Comparative analysis of rigidity across protein families.
We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks.
Wells
S A
SA
Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, UK.
Jimenez-Roldan
J E
JE
Römer
R A
RA
D018360:Crystallography, X-Ray; D045304:Cytochromes c / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry* / Q000145:classification*
D011506:Proteins; D045304:Cytochromes c