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Characterization of the conformational behavior of peptide Contryphan Vn: A theoretical study

2004; Wiley; Volume: 74; Issue: 6 Linguagem: Inglês

10.1002/bip.20090

1097-0282

M. D’Alessandro, Maurizio Paci, Andrea Amadei,

Photoreceptor and optogenetics research

Abstract In this work we report the study of a peptide, the Contryphan Vn produced by Conus ventricosus , a vermivorous cone snail living in the temperate Mediterranean sea. This cyclic peptide of nine residues is a ring closed by a Cys–Cys (Cys: cysteine) disulfide bond containing two proline (Pro) residues and two tryptophans (Trp), one of them being a D ‐Trp. We present a statistical mechanical characterization of the peptide, simulated in water for about 200 ns with classical molecular dynamics (MD). In recent years there has been a growing interest in the study of the mechanics and dynamics of biological molecules, and in particular for proteins and peptides, about the relationship between collective motions and the active conformations which exert the biological function. To this aim we used the essential dynamics analysis on the MD trajectory and extracted, from the total fluctuations of the molecule, the dominant dynamical modes responsible of the principal conformational transitions. The Contryphan Vn small size allowed us to investigate in details the all‐atoms dynamics and the corresponding thermodynamics in conformational space defined by the most significant intramolecular motions. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004