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Retrospective Theses and Dissertations

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Understanding Protein Motions By Computational Modeling And Statistical Approaches, Lei Yang Jan 2008

Understanding Protein Motions By Computational Modeling And Statistical Approaches, Lei Yang

Retrospective Theses and Dissertations

Because of its appealing simplicity, the elastic network model (ENM) has been widely accepted and applied to study many molecular motion problems, such as the molecular mechanisms of chaperonin GroEL-GroES function, allosteric changes in hemoglobin, ribosome motions, motor-protein motions, and conformational changes in general. In this dissertation, the ENM is employed to study various protein dynamics problems, and its validity is also examined by comparing with experimental data. First, we apply principal component analysis (PCA) to identify the essential protein motions from multiple structures (X-ray, NMR and MD) of the HIV-1 protease. We find significant similarities between the first few ...