DOI: 10.1002/pro.5560041206. Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding

Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding

10.1002/pro.5560041206

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractAtomic solvation parameters (ASP) are widely used to estimate the solvation contribution to the thermodynamic stability of proteins as well as the free energy of association for protein‐ligand complexes. They are also included in several molecular mechanics computer programs. In this work, a total of eight atomic solvation parametric sets has been employed to calculate the solvation contribution to the free energy of folding ΔGs for 17 proteins. A linear correlation between ΔGs and the number of residues in each protein was found for each ASP set. The calculations also revealed a great variety in the absolute value and in the sign of ΔGs values such that certain ASP sets predicted the unfolded state to be more stable than the folded, whereas others yield precisely the opposite. Further, the solvation contribution to the free energy of association of helix pairs and to the disassociation of loops (connection between secondary structural elements in proteins) from the protein tertiary structures were computed for each of the eight ASP sets and discrepancies were evident among them.

Bibliography

Juffer, A. H., Eisenhaber, F., Hubbard, S. J., Walther, D., & Argos, P. (1995). Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding. Protein Science, 4(12), 2499â2509. Portico.

Authors 5

André H. Juffer (first)
Frank Eisenhaber (additional)
Simon J. Hubbard (additional)
Dirk Walther (additional)
Patrick Argos (additional)

References 59 Referenced 70

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Dates

Type	When
Created	16 years, 6 months ago (Feb. 9, 2009, 9:30 p.m.)
Deposited	1 year, 9 months ago (Oct. 26, 2023, 5:08 p.m.)
Indexed	2 weeks, 6 days ago (Aug. 2, 2025, 1:01 a.m.)
Issued	29 years, 8 months ago (Dec. 1, 1995)
Published	29 years, 8 months ago (Dec. 1, 1995)
Published Online	16 years, 7 months ago (Dec. 31, 2008)
Published Print	29 years, 8 months ago (Dec. 1, 1995)

Funders 0

None

BibTeX

@article{Juffer_1995, title={Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding}, volume={4}, ISSN={1469-896X}, url={http://dx.doi.org/10.1002/pro.5560041206}, DOI={10.1002/pro.5560041206}, number={12}, journal={Protein Science}, publisher={Wiley}, author={Juffer, André H. and Eisenhaber, Frank and Hubbard, Simon J. and Walther, Dirk and Argos, Patrick}, year={1995}, month=dec, pages={2499–2509} }

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