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Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding
Author(s) -
Juffer André H.,
Eisenhaber Frank,
Hubbard Simon J.,
Walther Dirk,
Argos Patrick
Publication year - 1995
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560041206
Subject(s) - solvation , implicit solvation , chemistry , protein folding , folding (dsp implementation) , computational chemistry , crystallography , thermodynamics , chemical physics , molecule , physics , biochemistry , organic chemistry , electrical engineering , engineering
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 in 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.