Surveying structural flexibility on a proteomic scale
An area of focus in the lab is analyzing small populations of structures in
terms of their detailed 3D-geometry and physical properties. Here, we try to
interpret macromolecular motions in terms of packing. We have set up a database
of macromolecular motions and coupled it with simulation tools to interpolate
between structural conformations; the database also has tools to predict likely
motions based on simple models, such as normal modes and localized hinges
connecting rigid domains. Part of this project involves devising a system for
characterizing motions in a highly standardized fashion. Our motions
classification scheme is motivated by the fact that protein interiors are packed
exceedingly tightly, and the tight packing can greatly constrains a protein's
mobility. We have developed tools for measuring and comparing the packing
efficiency at different interfaces (e.g. inter-domain, protein surface,
helix-helix, protein vs. RNA) using specialized geometric constructions (e.g.
# The citation for the FlexOracle hinge predictor is SC Flores, MB Gerstein
(2007). BMC Bioinformatics 8: 215.
# Flores, Echols, Milburn, Hespenheide, Keating, Lu, Wells, Yu, Thorpe, Gerstein
(2006). Nucleic Acids Res. 34:D296-301.
SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). "Hinge Atlas: relating
protein sequence to sites of structural flexibility." BMC Bioinformatics 8: 167