Inverse enzyme isotope effects in human purine nucleoside phosphorylase with heavy asparagine labels

• Published in: Proceedings of the National Academy of Sciences - PNAS 2018-07, Vol.115 (27), p.E6209-E6216
• Main Authors: Harijan, Rajesh K., Zoi, Ioanna, Antoniou, Dimitri, Schwartz, Steven D., Schramm, Vern L.
• Format: Article
• Language: English
• Subjects: Amino acids; Asparagine; Asparagine - chemistry; Asparagine - genetics; Asparagine - metabolism; Barriers; Biological Sciences; Catalysis; Enzymes; Humans; Isotope Labeling; Isotopes; Kinetics; Labels; Nucleosides; Organic chemistry; Phosphorylase; PNAS Plus; Proteins; Purine-Nucleoside Phosphorylase - chemistry; Purine-Nucleoside Phosphorylase - genetics; Purine-Nucleoside Phosphorylase - metabolism; Reaction kinetics; Sampling; Steady state; Substrates
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1805416115

Transition path-sampling calculations with several enzymes have indicated that local catalytic site femtosecond motions are linked to transition state barrier crossing. Experimentally, femtosecond motions can be perturbed by labeling the protein with amino acids containing 13C, 15N, and nonexchangeable ²H. A slowed chemical step at the catalytic site with variable effects on steady-state kinetics is usually observed for heavy enzymes. Heavy human purine nucleoside phosphorylase (PNP) is slowed significantly (k chem light/k chem heavy = 1.36). An asparagine (Asn243) at the catalytic site is involved in purine leaving-group activation in the PNP catalytic mechanism. In a PNP produced with isotopically heavy asparagines, the chemical step is faster (k chem light/k chem heavy = 0.78). When all amino acids in PNP are heavy except for the asparagines, the chemical step is also faster (k chem light/k chem heavy = 0.71). Substrate-trapping experiments provided independent confirmation of improved catalysis in these constructs. Transition path-sampling analysis of these partially labeled PNPs indicate altered femtosecond catalytic site motions with improved Asn243 interactions to the purine leaving group. Altered transition state barrier recrossing has been proposed as an explanation for heavy-PNP isotope effects but is incompatible with these isotope effects. Rate-limiting product release governs steady-state kinetics in this enzyme, and kinetic constants were unaffected in the labeled PNPs. The study suggests that mass-constrained femtosecond motions at the catalytic site of PNP can improve transition state barrier crossing by more frequent sampling of essential catalytic site contacts.