A minimal proteinlike lattice model: an alpha-helix motif.
A simple protein model of a four-helix bundle motif on a face-centered cubic lattice has been studied. Total energy of a conformation includes attractive interactions between hydrophobic residues, repulsive interactions between hydrophobic and polar residues, and a potential that favors helical turns. Using replica exchange Monte Carlo simulations we have estimated a set of parameters for which the native structure is a global minimum of conformational energy. Then we have shown that all the above types of interactions are necessary to guarantee the cooperativity of folding transition and to satisfy the thermodynamic hypothesis.
Pokarowski
Piotr
P
Institute of Applied Mathematics and Mechanics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland. pokar@mimuw.edu.pl
Droste
Karol
K
Kolinski
Andrzej
A
D000465:Algorithms; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins