Publication Date:
2014-12-02
Description:
Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (Δ G vdw ) that scales linearly with solvent-accessible surface area ( A ). In a previous study, we argued that Δ G vdw , as well as its attractive (Δ G att ) and repulsive (Δ G rep ) components, was not simply a linear function of A . We found that the surface tensions, γ rep , γ att , and γ vdw , gotten from Δ G rep , Δ G att , and Δ G vdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γ rep . Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γ rep for the intact decaglycines. Finally, γ att for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γ vdw (−74 and −56 cal/mol/Å 2 for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that Δ G vdw favors extended rather than compact structures for decaglycine. We find that Δ G rep and Δ G vdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.
Print ISSN:
0021-9606
Electronic ISSN:
1089-7690
Topics:
Chemistry and Pharmacology
,
Physics
