistry B
Volume108
Issue number49
DOIs
Publication statusPublished - 2004 Dec 9

Fingerprint

Solvation
replicas
Peptides
Free energy
peptides
Monte Carlo method
Methionine Enkephalin
Monte Carlo methods
aqueous solutions
solvation
Molecules
Water
free energy
molecules
interactions
water
Conformations
energy
Temperature
temperature

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution. / Mitsutake, Ayori; Kinoshita, Masabiro; Okamoto, Yuko; Hirata, Fumio.

In: Journal of Physical Chemistry B, Vol. 108, No. 49, 09.12.2004, p. 19002-19012.

Research output: Contribution to journalArticle

@article{eaaf0a0f6b834d41a833922f84e78fab,
title = "Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution",
abstract = "This article reports the first attempt to combine the replica-exchange Monte Carlo method and the reference interaction site model (RISM) theory for simulating a peptide molecule in aqueous solution. The energy function is the sum of the conformational energy and the solvation free energy. The solvation free energy for a fixed conformation of the peptide molecule is calculated using the RISM theory. The replica-exchange method is modified so that the dependence of the energy function on the temperature can be incorporated. The effectiveness of the combined approach is demonstrated for Met-enkephalin in water. It is argued that the number of replicas required for a peptide molecule immersed in water is drastically reduced by employing the combined approach. Solvation properties and free energy surfaces of Met-enkephalin in water are discussed.",
author = "Ayori Mitsutake and Masabiro Kinoshita and Yuko Okamoto and Fumio Hirata",
year = "2004",
month = "12",
day = "9",
doi = "10.1021/jp047824d",
language = "English",
volume = "108",
pages = "19002--19012",
journal = "Journal of Physical Chemistry B Materials",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "49",

}

TY - JOUR

T1 - Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution

AU - Mitsutake, Ayori

AU - Kinoshita, Masabiro

AU - Okamoto, Yuko

AU - Hirata, Fumio

PY - 2004/12/9

Y1 - 2004/12/9

N2 - This article reports the first attempt to combine the replica-exchange Monte Carlo method and the reference interaction site model (RISM) theory for simulating a peptide molecule in aqueous solution. The energy function is the sum of the conformational energy and the solvation free energy. The solvation free energy for a fixed conformation of the peptide molecule is calculated using the RISM theory. The replica-exchange method is modified so that the dependence of the energy function on the temperature can be incorporated. The effectiveness of the combined approach is demonstrated for Met-enkephalin in water. It is argued that the number of replicas required for a peptide molecule immersed in water is drastically reduced by employing the combined approach. Solvation properties and free energy surfaces of Met-enkephalin in water are discussed.

AB - This article reports the first attempt to combine the replica-exchange Monte Carlo method and the reference interaction site model (RISM) theory for simulating a peptide molecule in aqueous solution. The energy function is the sum of the conformational energy and the solvation free energy. The solvation free energy for a fixed conformation of the peptide molecule is calculated using the RISM theory. The replica-exchange method is modified so that the dependence of the energy function on the temperature can be incorporated. The effectiveness of the combined approach is demonstrated for Met-enkephalin in water. It is argued that the number of replicas required for a peptide molecule immersed in water is drastically reduced by employing the combined approach. Solvation properties and free energy surfaces of Met-enkephalin in water are discussed.

UR - http://www.scopus.com/inward/record.url?scp=10844229323&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=10844229323&partnerID=8YFLogxK

U2 - 10.1021/jp047824d

DO - 10.1021/jp047824d

M3 - Article

VL - 108

SP - 19002

EP - 19012

JO - Journal of Physical Chemistry B Materials

JF - Journal of Physical Chemistry B Materials

SN - 1520-6106

IS - 49

ER -