Modeling and Simulating Biomolecular Machineries at Atomic Scale and Beyond
Yu, Jin
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https://hdl.handle.net/2142/80558
Description
Title
Modeling and Simulating Biomolecular Machineries at Atomic Scale and Beyond
Author(s)
Yu, Jin
Issue Date
2007
Doctoral Committee Chair(s)
Schulten, Klaus
Department of Study
Physics
Discipline
Physics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biophysics, General
Language
eng
Abstract
Biomolecular machineries are molecular complexes endowed with sophisticated machine-like functions inside living organisms. Understanding how these machineries achieve their functions at the microscopic structural level could be essential for understanding fundamental principles of life as well as for engineering molecular devices for the purpose of technology advancement and medical research. This work describes a computational research investigating three biomolecular systems which are simple and ubiquitous, namely, (1) a DNA helicase PcrA, a prototype molecular motor traveling along DNA, for which we have provided evidence for an alternating domain mobilities mechanism that controls the directional translocation; (2) a membrane channel protein Aquaporin-1 (AQP1), conducting water through its individual monomeric pores, for which we have proposed a feasible mechanism of gating and ion conduction in its tetramerical central pore; (3) a four-way DNA junction (Holliday junction), a central intermediate in homologous recombination, for which we have constructed a minimum geometric model and deduced a schematic framework of its conformer transition. The studies have been conducted mainly by modeling the molecular systems at the atomic scale and simulating them using molecular dynamics (MD) techniques. Since physiological functions of those systems usually involve time scales much longer that can currently achieve through atomic-scale MD simulations, other computational approaches have also been adopted to complement the atomistic descriptions. In particular, the study of PcrA helicase systematically implemented a variety of computational techniques and gives a comprehensive example of how to investigate a biomolecular machine working across multiple time and length scales. All the studies were conducted in close contact with experimental research, and the validity of the studies can be directly tested through experiments.
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