Stochastic Prediction of Peptide Secondary Structure Based on Molecular Dynamics Simulation Performed for Nano-second-Effectiveness of the %stickiness Approach Represented by Triangle Map Mode.

Shinichi MURAYAMA, Chuya YOSHIDA, Takashi AOYAMA, Satoshi URATA and Koichi NISHIGAKI*

Department of Functional Materials Science, Saitama University
255 Shimo-okubo, Sakura-ku, Saitama, Saitama 338-8570, Japan

(Received: May 10, 2006; Accepted for publication: July 7, 2006; Published on Web: September 4, 2006)

Nano-second (ns) MD simulations of peptides, which are known to be insufficient to obtain stable structures, were confirmed to provide faint secondary structure (especially, a-helix) images through a novel approach termed triangle map representation of %stickiness (TMR-%s). %stickiness is a measure formerly introduced to describe dynamic conformation changes of biopolymers. In TMR-%s representation, the a-helix forming propensity of a peptide was expressed as an off-diagonal dotted line, indicating a-helix intrinsic interactions. The coordinate information derived from %s and radius of gyration (Rg) of a peptide calculated from ns-MD results could be converted to a probability matrix of secondary peptide structure formation.

Keywords: ns-MD, Chou-Fasman parameter, a-helix, %stickiness, Triangle map representation, Secondary structure prediction

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