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Snapshots and Springs: Analyzing and Reproducing the Motions of Molecules

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dc.contributor.advisor Shehu, Amarda
dc.contributor.author Morris, David
dc.creator Morris, David
dc.date 2017-08-24
dc.date.accessioned 2018-05-14T18:29:02Z
dc.date.available 2018-05-14T18:29:02Z
dc.identifier doi:10.13021/G8668K
dc.identifier.uri http://hdl.handle.net/1920/10917
dc.description.abstract Nearly all cellular processes involve proteins structurally rearranging to accommodate molecular partners. The energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. Reconstruct- ing a proteins energy landscape holds the key to characterizing the structural dynamics and its regulation of protein function. In practice, the disparate spatio-temporal scales spanned by the slow dynamics challenge wet and dry laboratories. The growing number of deposited structures for proteins central to human biology presents an opportunity to infer the relevant dynamics. Recent computational efforts using extrinsic modes of motion as variables have successfully reconstructed detailed energy landscapes of several medium-size proteins. Here we investigate the extent to which one can reconstruct the energy landscape of a protein in the absence of sufficient, wet-laboratory structural data. We do so by integrating intrinsic modes of motion extracted off a single structure in a stochastic optimization framework that supports the plug-and-play of different variable selection strategies. We demonstrate that, while knowledge of more wet-laboratory structures yields better-reconstructed landscapes, precious information can be obtained even when one structural model is available. The presented work opens up interesting venues of research on structure-based inference of dynamics. Added data with a second protein suggests that the findings are not specific to the molecules analyzed. en_US
dc.language.iso en en_US
dc.subject protein dynamics en_US
dc.subject energy landscape en_US
dc.subject sampling en_US
dc.subject normal mode analysis en_US
dc.title Snapshots and Springs: Analyzing and Reproducing the Motions of Molecules en_US
dc.type Thesis en_US
thesis.degree.name Master of Science in Computer Science en_US
thesis.degree.level Master's en_US
thesis.degree.discipline Computer Science en_US
thesis.degree.grantor George Mason University en_US


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