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BP: Fachverband Biologische Physik

BP 7: Poster I

BP 7.31: Poster

Monday, March 23, 2009, 17:45–20:00, P3

Pebble-game rigidity analysis of protein crystal structures is highly sensitive to small structural variations — •Emilio Jimenez, Stephen Wells, and Rudolf Roemer — Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK

Rigidity analysis using the ``pebble game'' can usefully be applied to protein crystal structures to obtain information on protein folding, assembly and the structure-function relationship. However, previous work using this technique has not made clear how sensitive rigidity analysis is to small structural variations. We present a comparative study in which pebble-game rigidity analysis is applied to multiple structures, derived from different organisms and different conditions of crystallisation, for each of several different proteins. It appears that the results are highly sensitive to relatively small structural variations.

We find that rigidity analysis is best used as a comparative tool to highlight the effects of structural variation. We advise caution when using pebble-game rigidity analysis as a coarse-graining method in biophysical modelling of proteins. Our comparative use of multiple protein structures brings out a previously unnoticed peculiarity in the rigidity of trypsin.