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Ball, R. C. and Fink, Thomas M. A. (2000) Kinetic capacity of a protein. Working Paper. Cornell University Library, Cornell.
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Official URL: http://arxiv.org/abs/cond-mat/0008475v1
Abstract
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum basin of attraction, as parametrised in our model, depends on the number of amino acid species as ln A, independent of protein length. We argue that the extent to which the protein energy landscape can be manipulated is fixed, effecting a trade-off between well breadth, well depth and well number. This clarifies the scope and limits of protein and heteropolymer function.
| Item Type: | Working or Discussion Paper (Working Paper) |
|---|---|
| Subjects: | Q Science > QC Physics |
| Divisions: | Faculty of Science > Physics |
| Library of Congress Subject Headings (LCSH): | Chemical kinetics, Proteins |
| Publisher: | Cornell University Library |
| Place of Publication: | Cornell |
| Date: | August 2000 |
| Number of Pages: | 5 |
| Status: | Not Peer Reviewed |
| Access rights to Published version: | Open Access |
| References: | [1] Thomas M. A. Fink and Robin C. Ball, submitted to Phys. Rev. Lett. (2000). [2] Ken A. Dill and Sun Chan, Nature Struct. Biol. 4, 10 (1997). [3] E. I. Shakhnovich, Phys. Rev. Lett. 72, 3907 (1994). [4] A. M. Gutin, V. I. Abkevich and E. I. Shakhnovich, Proc. Natl. Acad. Sci. USA 92, 1282 (1995). [5] Thomas M. Fink and Robin C. Ball, Physica D 107, 199 (1997). [6] Thomas M. A. Fink, Inverse Protein Folding, Hierarchical Optimisation and Tie Knots, Ph.D. thesis, University of Cambridge (1998). [7] J.-R. Garel, T. Garel and H. Orland, J. Phys. France, 50, 3067 (1989). [8] Pierre-Gilles de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, UK, 1979). [9] Vijay S. Pande et al., J. Phys. A: Math. Gen. 27, 6231 (1994). [10] Stanley B. Prusiner, Proc. Natl. Acad. Sci. USA, 95, 13363 (1998). [11] Paul M. Harrison et al., J. Mol. Biol. 286, 593 (1999). |
| URI: | http://wrap.warwick.ac.uk/id/eprint/35726 |
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