An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides

Journal of Chemical Theory and Computation
Irene Maffucci, Alessandro Contini

Abstract

Replica exchange molecular dynamics simulations were performed to test the ability of six AMBER force fields and three implicit solvent models of predicting the native conformation of two helical peptides, three β-hairpins, and three intrinsically disordered peptides. Although a combination of the force field and implicit solvation models able to accurately predict the native structure of all the considered peptides was not identified, we found that the GB-Neck2 model seems to well compensate for some of the conformational biases showed by ff96 and ff99SB/ildn/ildn-φ. Indeed, the force fields of the ff99SB series coupled with GB-Neck2 reasonably discriminated helices from disordered peptides, while a good prediction of β-hairpin conformations was only achieved by performing two independent simulations: one with the ff96/GB-Neck2 combination and the other with GB-Neck2 coupled with any of the ff99SB/ildn/ildn-φ force fields.

References

Apr 5, 1987·Journal of Molecular Biology·S Vijay-KumarW J Cook
Sep 1, 1994·Nature Structural Biology·F J BlancoL Serrano
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jul 6, 2000·Nature Structural Biology·R R RustandiD J Weber
May 2, 2001·Proceedings of the National Academy of Sciences of the United States of America·A G CochranM A Starovasnik
Oct 17, 2001·Journal of Molecular Biology·B ZagrovicV Pande
Nov 17, 2001·Chemical Reviews·J VenkatramanP Balaram
Feb 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Angel E García, Kevin Y Sanbonmatsu
Sep 19, 2002·Journal of the American Chemical Society·Carlos SimmerlingAdrian E Roitberg
Sep 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ruhong Zhou, Bruce J Berne
Mar 14, 2003·Journal of Molecular Biology·Shibasish ChowdhuryYong Duan
Jun 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jed W Pitera, William Swope
Mar 2, 2005·Nature Reviews. Molecular Cell Biology·H Jane Dyson, Peter E Wright
Sep 28, 2005·Proceedings of the National Academy of Sciences of the United States of America·Luca Domenico D'AndreaCarlo Pedone
Nov 1, 2006·Protein Science : a Publication of the Protein Society·Thu Zar Lwin, Ray Luo
Feb 1, 2007·Chemical Society Reviews·Jessica M DavisAndrew D Hamilton
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Hongxing LeiYong Duan
Mar 27, 2007·Current Opinion in Structural Biology·Hongxing Lei, Yong Duan
Jul 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·S Banu OzkanKen A Dill
Dec 14, 2007·Nature·James A Wells, Christopher L McClendon
Jan 18, 2008·Genome Biology·Benjamin Schuster-Böckler, Alex Bateman
Mar 15, 2008·Biophysical Journal·Peter L FreddolinoKlaus Schulten
May 6, 2008·Biophysical Journal·Robert B BestGerhard Hummer
May 13, 2008·The Journal of Physical Chemistry. B·M Scott ShellKen A Dill
Jul 10, 2008·Structure·Feng DingNikolay V Dokholyan
Aug 9, 2008·Physical Chemistry Chemical Physics : PCCP·Alexandra Patriksson, David van der Spoel
Aug 14, 2008·The Journal of Physical Chemistry. B·Nevena TodorovaIrene Yarovsky
Feb 14, 2009·Journal of the American Chemical Society·Jianhan Chen
Jun 17, 2009·Journal of Medicinal Chemistry·Nicola FerriAlessandro Contini
Jan 8, 2010·Journal of Molecular Biology·Thomas H CharpentierDavid J Weber
Apr 22, 2010·Proteins·Kresten Lindorff-LarsenDavid E Shaw
Jun 12, 2010·The Journal of Physical Chemistry. B·Robert B Best, Jeetain Mittal
Jul 21, 2010·Biophysical Journal·Oliver F LangeBert L de Groot
Aug 3, 2010·Journal of Molecular Graphics & Modelling·John E StoneKlaus Schulten
Oct 16, 2010·Science·David E ShawWilly Wriggers
Nov 1, 2009·Nature Chemistry·Stefano PieracciniMaurizio Sironi
May 5, 2011·Biophysical Journal·Stefano PianaDavid E Shaw
May 10, 2011·The Journal of Chemical Physics·Jan-Hendrik PrinzFrank Noé

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Citations

Aug 9, 2016·Journal of Chemical Information and Modeling·Irene Maffucci, Alessandro Contini
Oct 13, 2016·Journal of Chemical Theory and Computation·Melina K RobinsonM Scott Shell
May 13, 2017·Journal of Chemical Theory and Computation·Piotr Setny, Anita Dudek
Jun 15, 2017·Journal of Chemical Information and Modeling·Yunhui GeVincent A Voelz
May 4, 2017·Chemistry : a European Journal·Raffaella BucciMaria Luisa Gelmi
Aug 8, 2017·Organic & Biomolecular Chemistry·Luciano RicciErnesto G Occhiato
Sep 12, 2019·Physical Chemistry Chemical Physics : PCCP·Nivedita DuttaAnsuman Lahiri
Feb 27, 2018·Physical Chemistry Chemical Physics : PCCP·Qiang Shao, Weiliang Zhu
Aug 3, 2018·Biochimica Et Biophysica Acta. General Subjects·Bin SunPeter M Kekenes-Huskey
Apr 18, 2017·The Journal of Physical Chemistry. B·Nguyen Hoang LinhMai Suan Li
Nov 10, 2017·Journal of Chemical Theory and Computation·Qiang Shao, Weiliang Zhu
Nov 16, 2018·The Journal of Physical Chemistry. B·Jerelle A Joseph, David J Wales
Nov 10, 2021·Journal of Computational Chemistry·Zirui ShuChangjun Chen

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