Probing protein mechanics: residue-level properties and their use in defining domains.
It is becoming clear that, in addition to structural properties, the mechanical properties of proteins can play an important role in their biological activity. It nevertheless remains difficult to probe these properties experimentally. Whereas single-molecule experiments give access to overall mechanical behavior, notably the impact of end-to-end stretching, it is currently impossible to directly obtain data on more local properties. We propose a theoretical method for probing the mechanical properties of protein structures at the single-amino acid level. This approach can be applied to both all-atom and simplified protein representations. The probing leads to force constants for local deformations and to deformation vectors indicating the paths of least mechanical resistance. It also reveals the mechanical coupling that exists between residues. Results obtained for a variety of proteins show that the calculated force constants vary over a wide range. An analysis of the induced deformations provides information that is distinct from that obtained with measures of atomic fluctuations and is more easily linked to residue-level properties than normal mode analyses or dynamic trajectories. It is also shown that the mechanical information obtained by residue-level probing opens a new route for defining so-called dynamical domains within protein structures.
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Isabelle
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Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris 75005, France.
Cailliez
Fabien
F
Lavery
Richard
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D001703:Biophysics / Q000379:methods*; D002147:Calmodulin / Q000737:chemistry; D003198:Computer Simulation; D019992:Databases as Topic; D006859:Hydrogen / Q000737:chemistry; D008836:Micrococcal Nuclease / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000502:physiology*; D012984:Software; D013696:Temperature
D002147:Calmodulin; D011506:Proteins; D006859:Hydrogen; D008836:Micrococcal Nuclease