Title page for ETD etd-04242007-134829

Type of Document Dissertation
Author Ruscio, Jory Zmuda
Author's Email Address jzmuda@vt.edu
URN etd-04242007-134829
Title Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution
Degree PhD
Department Genetics, Bioinformatics, and Computational Biology
Advisory Committee
Advisor Name Title
Bevan, David R. Committee Co-Chair
Onufriev, Alexey V. Committee Co-Chair
Esen, Asim Committee Member
Murali, T. M. Committee Member
Sandu, Adrian Committee Member
  • nucleosome core particle
  • myoglobin
  • beta-glucosidases
  • molecular dynamics
Date of Defense 2007-04-06
Availability unrestricted
While experiments provide valuable information about biological molecules, current technology cannot yet monitor atomic fluctuations at relevant time scales. Theoretical computational simulations are able to model the appropriate interactions at atomic resolution. Computational techniques have become widely used for identifying interactions in biological systems. Such methods have proven quite accurate in their ability to reproduce experimental data and also in screening and predicting pertinent activities. Molecular modeling employs theoretical and computational techniques to elucidate biologically relevant information from macromolecular structures. Three biological systems, the nucleosome core particle, myoglobin and glycosyl hydrolase family 1 beta-glucosidases will be examined with molecular modeling methods. Results of our analyses provide information about DNA flexibility and packaging, internal migration of ligands in a small protein, and substrate specificity of an enzyme system.

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