Methods for investigating conformational change in biomolecular simulations

Abstract

A series of simulations of the Syrian hamster prion protein and three point mutated variants thereof are presented.  These simulations are analysed using root mean square deviations, dynamical cross correlation maps, secondary structure versus time plots and hydrogen bonding profiles.  The results of these analyses are discussed.  A problem identified during the interpretation of the prion protein trajectories was the lack of sufficiently subtle analytic tool.  To remedy this, the recently proposed Hilbert Huang Transform (HHT) method was considered as a basis for the development of new techniques.  The HHT is examined in depth, some improvements to it are proposed, and a number of issues with its use and interpretation are identified.  A set of new analysis tools based on the HHT and wavelet methods are then proposed, and these are tested on a set of dihydrofolate reductase simulations performed by other workers.  The results are encouraging and a series of proposals for future research work based on the findings are made.

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