DOI: 10.1063/1.476842. Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model

Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model

10.1063/1.476842

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

A rapid and effective method for obtaining thermodynamic quantities for Hamiltonians whose configurational space has not been examined through a direct simulation has been developed. This approach extends the scope of the weighted histogram analysis method and is applied to the exploration of the balance of forces within the off-lattice Honeycutt–Thirumalai 46-mer beta-barrel model. Specificity is introduced into the long range hydrophobic interactions by scaling back the non-native attractive component of the hydrophobic interactions through a scaling factor λ (0&lt;λ&lt;1). Thermodynamic properties for incremental values of λ are extrapolated from the sampling of the original (λ=1) Hamiltonian. The results were found to be in good agreement with the thermodynamic signatures obtained by direct simulations. Decreasing the strength of the non-native attractive hydrophobic interactions leads to a more cooperative folding with the folding and collapse temperatures nearly coinciding at λ=0.0. The free energy surfaces were also seen to become progressively smoother while retaining a pronounced native well. Thus, this methodology may be used in the development, refinement, and exploration of folding for off-lattice protein models.

Bibliography

Shea, J.-E., Nochomovitz, Y. D., Guo, Z., & Brooks, C. L. (1998). Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist Î²-barrel model. The Journal of Chemical Physics, 109(7), 2895â2903.

Authors 4

Joan-Emma Shea (first)
Yigal D. Nochomovitz (additional)
Zhuyan Guo (additional)
Charles L. Brooks (additional)

References 30 Referenced 86

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Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 8:17 a.m.)
Deposited	1 year, 6 months ago (Feb. 6, 2024, 2:56 a.m.)
Indexed	2 months, 1 week ago (June 27, 2025, 6:51 a.m.)
Issued	27 years ago (Aug. 15, 1998)
Published	27 years ago (Aug. 15, 1998)
Published Print	27 years ago (Aug. 15, 1998)

Funders 0

None

BibTeX

@article{Shea_1998, title={Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model}, volume={109}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.476842}, DOI={10.1063/1.476842}, number={7}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Shea, Joan-Emma and Nochomovitz, Yigal D. and Guo, Zhuyan and Brooks, Charles L.}, year={1998}, month=aug, pages={2895–2903} }

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