Mittagsseminar (in cooperation with J. Lengler, A. Steger, and D. Steurer)

Date and Time: Tuesday, April 10, 2007, 12:15 pm

Duration: This information is not available in the database

Location: OAT S15/S16/S17

Speaker: Jack Snoeyink (Univ. of North Carolina at Chapel Hill)

Questions for graph rigidity from modeling allostery

We can represent molecules (and mechanical linkages in general) as graphs whose vertices correspond to atoms and edges correspond to bonds or constraints between atoms. These graphs can be subjected to first-order rigidity analysis, which essentially counts degrees of freedom of first-order motions at vertices, subject to constraints imposed by edges. I'll introduce a pebble game of Jacobs & co-authors (95&97) as an appealing way to do this counting.

In `allosteric' proteins, binding a small molecule at one site (the allosteric site) affects whether or not another can bind at a second site (the active, or catalytic, site). It is interesting to explore whether this effect may be observed in rigidity analysis of graphs derived from specific allosterics protein. I'll show one example (7GPB), but mostly point out the questions about the pebble game that this type of modeling raises.

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