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Exploring repulsive interactions in a model helical peptide: A parallel tempering Monte Carlo study

J. Chem. Phys. 119, 9274 (2003); doi:10.1063/1.1613641

Issue Date: 1 November 2003

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Mayra Ocasio, Johnny R. Maury-Evertsz, Belinda Pastrana-Ríos, and Gustavo E. López
Center for Research in Protein Structure, Function, and Dynamics, and Department of Chemistry, University of Puerto Rico, at Mayagüez, P.O. Box 9019, Mayagüez, Puerto Rico 00681-9019
By implementing the parallel-tempering algorithm to the canonical ensemble, the conformational changes of an isolated Ac–W(RAAAR)5A–NH2 model peptide were determined. The interparticle interactions were modeled using a minimalist potential, i.e., a beadlike model that uses harmonic oscillators to describe covalent interactions and modified Lennard-Jones potentials to model nonbonding interactions. In particular, the interactions between arginines are modeled by repulsive interactions, causing a stabilization of the alpha-helix structure at low temperatures. The conformational changes were identified by anomalies in the constant volume heat capacity as a function of temperature. Namely, the temperature at which the constant volume heat capacity reached a maximum in the transition region was associated with the temperature at which a conformational change occurred. The transitions were also characterized by computing the radius of gyration of the peptide and the most probable isomeric structure obtained at a given temperature. Three changes were observed at low temperatures and one at high temperature. The low temperature transitions were analogous to the peptide folding, whereas the high temperature transition was related to the peptide unfolding. The results obtained were compared with experimental data generated from isotope edited Fourier transform infrared spectroscopy and two-dimensional correlation analysis for a similar peptide containing salt bridge interactions. ©2003 American Institute of Physics.
History: Received 8 July 2002; accepted 4 August 2003
Permalink: http://link.aip.org/link/?JCPSA6/119/9274/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.By
    Structure and bonding of biomolecules
  • 87.15.Cc
    Folding and sequence analysis of biomolecules
  • 05.10.Ln
    Monte Carlo methods (statistical physics/nonlinear dynamics)
  • 33.15.Bh
    General molecular conformation and symmetry; stereochemistry
  • 33.15.Hp
    Molecular barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
  • YEAR: 2003

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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