S A Wells et al 2009 Phys. Biol. 6 046005 doi:10.1088/1478-3975/6/4/046005
Comparative analysis of rigidity across protein families
S A Wells1, J E Jimenez-Roldan1,2 and R A Römer1
Show affiliationsWe 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.
- PACS
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87.15.B- Structure of biomolecules
36.20.Ey Conformation (statistics and dynamics)
36.20.Hb Configuration (bonds, dimensions)
87.15.K- Molecular interactions; membrane-protein interactions
- Subjects
- Dates
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Issue 4 (December 2009)
Received 20 May 2009, accepted for publication 17 August 2009
Published 22 September 2009
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Comparative analysis of rigidity across protein families
S A Wells et al 2009 Phys. Biol. 6 046005
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