Thesis Defense: "Modeling Ensembles of Beta-sheet Proteins"
Speaker: Charles O'Donnell , PhD Student - CSG-CSAIL
Date: April 27 2011
Time: 12:45PM to 2:30PM
Location: 32-G449 (Kiva)
Host: Professor Devadas, CSG-CSAIL-MIT
Contact: Sally O. Lee, 3-6837, sally@csail.mit.edu
Our ability to characterize protein structure and dynamics is vastly
outpaced by the speed of modern genetic sequencing, creating a growing
divide between our knowledge of biological sequence and structure.
Structural modeling algorithms offer the hope to bridge this gap through
computational exploration of the sequence determinants of structure
diversity.
In this thesis, we introduce new algorithms that enable the efficient
modeling of protein structure ensembles and their sequence variants.
These statistical mechanics-based constructions enable the
identification of all energetically likely sequence/structure states for
a family of proteins. Beyond improved structure predictions, this
approach enables a framework for mutational and comparative analysis as
well as the approximation of kinetic protein folding pathways.
We have applied these techniques to two protein types that are
notoriously difficult to characterize biochemically: transmembrane
beta-barrel proteins and amyloid fibrils. For these we advance the
state-of-the-art in structure prediction, mutational analysis, and
sequence alignment. Further, we have collaborated to apply these
methods to open scientific questions about amyloid fibrils and bacterial
biofilms.
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