DOI: 10.1063/1.477748. Pairwise contact potentials are unsuitable for protein folding

Pairwise contact potentials are unsuitable for protein folding

10.1063/1.477748

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

We demonstrate that pairwise contact potentials alone cannot be used to predict the native fold of a protein. Ideally, one would hope that a universal energy function exists, for which the native folds of all proteins are the respective ground states. Here we pose a much more restricted question: Is it possible to find a set of contact parameters for which the energy of the native contact map of a single protein (crambin) is lower than that of all possible physically realizable decoy maps? The set of maps we used was derived by energy minimization (not by threading). We seek such a set of parameters by perceptron learning, a procedure which is guaranteed to find such a set if it exists. We found that it is impossible to fine-tune contact parameters that will assign all alternative conformations higher energy than that of the native map. This finding proves that there is no pairwise contact potential that can be used to fold any given protein. Inclusion of additional energy terms, such as hydrophobic (solvation), hydrogen bond, or multibody interactions may help to attain foldability within specific structural families.

Bibliography

Vendruscolo, M., & Domany, E. (1998). Pairwise contact potentials are unsuitable for protein folding. The Journal of Chemical Physics, 109(24), 11101â11108.

Authors 2

Michele Vendruscolo (first)
Eytan Domany (additional)

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Dates

Type	When
Created	23 years ago (July 26, 2002, 8:46 a.m.)
Deposited	1 year, 6 months ago (Feb. 7, 2024, 8:13 a.m.)
Indexed	2 weeks, 2 days ago (Aug. 6, 2025, 8:16 a.m.)
Issued	26 years, 8 months ago (Dec. 22, 1998)
Published	26 years, 8 months ago (Dec. 22, 1998)
Published Print	26 years, 8 months ago (Dec. 22, 1998)

Funders 0

None

BibTeX

@article{Vendruscolo_1998, title={Pairwise contact potentials are unsuitable for protein folding}, volume={109}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.477748}, DOI={10.1063/1.477748}, number={24}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Vendruscolo, Michele and Domany, Eytan}, year={1998}, month=dec, pages={11101–11108} }

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