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dc.contributor.authorAllen, William Josephen
dc.date.accessioned2017-06-09T18:30:48Zen
dc.date.available2017-06-09T18:30:48Zen
dc.date.issued2011-03-23en
dc.identifier.otheretd-04062011-003404en
dc.identifier.urihttp://hdl.handle.net/10919/78000en
dc.description.abstractMolecular modeling is a term referring to the study of proteins, nucleic acids, lipids, and other bio- or macro- or small molecules at the atomistic level using a combination of computational methods, physico-chemical principles, and mathematical functions. It can be generally sub-divided into two areas: molecular mechanics, which is the treatment of atoms and bonds as Newtonian particles and springs, and quantum mechanics, which models electronic behaviors using the Schrödinger equation and wavefunctions. Each technique is a powerful tool that, when used alone or in combination with wet lab experiments, can yield useful results, the products of which have broad applications in studying human disease models, oxidative damage, and other biomolecular processes that are otherwise not easily observed by experiment alone. Within this document, we study seven different such systems. This includes the mode of inhibitor binding to the enzyme monoamine oxidase B, the active site mechanism of that same enzyme, the dynamics of the unstructured p53 C-terminal domain in complex with globular, structured proteins, the process of the viral protein B2 unbinding from double-stranded RNA, and a focus on the dynamics of a variable loop in the antigenic peanut protein Ara h 2. In addition to those conventional molecular modeling studies, several of which were done in tandem with wet lab experiment, we also discuss the validation of charges and charge group parameters for small molecules used in molecular mechanics, and the development of software for the analysis of lipid bilayer systems in molecular mechanics simulations. As computational resources continue to evolve, and as more structural information becomes available, these methods are becoming an integral part of the study of biomolecules in the context of disease.en
dc.language.isoen_USen
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectArachis Ara h 2 proteinen
dc.subjectmolecular modelingen
dc.subjectmonoamine oxidase Ben
dc.subjectp53 C-terminal domainen
dc.subjectB2 suppressor of RNA silencingen
dc.subjectlipid bilayer analysisen
dc.titlePractical Applications of Molecular Modeling Pertaining to Oxidative Damage and Diseaseen
dc.typeDissertationen
dc.contributor.departmentBiochemistryen
dc.description.degreePh. D.en
thesis.degree.namePh. D.en
thesis.degree.leveldoctoralen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.disciplineBiochemistryen
dc.contributor.committeechairBevan, David R.en
dc.contributor.committeememberLi, Jianyongen
dc.contributor.committeememberSmith, Edward J.en
dc.contributor.committeememberTanko, James M.en
dc.contributor.committeememberHelm, Richard F.en
dc.type.dcmitypeTexten
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-04062011-003404/en
dc.date.sdate2011-04-06en
dc.date.rdate2014-01-30en
dc.date.adate2011-04-27en


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