Monte Carlo simulation of protein folding with orientation-dependent monomer-monomer interactions.
We present the results of lattice Monte Carlo simulations of protein folding in the framework of a model taking into account (i) the dependence of the energy of interaction of amino-acid residues on their orientation and (ii) the rigidity of the polypeptide chain with respect to the formation of kinks. If the chain is flexible, the final protein structures are predicted to be compact. Increasing the energy cost of creation of kinks is found to favor the formation of flat structures mimicking an ideal antiparallel beta sheet. For compact structures, the kinetics of folding exhibit the standard two-phase regime (a rapid collapse to one of the metastable stable, followed by slow reconfiguration of the chain to the native structure). For flat structures, the transition to the native state is often gradual.
Zhdanov
V P
VP
Department of Applied Physics, Chalmers University of Technology, Göteborg, Sweden. zhdanov@catalysis.nsk.su
Kasemo
B
B
D000465:Algorithms; D003198:Computer Simulation; D007700:Kinetics; D008432:Mathematical Computing; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary