Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol
 
research article

Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol

Horta, Bruno A. C.
•
Lin, Zhixiong
•
Huang, Wei
Show more
2012
Journal Of Computational Chemistry

Considering N-methylacetamide (NMA) as a model compound, new interaction parameters are developed for the amide function in the GROMOS force field that are compatible with the recently derived 53A6OXY parameter set for oxygen-containing chemical functions. The resulting set, referred to as 53A6OXY+A, represents an improvement over earlier GROMOS force-field versions in the context of the pure-liquid properties of NMA, including the density, heat of vaporization, dielectric permittivity, self-diffusion constant and viscosity, as well as in terms of the Gibbs hydration free energy of this molecule. Assuming that NMA represents an adequate model compound for the backbone of peptides, 53A6OXY+A may be expected to also provide an improved description of polypeptide chains. As an initial test, simulations are reported for two beta-peptides characterized by very different folding properties in methanol. For these systems, earlier force-field versions provided good agreement with experimental NMR data, and the test shows that the improved description achieved in the context of NMA is not accompanied by any deterioration in the representation of the conformational properties of these peptides. (c) 2012 Wiley Periodicals, Inc.

  • Details
  • Metrics
Type
research article
DOI
10.1002/jcc.23021
Web of Science ID

WOS:000307078800001

Author(s)
Horta, Bruno A. C.
Lin, Zhixiong
Huang, Wei
Riniker, Sereina
Van Gunsteren, Wilfred F.
Huenenberger, Philippe H.
Date Issued

2012

Publisher

Wiley-Blackwell

Published in
Journal Of Computational Chemistry
Volume

33

Issue

24

Start page

1907

End page

1917

Subjects

computer simulation

•

molecular dynamics

•

force field

•

GROMOS

•

N-methylacetamide

•

peptide-backbone model

•

peptide folding

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
ISIC  
Available on Infoscience
February 27, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/89489
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés