Pseudo-dynamic contact surface areas: estimation of apolar bonding.
A new Monte Carlo based algorithm has been written for the computation of pseudo-dynamic contact surface areas. The linear correlation of this contact area with solute transfer free energies (water leads to organic liquid) is established for apolar amino acid side chains. The slope of these linear plots, deltaGosp, is a unitary free energy which has potential use in the estimation of apolar bond free energies in proteins. The magnitude of deltaGosp is dependent upon the nature of the organic solvent involved in the transfer process, varying from 86 to 130 cal/A2. Analogues linear correlations with the same range of deltaGosp values are observed for inhibitors of protein-catalyzed reactions.
D000409:Alanine; D000596:Amino Acids; D004798:Enzymes / Q000378:metabolism; D008954:Models, Biological; D008968:Molecular Conformation; D011487:Protein Conformation; D013816:Thermodynamics
D000596:Amino Acids; D004798:Enzymes; D000409:Alanine