Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: distributions of phi.
The "coil library," consisting of the phi, psi values of residues outside secondary structure in high-resolution protein structures, has chiefly the beta, alpha(R), alpha(L), and polyproline II backbone conformations. In denatured proteins, the 20 aa have different average values of the (3)J(HN)alpha coupling constant, related to the backbone angle phi by the Karplus relation. Average (3)J(HN)alpha values obtained from the distributions of phi, g(phi), of the coil library agree with NMR results, and so the coil library can be and is being used to model denatured proteins. Here, Monte Carlo simulations of backbone conformations in denatured proteins are used to test two physics-based models: the random coil model of Brant and Flory [(1965) J. Am. Chem. Soc. 87, 2788-2791 and 2791-2800] and an electrostatic screening model (ESM) that includes electrostatic solvation. The random coil model represents hindered rotation about phi and psi backbone angles, nonbonded interactions, and dipole-dipole interactions. In the ESM, the nonbonded interactions term is replaced by the use of hard sphere repulsion and allowed regions in the Ramachadran maps. These models were tested by using the amino acid sequences of three small proteins. There are two main conclusions: (i) The g(phi) distributions of the coil library contain detailed, specific information, so that prediction of the g(phi) distributions of the different amino acids is a demanding test of the energy function. (ii) The ESM is partly successful in predicting the g(phi) distributions. Electrostatic solvation is primarily responsible, and steric clash between pairs of atoms connected by torsion angles is not responsible.
Avbelj
Franc
F
National Institute of Chemistry, Hajdrihova 19, Ljubljana Sl 1115, Slovenia.
Baldwin
Robert L
RL
D000596:Amino Acids; D006863:Hydrogen-Ion Concentration; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012996:Solutions; D012997:Solvents; D055672:Static Electricity
D000596:Amino Acids; D010455:Peptides; D011506:Proteins; D012996:Solutions; D012997:Solvents; C011083:polyproline