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

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 (kchemlight/kchemheavy = 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 (kchemlight/kchemheavy = 0.78). When all amino acids in PNP are heavy except for the asparagines, the chemical step is also faster (kchemlight/kchemheavy = 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.

Comparison of photoenolization and alcohol release from alkyl-substituted benzoyl benzoic esters

Photolysis of 1B in argon-saturated solutions yields 4B and releases methanol. Laser flash photolysis of 1B shows formation of biradical 2B, which has a lifetime of ~50 ns and a λmax at 330 nm. Biradical 2B undergoes an intersystem crossing to form photoenols E-3B and Z-3B with a λmax at 390 nm. Laser flash photolysis shows that the lifetimes of E-3B and Z-3B are affected by the solvent. Density functional theory calculations demonstrate that the transition-state barrier for a 1,5-H atom shift from Z-3B to regenerate 1B is affected by the ortho-alkyl substituents, whereas the stereoelectronics of the alkyl substituent affect the transition-state barrier of E-3B as it undergoes electrocyclic ring closure to form 4B. The photoreactivity of 1B was compared with its analogous methyl and isopropyl derivatives 1A and 1C, respectively, to better estimate the effect of the alkyl substituent on reactivity.

Folding initiation sites and protein folding.

The paper discusses the role of local structural preferences of protein segments in the folding of proteins. First a short overview of the local, secondary structures detected in peptides, protein fragments, denatured proteins and early folding intermediates is given. Next the discussion of their role in protein folding is presented based on recent literature and data obtained in our laboratory. In conclusion it is pointed out that, during folding, local structures populated at low levels in denatured state may facilitate the crossing of the folding transition state barrier, and consequently accelerate the rate limiting step in folding. However, the data show that this effect does not follow simple rules.