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

A. H. Juffer, F. Eisenhaber, S. J. Hubbard, D. Walther, P. Argos

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Atomic 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 ΔG(s) for 17 proteins. A linear correlation between ΔG(s) 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 the sign of ΔG(s) 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.
    Original languageEnglish
    Pages (from-to)2499-2509
    Number of pages10
    JournalProtein science
    Volume4
    Issue number12
    Publication statusPublished - 1995

    Keywords

    • atomic solvation parameters
    • helix docking
    • loop removal
    • protein folding
    • solvent contribution

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