Paper Citing NAMD - Abstract
Cherepanov, D.A.; Mulkidjanian, A.Y.
Proton transfer in Azotobacter vinelandii ferredoxin I: entatic Lys84 operates as elastic counterbalance for the proton-carrying Asp15
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1505:179-184, JUN 1 2001
In ferredoxin I from Azotoacter vinelandii. the reduction of a [3Fe-4S] iron-sulphur cluster is coupled with the protonation of the mu S-2 sulphur atom that is approx. 6 Angstrom away from the protein boundary. The recent study of the site-specific mutants of ferredoxin I led to the conclusion that a particular surface aspartic residue (Asp15) is solely responsible for the proton transfer to the mu S-2 atom by rapid penetrative excursions' (K. Chen, J. Hirst, R. Camba, C.A. Bonagura, C.D. Stout, B.K. Burgess, F.A. Armstrong. Nature 405 (2000) 814-817). In the same paper it has been reported that the replacement of Asp15 by glutamate led to the blockage of the enzyme, although glutamate, with its longer and more flexible side chain, should apparently do even better as a mobile proton carrier than aspartate. We tackled this puzzling incompetence of Glu15 by molecular dynamics simulations. It was revealed that the conformational alterations of Asp15 are energetically balanced by the straining of the nearby Lys84 side chain in wild-type ferredoxin I but not in the Asp15 --> Glu mutant. Lys84 in ferredoxin I of A. vinelandii seems to represent the first case where the strained (entatic) conformation of a particular amino acid side chain could be directly identified in the ground state of an enzyme and assigned to a distinct mechanism of energy balance during the catalytic transition. (C) 2001 Elsevier Science B.V. All rights reserved.
