title: Investigation of formate transport through the substrate channel of formate dehydrogenase by steered molecular dynamics simulations.
abstract: 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.
authors.affiliation: Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia.
authors.forename: D K
authors.initials: DK
authors.lastname: Nilov
authors.forename: I G
authors.initials: IG
authors.lastname: Shabalin
authors.forename: V O
authors.initials: VO
authors.lastname: Popov
authors.forename: V K
authors.initials: VK
authors.lastname: Svedas
mesh_terms: D001120:Arginine / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D005560:Formate Dehydrogenases / Q000737:chemistry* / Q000378:metabolism*; D017136:Ion Transport; D026901:Membrane Transport Proteins / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D013379:Substrate Specificity
chemical_list: D026901:Membrane Transport Proteins; D001120:Arginine; D005560:Formate Dehydrogenases