A molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix–coil transitions

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