화학공학소재연구정보센터
Journal of Physical Chemistry, Vol.100, No.7, 2555-2563, 1996
Molecular-Dynamics Simulations of Cyclic and Linear Dpdpe - Influence of the Disulfide Bond on Peptide Flexibility
Three 1 ns simulations of the solvated DPDPE peptide have been performed, one for the cyclic and two for the linear forms. The trajectories allow us to describe the conformations explored by DPDPE and DPDPE(SH)(2) in aqueous solution on the 1 ns time scale, to quantify the conformational constraints imposed by the presence of the disulfide bond by comparing the conformational flexibility of the cyclic and acyclic peptides, evaluate several physical properties (NMR vicinal coupling constants, diffusion coefficients, and dipole moments of the peptides), and to suggest relations between the calculated properties and biological function. The cyclic peptide, while retaining the general structural features found previously-the presence of a hydrophobic and a hydrophilic face and a parallel arrangement of peptide dipoles, explores four major conformers during the 1 ns simulation. In two independent simulations, started from an extended and a cycliclike structure, the linear peptide is found to be about twice as structurally flexible as the cyclic form. Both DPDPE(SH)(2) trajectories converge to essentially the same final structure, a type IV beta-turn. This indicates both that a stable, representative conformation of the linear peptide has been found and that the cyclic-like structure is unfavorable when the disulfide bond is not present.