Understanding Protein Cold Denaturation with Molecular Dynamics Simulations
| dc.contributor.author | Bui, Pho | |
| dc.date.accessioned | 2018-03-26T20:10:10Z | |
| dc.date.available | 2018-03-26T20:10:10Z | |
| dc.date.created | 2015-10-23 | |
| dc.date.issued | 2018-03-26 | |
| dc.description.abstract | The deformation of proteins under the impact of high temperature has been the main interest of many biochemical researches. However, very little is known about protein’s behavior at low temperature. In recent years, when the computation power is dramatically improved to allow the simulations of seemingly impossible experimental conditions, cold denaturation starts raising questions in the curious mind of scientists. My summer research aimed at modifying a coarse-grained implicit-solvent protein model so that it could correctly capture all the side chain-side chain and side chain-backbone interactions, using the basic theories of Molecular Dynamics (MD) simulations. The model that I was working on originated from the previously proven models, namely Warshel and Mercedes-Benz. I experimented with building in a new parameter that took into account the temperature-dependent hydration enthalpy of the system. While the project currently requires some revision, the ultimate goal is to create a model which denatures at low temperature. I envision the next step to be the incorporation of the crowding agents, which mimic the cellular environment, allowing more precise understanding of proteins’ behavior in vivo. | |
| dc.description.panabstract | New research paradigms rely on existing knowledge of protein structure, behavior, and genomic data. This panel brings together four scientists who visualized the basic building blocks of life from genetic code to protein structure in the quest to answer some of the most challenging questions in human health. Using big data, toxicant-resistant fish, and mechanisms of drug discovery, each utilized unique methods to visualize the basic components of life including computer modeling, genomic sequencing, luminescence, and bacterial growth. This panel hopes to show possible applications of knowledge and skills gained in class as well as to impress one of the main principles of research: significant achievements are made possible through interdisciplinary collaboration that involves trials, failures, and optimization. | |
| dc.identifier.uri | http://hdl.handle.net/10166/4570 | |
| dc.language.iso | en_US | |
| dc.rights.restricted | public | |
| dc.title | Understanding Protein Cold Denaturation with Molecular Dynamics Simulations | |
| dc.title.alternative | Trails, Failures, and Optimizations: The Cycle to Visualize the Basic Building Blocks of Life |
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