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The Role of Mutations in Protein Structural Dynamics and Function: A Multi-scale Computational Approach


Abstract Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding is explored using a multi-scale modeling method including (i) geometric constraint based simulations that efficiently search for native like topologies and (ii) reservoir replica exchange molecular dynamics, which identify the low free energy structures and refines these structures toward the native conformation. A test set of eight proteins and three ancestral steroid receptor proteins are folded to 2.7Å all-ato... (more)
Created Date 2011
Contributor Glembo, Tyler (Author) / Ozkan, Sefika B (Advisor) / Thorpe, Michael F (Committee member) / Ros, Robert (Committee member) / Kumar, Sudhir (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Subject Biophysics / dynamics / evolution / function / mutation / protein / structure
Type Doctoral Dissertation
Extent 190 pages
Language English
Copyright
Reuse Permissions All Rights Reserved
Note Ph.D. Physics 2011
Collaborating Institutions Graduate College / ASU Library
Additional Formats MODS / OAI Dublin Core / RIS


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Description Dissertation/Thesis