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| - Two-Dimensional Correlation Analysis of Peptide Unfolding: Molecular DynamicsSimulations of β Hairpins
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| - We have studied the mechanism of formation of a 16-residue β hairpin from the protein GB1 using moleculardynamics simulations in an aqueous environment. Essential dynamics (ED) analysis was performed on thecombined trajectories of two separate simulations at five different temperatures. Generalized 2D correlationanalysis was performed using the displacements from the ED analysis as a dynamic spectrum. The results ofthe 2D correlation analysis illustrate the correlated structural changes as the temperature is increased. Theasynchronous 2D correlation spectrum reveals the existence of sequential events in the unfolding of the peptide.The order of structural changes suggested by such an analysis support the hydrophobic collapse mechanismof folding for the β-hairpin fragment of protein GB1. The 2D correlation method combined with ED analysiscan provide a useful scheme for studying the characteristics of dynamical structural changes which are importantin understanding the function of protein and the mechanism of protein folding.
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