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Investigation of Formate Transport through the Substrate Channel of Formate Dehydrogenase by Steered Molecular Dynamics Simulations

D. K. Nilov1, I. G. Shabalin2, V. O. Popov2, and V. K. Švedas1,3*

1Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1, Bldg. 73, 119991 Moscow, Russia; fax: (495) 939-2355; E-mail: vytas@belozersky.msu.ru

2Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia; fax: (495) 954-2732

3Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, Bldg. 40, 119991 Moscow, Russia; fax: (495) 939-2355

* To whom correspondence should be addressed.

Received August 4, 2010; Revision received September 30, 2010
Steered molecular dynamics simulation has revealed the mechanism of formate transport via the substrate channel of formate dehydrogenase. It is shown that the structural organization of the channel promotes the transport of formate anion in spite of the fact that the channel is too narrow even for such a small molecule. The conformational mobility of Arg284 residue, one of the residues forming the wall of the substrate channel, provides for the binding and delivery of formate to the active site.
KEY WORDS: formate dehydrogenase, substrate channel, steered molecular dynamics

DOI: 10.1134/S0006297911020027