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Access Type

WSU Access

Date of Award

January 2022

Degree Type


Degree Name



Chemical Engineering and Materials Science

First Advisor

Korosh Torabi


The intrinsic dynamics of proteins can be used to analyze the thermal fluctuations, functional modes, collective motions, and correlated movements. The principal component analysis (PCA) and normal mode analysis (NMA) of elastic network model (ENM) are important tools for characterizing intrinsic dynamics. Various ENMs have been created based on different hypotheses and applications. In this dissertation, we created an evaluation benchmark for ENMs on their performance in predicting the thermal fluctuations, the dynamic cross-correlations, and the functional modes. Different coarse-grained ENMs are revisited and tested by our evaluation benchmarks. Anisotropic network model (ANM) was applied to Myosin V motor domains. The analysis reveals the correlated behaviors in myosin V motors during the detachment process. A set of ENM perturbation methods are developed. These perturbation methods could reveal hot spots and hinges in proteins. They were tested and applied on myosin II and myosin 1b.

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