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. [10.1021/acs.jctc.5b01211]

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
Primo
;
A. Contini
2016

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 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.
free-energy landscape; molecular-dynamics simulations; generalized-ensemble simulations; alpha-amino-acids; folding simulations; side-chain; backbone parameters; solvation model; protein; design
Settore CHIM/06 - Chimica Organica
Sintesi e applicazioni biomediche di peptidomimetici in campo oncologico
19-gen-2016
Article (author)
File in questo prodotto:
File Dimensione Formato  
paper_peptide_folding_ff-igb_22-12.pdf

accesso riservato

Tipologia: Pre-print (manoscritto inviato all'editore)
Dimensione 1.94 MB
Formato Adobe PDF
1.94 MB Adobe PDF   Visualizza/Apri   Richiedi una copia
acs%2Ejctc%2E5b01211.pdf

accesso riservato

Tipologia: Publisher's version/PDF
Dimensione 7.55 MB
Formato Adobe PDF
7.55 MB Adobe PDF   Visualizza/Apri   Richiedi una copia
Pubblicazioni consigliate

Caricamento pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/363443
Citazioni
  • ???jsp.display-item.citation.pmc??? 8
  • Scopus 30
  • ???jsp.display-item.citation.isi??? 29
social impact