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Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins


Abstract In a typical living cell, millions to billions of proteins—nanomachines that fluctuate and cycle among many conformational states—convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics... (more)
Created Date 2017
Contributor Seyler, Sean Lee (Author) / Beckstein, Oliver (Advisor) / Chamberlin, Ralph (Committee member) / Matyushov, Dmitry (Committee member) / Thorpe, Michael F (Committee member) / Vaiana, Sara (Committee member) / Arizona State University (Publisher)
Subject Biophysics / Computational physics / Fluid mechanics / adenylate kinase / conformational transitions / enhanced sampling / fluctuating hydrodynamics / molecular dynamics / path similarity analysis
Type Doctoral Dissertation
Extent 245 pages
Language English
Copyright
Reuse Permissions All Rights Reserved
Note Doctoral Dissertation Physics 2017
Collaborating Institutions Graduate College / ASU Library
Additional Formats MODS / OAI Dublin Core / RIS


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Description Dissertation/Thesis