Graduate Training in Neuroscience
University of Washington
Professor, Department of Bioengineering; Adjunct, Department of Biochemistry; Adjunct, Biomedical & Health Informatics
Our overall goal is to perform realistic molecular modeling studies of the links between dynamics, stability, function, and folding of proteins and peptide-based biomaterials in solution. Although much is known of the structural details of the native folded state, the details of the folding and unfolding process remain elusive. An understanding of protein dynamics and folding has important implications for all biological processes, including protein degradation, translocation, aging, and human diseases, as well as genomics, biotechnology, and the pharmaceutical industry. Given that experimental approaches only provide limited amounts of information for the structural transitions and interactions occurring during protein folding, we are using computer simulation methods to complement and extend experiment.
While we investigate the general features of how proteins fold and unfold, we are also involved in the study of protein misfolding, actually it is typically unfolding, that leads to disease, particularly amyloid diseases. The molecular details of this process remain inaccessible to experiment, which has greatly hampered our ability to design drugs to treat these patients. Consequently, we are employing detailed, atomic-resolution molecular dynamics simulations to characterize conformational changes linked to disease. In particular, we are focusing on the prion protein responsible for transmissible spongiform encephalopathies; transthyretin, which is involved in systemic amyloid diseases; and polyglutamine repeats implicated in Huntington's Disease. The resulting pathological conformations are being used to address species barriers and infectivity associated with the prion protein. Also, they are being used for drug design studies.