Paper Citing NAMD - Abstract
Fuentealba, Matias; Munoz, Rodrigo; Maturana, Pablo; Krapp, Adriana; Cabrera, Ricardo
Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies
PLOS ONE, 11 Art. No. e0152403, MAR 24 2016
Glucose 6-Phosphate Dehydrogenases (G6PDHs) from different sources show varying specificities towards NAD(+) and NADP(+) as cofactors. However, it is not known to what extent structural determinants of cofactor preference are conserved in the G6PDH family. In this work, molecular simulations, kinetic characterization of site-directed mutants and phylogenetic analyses were used to study the structural basis for the strong preference towards NADP(+) shown by the G6PDH from Escherichia coli. Molecular Dynamics trajectories of homology models showed a highly favorable binding energy for residues K18 and R50 when interacting with the 2'-phosphate of NADP(+), but the same residues formed no observable interactions in the case of NAD(+). Alanine mutants of both residues were kinetically characterized and analyzed with respect to the binding energy of the transition state, according to the k(cat)/K-M value determined for each cofactor. Whereas both residues contribute to the binding energy of NADP(+), only R50 makes a contribution (about-1 kcal/mol) to NAD(+) binding. In the absence of both positive charges the enzyme was unable to discriminate NADP(+) from NAD(+). Although kinetic data is sparse, the observed distribution of cofactor preferences within the phylogenetic tree is sufficient to rule out the possibility that the known NADP(+)-specific G6PDHs form a monophyletic group. While the beta 1-alpha 1 loop shows no strict conservation of K18, (rather, S and T seem to be more frequent), in the case of the beta 2-alpha 2 loop, different degrees of conservation are observed for R50. Noteworthy is the fact that a K18T mutant is indistinguishable from K18A in terms of cofactor preference. We conclude that the structural determinants for the strict discrimination against NAD(+) in the case of the NADP(+)-specific enzymes have evolved independently through different means during the evolution of the G6PDH family. We further suggest that other regions in the cofactor binding pocket, besides the beta 1-alpha 1 and beta 2-alpha 2 loops, play a role in determining cofactor preference.
