ALPHA-HELIX FORMATION IN C-PEPTIDE RNASE-A INVESTIGATED BY PARALLEL TEMPERING SIMULATIONS

Gökhan Gökoğlu () and Tarik Çeli̇k ()
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Gökhan Gökoğlu: Department of Physics Engineering, Hacettepe University, 06800 Beytepe, Ankara, Turkey
Tarik Çeli̇k: Turkish Academy of Sciences, Piyade Sokak No. 27, 06550 Çankaya, Ankara, Turkey

International Journal of Modern Physics C (IJMPC), 2007, vol. 18, issue 01, 91-98

Abstract: We have performed parallel tempering simulations of a 13-residue peptide fragment of ribonuclease-A, c-peptide, in implicit solvent with constant dielectric permittivity. This peptide has a strong tendency to form α-helical conformations in solvent as suggested by circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments. Our results demonstrate that 5th and 8–12 residues are in the α-helical region of the Ramachandran map for global minimum energy state in solvent environment. Effects of salt bridge formation on stability of α-helix structure are discussed.

Keywords: Parallel tempering; generalized ensembles; c-peptide ribonuclease-A; 82.20.Wt; 02.70.Uu; 87.15.Cc (search for similar items in EconPapers)
Date: 2007
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DOI: 10.1142/S0129183107010292

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