Repository: Freie Universit├Ąt Berlin, Math Department

What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation.

Keller, B. and Gattin, Z. and van Gunsteren, W. F. (2010) What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation. PROTEINS: Structure, Function, and Bioinformatics, 78 (7). pp. 1677-1690.

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Official URL: http://dx.doi.org/10.1002/prot.22685

Abstract

Beta-peptides are analogs of natural alpha-peptides and form a variety of remarkably stable structures. Having an additional carbon atom in the backbone of each residue, their folded conformation is not only influenced by the side-chain sequence but also and foremost by their substitution pattern. The precise mechanism by which the side chains interact with the backbone is, however, hitherto not completely known. In order to unravel the various effects by which the side chains influence the backbone conformation, we quantify to which extent the dihedral angles of a beta^3-substited peptide with an additional methyl group on the central C_alpha-atom can be regarded as independent degrees of freedom and analyze the distributions of these dihedral angles. We also selectively capture the steric effect of substituents on the C_alpha- and C_beta-atoms of the central residue by alchemically changing them into dummy atoms, which have no non-bonded interactions. We find that the folded state of the beta^3-peptide is primarily stabilized by a steric exclusion of large parts of the unfolded state (entropic effect) and only subsequently by mutual dependence of the psi-dihedral angles (enthalpic effect). The folded state of beta-peptides is stabilized by a different mechanism than that of alpha-peptides.

Item Type:Article
Subjects:Physical Sciences > Physics > Mathematical & Theoretical Physics > Computational Physics
Physical Sciences > Chemistry > Physical Chemistry
Biological Sciences > Molecular Biology
Divisions:Department of Mathematics and Computer Science > Institute of Mathematics > Comp. Molecular Biology
Department of Mathematics and Computer Science > Institute of Mathematics > BioComputing Group
ID Code:840
Deposited By: BioComp Admin
Deposited On:12 Mar 2010 11:37
Last Modified:03 Mar 2017 14:40

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