Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c.
A new method for simulating the folding process of a protein is reported. The method is based on the essential dynamics sampling technique. In essential dynamics sampling, a usual molecular dynamics simulation is performed, but only those steps, not increasing the distance from a target structure, are accepted. The distance is calculated in a configurational subspace defined by a set of generalized coordinates obtained by an essential dynamics analysis of an equilibrated trajectory. The method was applied to the folding process of horse heart cytochrome c, a protein with approximately 3000 degrees of freedom. Starting from structures, with a root-mean-square deviation of approximately 20 A from the crystal structure, the correct folding was obtained, by utilizing only 106 generalized degrees of freedom, chosen among those accounting for the backbone carbon atoms motions, hence not containing any information on the side chains. The folding pathways found are in agreement with experimental data on the same molecule.
Daidone
Isabella
I
Department of Chemistry, University of Rome "La Sapienza," Roma, Italy.
Amadei
Andrea
A
Roccatano
Danilo
D
Nola
Alfredo Di
AD
D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D045304:Cytochromes c / Q000737:chemistry*; D004789:Enzyme Activation; D006736:Horses; D008958:Models, Molecular; D009038:Motion; D009206:Myocardium / Q000378:metabolism*; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding
D045304:Cytochromes c