Modeling ensembles of beta-sheet folds
Speaker: Charles W. O'Donnell , MIT
Date: April 22 2009
Time: 11:30AM to 1:00PM
Location: Stata Center 32-G575
Host: Bonnie Berger & Peter Clote, MIT - BC
Contact: Patrice Macaluso, 617.253.3037, macaluso@csail.mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/Determining the physical structure of a protein or protein complex is one the best ways to understand its mechanism and function. To assist in this goal, software structure modeling tools typically use sequence data (only) to predict a single most likely protein conformation. We present here algorithmic techniques for the prediction of a Boltzmann
ensemble of protein structures, that is, the statistical mechanical set
of all likely protein conformations that may exist at once. This is
achieved by a hypothesis-driven strategy, incorporating experimental
knowledge and allowing for an exhaustive search of conformational
space.
We demonstrate that in the case of transmembrane beta-barrel proteins,
an important class of proteins that can act as cellular gatekeepers, our
tools give high predictive accuracy, while also enabling the prediction
of macroscopic properties. We then illustrate the generality of these
techniques to other beta-sheet folds with their application to amyloid
fibrils.
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