Regensburg 2010 – scientific programme

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BP: Fachverband Biologische Physik

BP 23: Biopolymers

BP 23.4: Talk

Thursday, March 25, 2010, 11:00–11:15, H43

Comparative analysis of rigidity across protein families — •Jose Emilio Jimenez, Stephen Wells, and Rudolf Römer — Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, UK

Protein rigidity analysis using the coarse graining FIRST/FRODA software package [1] has provided valuable insights in identifying the most flexible region of a protein [2]. Using the flexibility/rigidity restrictions given by FIRST/FRODA together with normal mode calculations makes it possible to simulate low frequency conformational changes in proteins at much lower computational cost than conventional molecular-dynamics methods.

Here we present a comparative study of rigidity across protein families that show two distinctive behaviors in their rigidity dilution patterns of proteins as hydrogen bonds are removed from weakest to strongest, one of sudden loss of rigidity and one of smooth transition [3]. This result highlights that choosing the energy cut off value should not be based on a numerical standard but chosen individually for each protein according to its rigidity pattern.

[1] S A Wells, et al, Constrained geometric simulation of diffusive motion in proteins. Physical Biology, 2, S127-S136, 2005 [2] D J Jacobs, et al. Protein flexibility predictions using graph theory. PROTEINS: Struct., Func. and Gen., 44:150*165, 2001. [3] S A Wells, J E Jimenez-Roldan and R A Römer. Comparative analysis of rigidity across protein families Phys. Biol. 6 046005, 2009