Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

✍ Scribed by Dudek, Michael J.; Ramnarayan, K.; Ponder, Jay W.

• Publisher: John Wiley and Sons
• Year: 1998
• Tongue: English
• Weight: 667 KB
• Volume: 19
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(19980415)19:5<548::aid-jcc7>3.0.co;2-m

✦ Synopsis

A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures. For 9 of 10 predictions, the native backbone conformation is identified correctly. Electrostatic energy is modeled as a pairwise sum of interactions between anisotropic atomic charge densities. Model repulsion energy has a softness similar to that seen in ab initio data. Intrinsic torsional energy is modeled as a sum over pairs of adjacent torsion angles of 2-dimensional Fourier series. Hydrophobic energy is that of a hydration shell model. The remainder of hydration free energy is obtained as the energetic effect of a continuous dielectric medium. Parameters are adjusted to reproduce the following data: a complete set of ab initio energy surfaces, meaning one for each pair of adjacent torsion angles of each blocked amino acid; experimental crystal structures and sublimation energies for nine model compounds; ab initio energies over 1014 conformations of 15 small-molecule dimers; and experimental hydration free energies for 48 model compounds. All ab initio data is at the Hartree᎐Fockr6᎐31G U level.