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Kinetic capacity of a protein

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Ball, Robin and Fink, Thomas M. A. (2000) Kinetic capacity of a protein. Working Paper. Cornell: Cornell University Library.

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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

Official Date:

August 2000

Dates:

Date	Event
August 2000	Submitted

Number of Pages:

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Not Peer Reviewed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).