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 beta-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-phi. Indeed, the force fields of the ff99SB series coupled with GB-Neck2 reasonably discriminated helices from disordered peptides, while a good prediction of beta-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-phi force fields.
An updated test of AMBER force fields and implicit solvent models in predicting the secondary structure of helical, beta-hairpin, and intrinsically disordered peptides / I. Maffucci, A. Contini. - In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. - ISSN 1549-9618. - 12:2(2016), pp. 714-727.
|Titolo:||An updated test of AMBER force fields and implicit solvent models in predicting the secondary structure of helical, beta-hairpin, and intrinsically disordered peptides|
MAFFUCCI, IRENE (Primo)
CONTINI, ALESSANDRO (Corresponding)
|Parole Chiave:||free-energy landscape; molecular-dynamics simulations; generalized-ensemble simulations; alpha-amino-acids; folding simulations; side-chain; backbone parameters; solvation model; protein; design|
|Settore Scientifico Disciplinare:||Settore CHIM/06 - Chimica Organica|
|Progetto:||Sintesi e applicazioni biomediche di peptidomimetici in campo oncologico|
|Data di pubblicazione:||2016|
|Data ahead of print / Data di stampa:||19-gen-2016|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1021/acs.jctc.5b01211|
|Appare nelle tipologie:||01 - Articolo su periodico|