Potential energy surface of alanine polypeptide chains

Journal Article · Wed Feb 15 04:00:00 EST 2006 · Journal of Experimental and Theoretical Physics

DOI:https://doi.org/10.1134/S1063776106020129· OSTI ID:21067735

Yakubovitch, A V; Solov'yov, A V ^[1]; Greiner, W ^[2]

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1. Russian Academy of Sciences, Ioffe Physicotechnical Institute (Russian Federation)
2. Johann Wolfgang Goethe University, Frankfurt Institute of Advanced Studies (Germany)

The multidimensional potential energy surfaces of the peptide chains consisting of three and six alanine (Ala) residues have been studied with respect to the degrees of freedom related to the twist of these molecules relative to the peptide backbone (these degrees of freedom are responsible for the folding of such peptide molecules and proteins). The potential energy surfaces have been calculated ab initio within the framework of the density functional theory taking into account all electrons in the system. The probabilities of transitions between various stable conformations of polypeptide molecules are evaluated. The results are compared to the data obtained by molecular dynamics simulations and to the available experimental data. The influence of the secondary structure of the polypeptide chain on its conformational properties with respect to rotations has been studied. It is shown that, in a chain of six amino acid (Ala) residues, the secondary structure type (helix or sheet conformation) influences the stable isomer states of the polypeptide.

• OSTI ID: 21067735
• Journal Information: Journal of Experimental and Theoretical Physics, Journal Name: Journal of Experimental and Theoretical Physics Journal Issue: 2 Vol. 102; ISSN JTPHES; ISSN 1063-7761
• Country of Publication: United States
• Language: English

Related Subjects

71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
ALANINES
DEGREES OF FREEDOM
DENSITY FUNCTIONAL METHOD
ELECTRONS
EXPERIMENTAL DATA
ISOMERS
MOLECULAR DYNAMICS METHOD
MOLECULES
POLYPEPTIDES
POTENTIAL ENERGY
PROBABILITY
SIMULATION
SURFACES