August 14, 2012

Onur Varol, M.S. 2012

Current position: PhD Student, School of Informatics and Computing, Indiana University Bloomington. (website, email).
M.S. Thesis: Modal Analysis of Myosin II and Identification of Functionally Important Sites. Koç University, Department of Computer Engineering. June, 2012. (PDF, Presentation).

Analysis of protein dynamics uses structural and fluctuation based methods. Fluctuation analysis of protein dynamics has proven to be a rewarding venue of research. Mass and spring models are used in previous research commonly. However, fluctuations of this models are based on purely harmonic which has significant gap between the experimental results. Deviations from harmonicity mostly observe in slow, collective modes. Corrections like anharmonic modal decomposition are first step in order to minimize this gap. The contribution of the higher-order corrections is limited because of the interacting modes. Mode-coupling corrections which yield valuable information on means of energy transfer and allostery.

In this work, molecular dynamic results of Dictyostelium discoideum myosin II motor domain is used as test ground. Mode fluctuation distributions produced using MD results, fully harmonic models and a model with anharmonic corrections. Tensorial hermite polynomials are used in order to obtain distributions of modal fluctuations. Fluctuations on modal space are transformed back into real space and distribution of residual fluctuations is compared using KL divergence. Analysis results for ligand-bound and free myosin dynamics are used in order to demonstrate that the mode-coupling contributions alone highlight functionally important sites.

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