TY - JOUR
T1 - Inverse enzyme isotope effects in human purine nucleoside phosphorylase with heavy asparagine labels
AU - Harijan, Rajesh K.
AU - Zoi, Ioanna
AU - Antoniou, Dimitri
AU - Schwartz, Steven D.
AU - Schramm, Vern L.
N1 - Funding Information:
ACKNOWLEDGMENTS. We acknowledge Dr. Javier Suarez for insightful discussions. The use of the facilities and expertise of the Albert Einstein College of Medicine Proteomics Core Facility is gratefully acknowledged. We thank Dr. Jennifer T. Aguilan from the Proteomics Laboratory at the Albert Einstein College of Medicine for analysis of the nano-UPLC-MS/MS data for PNPs. All computer simulations were performed at the University of Arizona High-Performance Computing Center on a Lenovo NeXtScale nx360 M5 supercomputer. This research was supported through NIH Program Project Grant GM068036 (to V.L.S. and S.D.S.) and Research Grant GM041916.
Funding Information:
We acknowledge Dr. Javier Suarez for insightful discussions. The use of the facilities and expertise of the Albert Einstein College of Medicine Proteomics Core Facility is gratefully acknowledged. We thank Dr. Jennifer T. Aguilan from the Proteomics Laboratory at the Albert Einstein College of Medicine for analysis of the nano-UPLC-MS/MS data for PNPs. All computer simulations were performed at the University of Arizona High-Performance Computing Center on a Lenovo NeXtScale nx360 M5 supercomputer. This research was supported through NIH Program Project Grant GM068036 (to V.L.S. and S.D.S.) and Research Grant GM041916.
Publisher Copyright:
© 2018 National Academy of Sciences. All Rights Reserved.
PY - 2018/7/3
Y1 - 2018/7/3
N2 - 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 (kchem light/ kchem 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 (kchem light/kchem heavy = 0.78). When all amino acids in PNP are heavy except for the asparagines, the chemical step is also faster (kchem light/kchem 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.
AB - 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 (kchem light/ kchem 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 (kchem light/kchem heavy = 0.78). When all amino acids in PNP are heavy except for the asparagines, the chemical step is also faster (kchem light/kchem 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.
KW - Born–Oppenheimer enzymes
KW - Heavy-enzyme isotope effects
KW - Promoting vibrations
KW - Transition path sampling
KW - Transition state structure
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U2 - 10.1073/pnas.1805416115
DO - 10.1073/pnas.1805416115
M3 - Article
C2 - 29915028
AN - SCOPUS:85049366618
SN - 0027-8424
VL - 115
SP - E6209-E6216
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 27
ER -