J C Phillips 2004 J. Phys.: Condens. Matter 16 S5065 doi:10.1088/0953-8984/16/44/004
Constraint theory and hierarchical protein dynamics
J C Phillips
Show affiliationsThe complexity and functionality of proteins requires that they occupy an exponentially small fraction of configuration space (perhaps 10−300). How did evolution manage to create such unlikely objects? Thorpe has solved the static half of this problem (known in protein chemistry as Levinthal's paradox) by observing that for stress-free chain segments the complexity of optimally constrained elastic networks scales not with expN (where 
–1000 is the number of amino acids in a protein), but only with N. Newman's results for diffusion in N-dimensional spaces provide suggestive insights into the dynamical half of the problem. He showed that the distribution of residence (or pausing) time between sign reversals changes qualitatively at 
. The overall sign of a protein can be defined in terms of a product of curvature and hydrophobic(philic) character over all amino acid residues. This construction agrees with the sizes of the smallest known proteins and prions, and it suggests a universal clock for protein molecular dynamics simulations.
- PACS
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36.20.-r Macromolecules and polymer molecules
- MSC
- Subjects
- Dates
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Issue 44 (10 November 2004)
Received 14 August 2004
Published 22 October 2004
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Constraint theory and hierarchical protein dynamics
J C Phillips 2004 J. Phys.: Condens. Matter 16 S5065
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