A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions.

摘要: An understanding of helix dynamics can aid in interpreting the motions proteins. The conformational transitions that occur also appear to play a role protein folding. Structural studies isolated peptides solution are just becoming available. However, detailed analysis helix-coil transition is still not available and will be difficult obtain experimentally. For these reasons, we performed long molecular simulation polyalanine at high temperature. Using this approach, description overall structure inherent flexibility chain as well structural picture changes occur. In way, address both equilibrium properties peptide mechanisms transitions. Our results correlate fairly with experimental data previous simulations aimed addressing alpha-helix dynamics. spends bulk its time fluctuating between different conformations intermediate contents. Transitions highly ordered disordered structures were rare, but they occurred rapidly. distribution favored collapsed states. Hence, our helical content from compact structures. conversion coil sequentially on residue-by-residue basis. there was local cooperativity; residue state facilitated after neighboring group became nonhelical. relevance folding discussed.