paper

Comparative analysis of rigidity across protein families

arXiv:0905.4232 · doi:10.1088/1478-3975/6/4/046005

Abstract

Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made clear how the set of hydrogen-bond constraints included in the rigidity analysis should be chosen, nor how sensitive the results of rigidity analysis are to small structural variations. We present a comparative study in which "pebble game" rigidity analysis is applied to multiple protein crystal structures, for each of six differen t protein families. We find that the mainchain 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 o f a particular protein. Our comparative approach highlights two different characteristic patterns ("sudden" or "gradual") for protein rigidity loss as constraints are re moved, in line with recent results on the rigidity transitions of glassy networks.

15 pages, 7 figures comprising 21 subfigures

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