Hydrophobic potential by pairwise surface area sum.
An approximate but rapid method for estimating hydrophobic energy is proposed. Aside from a scale factor, it is given by the pairwise sum of the surface area buried by each neighbor atom, but excluding those atoms in the same residue or in its sequence neighbor residues. This sum is found to be linearly related to the true buried area as calculated by the algorithm of Lee and Richards [1971, J. Mol. Biol., 55, 379-400], and to the contact potential of Miyazawa and Jernigan [1985, Macromolecules, 18, 534-552]. It correlates with experimental transfer free energies to approximately the same degree as that calculated using the true buried area. Furthermore, in a simple test of helix packing with ROP protein monomer, the new hydrophobic energy clearly discriminated one structure, with the lowest r.m.s. deviation from the crystal structure, against an exhaustive set of others.
Kurochkina
N
N
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Lee
B
B
D000596:Amino Acids / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry*; D013499:Surface Properties; D013816:Thermodynamics
D000596:Amino Acids; D001426:Bacterial Proteins; D011506:Proteins; D016601:RNA-Binding Proteins; C054243:Rop protein, ColE1 plasmid