title: Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases.
abstract: Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate-protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate.
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany. wade@embl-heidelberg.de
authors.forename: R C
authors.initials: RC
authors.lastname: Wade
authors.forename: R R
authors.initials: RR
authors.lastname: Gabdoulline
authors.forename: B A
authors.initials: BA
authors.lastname: Luty
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000378:metabolism*; D001665:Binding Sites; D002645:Chickens; D003198:Computer Simulation; D004058:Diffusion; D004926:Escherichia coli / Q000201:enzymology; D005656:Fungal Proteins / Q000378:metabolism*; D005986:Glyceraldehyde 3-Phosphate / Q000378:metabolism; D008958:Models, Molecular; D011485:Protein Binding; D015800:Protozoan Proteins / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D013045:Species Specificity; D055672:Static Electricity; D013379:Substrate Specificity; D014305:Triose-Phosphate Isomerase / Q000378:metabolism*; D014346:Trypanosoma brucei brucei / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D005656:Fungal Proteins; D015800:Protozoan Proteins; D005986:Glyceraldehyde 3-Phosphate; D014305:Triose-Phosphate Isomerase