Pu, JingzhiThomson, Karen J.Ge, HaiboSardar, RajeshLong, Eric C. (Eric Charles)2014-09-082014-09-082013https://hdl.handle.net/1805/5024http://dx.doi.org/10.7912/C2/2249Indiana University-Purdue University Indianapolis (IUPUI)The multi-protein complex of F0F1 ATP synthase has been of great interest in the fields of microbiology and biochemistry, due to the ubiquitous use of ATP as a biological energy source. Efforts to better understand this complex have been made through structural determination of segments based on NMR and crystallographic data. Some experiments have provided useful data, while others have brought up more questions, especially when structures and functions are compared between bacteria and species with chloroplasts or mitochondria. The epsilon subunit is thought to play a signi cant role in the regulation of ATP synthesis and hydrolysis, yet the exact pathway is unknown due to the experimental difficulty in obtaining data along the transition pathway. Given starting and end point protein crystal structures, the transition pathway of the epsilon subunit was examined through computer simulation.The purpose of this investigation is to determine the likelihood of one such proposed mechanism for the involvement of the epsilon subunit in ATP regulation in bacterial species such as E. coli.en-USATP synthasemolecular dynamicscomputer simulationCHARMMMolecular dynamics -- Research -- Analysis -- EvaluationAdenosine triphosphatase -- RegulationAdenosine triphosphatase -- Computer simulationComputational biologyEscherichia coli -- ResearchProteins -- StructureMolecular biology -- Mathematical modelsChemistry -- Data processingProteins -- ConformationCrystallography -- TechniqueMolecular dynamicsBioenergeticsComputer simulationThesis