Hydrophobic potential by pairwise surface area sum

Abstract

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.

Deuterium Spin Probes of Backbone Order in Proteins: 2H NMR Relaxation Study of Deuterated Carbon α Sites

“…The resulting alternating patterns of R Q ( D + ) rates (Figures 3d–f and Figures S1 of the Supporting Information) and S 2 C α D α values (Figures 6a,b, Figure S4 of the Supporting Information) are apparent in the helical regions of both proteins indicating that the backbone order as probed by 2 H spin relaxation at D α positions is likely to be related to the tightness of hydrophobic packing in protein cores. Specifically, the values of S 2 C α D α in the α-helix of ubiquitin (Figure 7c) are weakly but statistically significantly correlated with the buried surface area and the hydrophobic contact potential91,92 at C α positions (Pearson R > 0.5). We note that the `zigzag' patterns of R Q ( D + ) rates and the resulting S 2 C α D α values cannot be explained by the anisotropy of the global molecular tumbling, as the unique diffusion axis of ubiquitin subtends an angle of only ~10° relative to the α-helical axis.…”

Fast accurate evaluation of protein solvent exposure

“…It is common in calculating protein surface areas to exclude the area buried by the local tripeptide because the burial due to local covalent bonds does not change during folding (see ref. 13). A i,bb exposed ϩ A j,bb exposed Ϫ A ij,bb exposed is the area buried by the proximity of the two residues at i and j, excluding that buried by the backbone [see Fig.…”

ProVal: A protein‐scoring function for the selection of native and near‐native folds

“…The hydrophobic core potential was used to capture the propensity of most soluble proteins to form a nonsolvent‐accessible core consisting, almost exclusively, of hydrophobic residues. Many have developed similar functions 24, 28–30. A pseudopotential is calculated by placing a positive “hydrophilic charge” at the centroid of a given candidate conformation and a similar charge on the atom of each residue that is nearest to the centroid.…”