Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

Lirong Mou; Xiangyu Jia; Ya Gao; Yongxiu Li; John Z.H. Zhang; Ye Mei

doi:10.1142/S0219633614500266

Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

Lirong Mou
, Xiangyu Jia
, Ya Gao
, Yongxiu Li
, John Z.H. Zhang
, Ye Mei^*

^*Corresponding author for this work

Institute for Advanced Study in Precision Spectroscopy

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER03^2D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity C_v is only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER03^2D is an accurate force field that can be used for protein folding simulations.

Original language	English
Article number	1450026
Journal	Journal of Theoretical and Computational Chemistry
Volume	13
Issue number	4
DOIs	https://doi.org/10.1142/S0219633614500266
State	Published - Jun 2014

Keywords

AMBER force field
Trp-cage
coupled backbone torsion
folding mechanism
melting temperature

Access to Document

10.1142/S0219633614500266

Cite this

@article{c5f82750e22149508fbad71a9007d99d,

title = "Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions",

abstract = "A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER032D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity Cv is only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032D is an accurate force field that can be used for protein folding simulations.",

keywords = "AMBER force field, Trp-cage, coupled backbone torsion, folding mechanism, melting temperature",

author = "Lirong Mou and Xiangyu Jia and Ya Gao and Yongxiu Li and Zhang, \{John Z.H.\} and Ye Mei",

year = "2014",

month = jun,

doi = "10.1142/S0219633614500266",

language = "英语",

volume = "13",

journal = "Journal of Theoretical and Computational Chemistry",

issn = "0219-6336",

publisher = "World Scientific",

number = "4",

}

TY - JOUR

T1 - Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

AU - Mou, Lirong

AU - Jia, Xiangyu

AU - Gao, Ya

AU - Li, Yongxiu

AU - Zhang, John Z.H.

AU - Mei, Ye

PY - 2014/6

Y1 - 2014/6

N2 - A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER032D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity Cv is only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032D is an accurate force field that can be used for protein folding simulations.

AB - A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER032D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity Cv is only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032D is an accurate force field that can be used for protein folding simulations.

KW - AMBER force field

KW - Trp-cage

KW - coupled backbone torsion

KW - folding mechanism

KW - melting temperature

UR - https://www.scopus.com/pages/publications/84903819590

U2 - 10.1142/S0219633614500266

DO - 10.1142/S0219633614500266

M3 - 文章

AN - SCOPUS:84903819590

SN - 0219-6336

VL - 13

JO - Journal of Theoretical and Computational Chemistry

JF - Journal of Theoretical and Computational Chemistry

IS - 4

M1 - 1450026

ER -

Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this