A test of AMBER force fields in predicting the secondary structure of Α-helical and Β-hairpin peptides

Ya Gao; Chaomin Zhang; Xianwei Wang; Tong Zhu

doi:10.1016/j.cplett.2017.04.074

A test of AMBER force fields in predicting the secondary structure of Α-helical and Β-hairpin peptides

Ya Gao^*
, Chaomin Zhang
, Xianwei Wang
, Tong Zhu

^*Corresponding author for this work

School of Chemistry and Molecular Engineering

Shanghai University of Engineering Science
Zhejiang University of Technology

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

37 Scopus citations

Abstract

We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the α-helix successfully folded to its native state, while the further folding of the β-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures.

Original language	English
Pages (from-to)	112-118
Number of pages	7
Journal	Chemical Physics Letters
Volume	679
DOIs	https://doi.org/10.1016/j.cplett.2017.04.074
State	Published - 2017

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title = "A test of AMBER force fields in predicting the secondary structure of Α-helical and Β-hairpin peptides",

abstract = "We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the α-helix successfully folded to its native state, while the further folding of the β-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures.",

author = "Ya Gao and Chaomin Zhang and Xianwei Wang and Tong Zhu",

note = "Publisher Copyright: {\textcopyright} 2017 Elsevier B.V.",

year = "2017",

doi = "10.1016/j.cplett.2017.04.074",

language = "英语",

volume = "679",

pages = "112--118",

journal = "Chemical Physics Letters",

issn = "0009-2614",

publisher = "Elsevier B.V.",

}

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T1 - A test of AMBER force fields in predicting the secondary structure of Α-helical and Β-hairpin peptides

AU - Gao, Ya

AU - Zhang, Chaomin

AU - Wang, Xianwei

AU - Zhu, Tong

PY - 2017

Y1 - 2017

N2 - We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the α-helix successfully folded to its native state, while the further folding of the β-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures.

AB - We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the α-helix successfully folded to its native state, while the further folding of the β-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures.

UR - https://www.scopus.com/pages/publications/85018736119

U2 - 10.1016/j.cplett.2017.04.074

DO - 10.1016/j.cplett.2017.04.074

M3 - 文章

AN - SCOPUS:85018736119

SN - 0009-2614

VL - 679

SP - 112

EP - 118

JO - Chemical Physics Letters

JF - Chemical Physics Letters

ER -

A test of AMBER force fields in predicting the secondary structure of Α-helical and Β-hairpin peptides

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