Solvent entropy-driven searching for protein modeling examined and tested in simplified models.
Solvent entropy is a force to consider in protein folding and protein design but is difficult to model. It is investigated here in the context of the hp model: Two types of residues, hydrophobic and hydrophilic, are modeled on a lattice. Nine chains and two- and three-dimensional simulations are compared. We show that considering solvent entropy alone, efficient folding of lattice chains (identification of the native fold) can be achieved by an entropy-driven simulation on its own. Moreover, in a detailed comparison over a wide range of parameters, entropy-guided searching outperforms an energy-driven search in the model. The combination of energy- and entropy-driven search yields the most efficient searching. It is compared in detail with the above results, indicating also how this solvent shell model may advantageously be implemented in more complex protein modeling simulations.
König
R
R
European Molecular Biology Laboratory, Meyerhofstr. 1, Postfach 10 22 09, D-69012 Heidelberg, Germany.
Dandekar
T
T
D003198:Computer Simulation; D019277:Entropy; D006860:Hydrogen Bonding; D008433:Mathematics; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D014867:Water
D011506:Proteins; D012997:Solvents; D014867:Water