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Thermodynamic capacity of a protein
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Fink, Thomas M. A. and Ball, R. C. (2000) Thermodynamic capacity of a protein. Working Paper. Cornell University Library, Cornell.
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Official URL: http://arxiv.org/abs/cond-mat/0008474v1
Abstract
We show that a protein can be trained to recognise multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield network, the number of conformations which can be remembered by a protein sequence depends on the size of the amino acid alphabet as ln A, independent of protein length. This admits the possibility of certain proteins, such as prions, evolving to fold to independent stable conformations, as well as novel possibilities for protein and heteropolymer design.
| Item Type: | Working or Discussion Paper (Working Paper) |
|---|---|
| Subjects: | Q Science > QC Physics |
| Divisions: | Faculty of Science > Physics |
| Library of Congress Subject Headings (LCSH): | Proteins -- Thermal properties |
| 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| Status: | Not Peer Reviewed |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] Ken A. Dill and Sun Chan, Nature Struct. Biol. 4, 10 (1997). [2] Thomas M. A. Fink and Robin C. Ball, Physica D 107, 199 (1997). [3] Thomas M. A. Fink, Inverse Protein Folding, Hierarchical Optimisation and Tie Knots, Ph.D. thesis, University of Cambridge (1998). [4] D.J. Amit, Modeling Brain Function (Cambridge University Press, Cambridge, UK, 1989). [5] Stanley B. Prusiner, Proc. Natl. Acad. Sci. USA, 95, 13363 (1998). [6] Robin C. Ball and Thomas M. A. Fink, submitted to Phys. Rev. Lett. (2000). [7] E. I. Shakhnovich, Phys. Rev. Lett. 72, 3907 (1994). [8] A. M. Gutin, V. I. Abkevich and E. I. Shakhnovich, Proc. Natl. Acad. Sci. USA 92, 1282 (1995). [10] V. I. Abkevich, A. M. Gutin and E. I. Shakhnovich, Proteins: Struct. Function and Genetics 31, 335 (1998). [11] S. Miyazawa and R. Jernigan, J. Mol. Biol. 256, 623 (1996). [12] Vijay S. Pande et al., J. Phys. A: Math. Gen. 27, 6231 (1994). |
| URI: | http://wrap.warwick.ac.uk/id/eprint/35720 |
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