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Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c

Isabella Daidone ^*, Andrea Amadei , Danilo Roccatano  and Alfredo Di Nola ^*

^* Department of Chemistry, University of Rome "La Sapienza," Roma, Italy; Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata," Roma, Italy; and Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L'Aquila, L'Aquila, Italy

Correspondence: Address reprint requests to Alfredo Di Nola, Fax: 39-0-649-0324; E-mail: dinola{at}degas.chem.uniroma1.it.

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 3000° of freedom. Starting from structures, with a root-mean-square deviation of 20 Å 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.

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