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

Chemistry

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

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 (US)
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

ASJC Scopus subject areas

Computer Science Applications
Physical and Theoretical Chemistry
Computational Theory and Mathematics

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10.1142/S0219633614500266

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@article{287b0007673648e4a7faaf12ab542b81,

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",

note = "Funding Information: This work is supported by the National Natural Science Foundation of China (Grant Nos. 10974054, 20933002 and 21173082) and the Shanghai PuJiang Program (09PJ1404000). We thank Supercomputer Center of East China Normal University for CPU time support.",

year = "2014",

month = jun,

doi = "10.1142/S0219633614500266",

language = "English (US)",

volume = "13",

journal = "Journal of Theoretical and Computational Chemistry",

issn = "0219-6336",

publisher = "World Scientific Publishing Co. Pte Ltd",

number = "4",

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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

N1 - Funding Information: This work is supported by the National Natural Science Foundation of China (Grant Nos. 10974054, 20933002 and 21173082) and the Shanghai PuJiang Program (09PJ1404000). We thank Supercomputer Center of East China Normal University for CPU time support.

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

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DO - 10.1142/S0219633614500266

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JO - Journal of Theoretical and Computational Chemistry

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ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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