Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems.

Ab initio chemical shielding calculations greatly facilitate the interpretation of nuclear magnetic resonance (NMR) chemical shifts in biological systems, but the large sizes of these systems requires approximations in the chemical models used to represent them. Achieving good convergence in the predicted chemical shieldings is necessary before one can unravel how other complex structural and dynamical factors affect the NMR measurements. Here, we investigate how to balance trade-offs between using a better basis set or a larger cluster model for predicting the chemical shieldings of the substrates in two representative examples of protein-substrate systems involving different domains in tryptophan synthase: the N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F9) ligand which binds in the α active site, and the 2-aminophenol quinonoid intermediate formed in the ß active site. We first demonstrate that a chemically intuitive three-layer, locally dense basis model that uses a large basis on the substrate, a medium triple-zeta basis to describe its hydrogen-bonding partners and/or surrounding van der Waals cavity, and a crude basis set for more distant atoms provides chemical shieldings in good agreement with much more expensive large basis calculations. Second, long-range quantum mechanical interactions are important, and one can accurately estimate them as a small-basis correction to larger-basis calculations on a smaller cluster. The combination of these approaches enables one to perform density functional theory NMR chemical shift calculations in protein systems that are well-converged with respect to both basis set and cluster size.

Protonation states of the tryptophan synthase internal aldimine active site from solid-state NMR spectroscopy: direct observation of the protonated Schiff base linkage to pyridoxal-5'-phosphate.

The acid-base chemistry that drives catalysis in pyridoxal-5'-phosphate (PLP)-dependent enzymes has been the subject of intense interest and investigation since the initial identification of PLP's role as a coenzyme in this extensive class of enzymes. It was first proposed over 50 years ago that the initial step in the catalytic cycle is facilitated by a protonated Schiff base form of the holoenzyme in which the linking lysine ε-imine nitrogen, which covalently binds the coenzyme, is protonated. Here we provide the first (15)N NMR chemical shift measurements of such a Schiff base linkage in the resting holoenzyme form, the internal aldimine state of tryptophan synthase. Double-resonance experiments confirm the assignment of the Schiff base nitrogen, and additional (13)C, (15)N, and (31)P chemical shift measurements of sites on the PLP coenzyme allow a detailed model of coenzyme protonation states to be established.

Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states.

The allosteric regulation of substrate channeling in tryptophan synthase involves ligand-mediated allosteric signaling that switches the α- and ß-subunits between open (low activity) and closed (high activity) conformations. This switching prevents the escape of the common intermediate, indole, and synchronizes the α- and ß-catalytic cycles. (19)F NMR studies of bound α-site substrate analogues, N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F6) and N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), were found to be sensitive NMR probes of ß-subunit conformation. Both the internal and external aldimine F6 complexes gave a single bound peak at the same chemical shift, while α-aminoacrylate and quinonoid F6 complexes all gave a different bound peak shifted by +1.07 ppm. The F9 complexes exhibited similar behavior, but with a corresponding shift of -0.12 ppm. X-ray crystal structures show the F6 and F9 CF3 groups located at the α-ß subunit interface and report changes in both the ligand conformation and the surrounding protein microenvironment. Ab initio computational modeling suggests that the change in (19)F chemical shift results primarily from changes in the α-site ligand conformation. Structures of α-aminoacrylate F6 and F9 complexes and quinonoid F6 and F9 complexes show the α- and ß-subunits have closed conformations wherein access of ligands into the α- and ß-sites from solution is blocked. Internal and external aldimine structures show the α- and ß-subunits with closed and open global conformations, respectively. These results establish that ß-subunits exist in two global conformational states, designated open, where the ß-sites are freely accessible to substrates, and closed, where the ß-site portal into solution is blocked. Switching between these conformations is critically important for the αß-catalytic cycle.

Free-radical-induced oxidative and reductive degradation of sulfa drugs in water: absolute kinetics and efficiencies of hydroxyl radical and hydrated electron reactions.

Absolute rate constants and degradation efficiencies for hydroxyl radical and hydrated electron reactions with four different sulfa drugs in water have been evaluated using a combination of electron pulse radiolysis/absorption spectroscopy and steady-state radiolysis/high-performance liquid chromatography measurements. For sulfamethazine, sulfamethizole, sulfamethoxazole, and sulfamerazine, absolute rate constants for hydroxyl radical oxidation were determined as (8.3 +/- 0.8) x 10(9), (7.9 +/- 0.4) x 10(9), (8.5 +/- 0.3) x 10(9), and (7.8 +/- 0.3) x 10(9) M(-1) s(-1), respectively, with corresponding degradation efficiencies of 36% +/- 6%, 46% +/- 8%, 53% +/- 8%, and 35% +/- 5%. The reduction of these four compounds by their reaction with the hydrated electron occurred with rate constants of (2.4 +/- 0.1) x 10(10), (2.0 +/- 0.1) x 10(10), (1.0 +/- 0.03) x 10(10), and (2.0 +/- 0.1) x 10(10) M(-1) s(-1), respectively, with efficiencies of 0.5% +/- 4%, 61% +/- 9%, 71% +/- 10%, and 19% +/- 5%. We propose that hydroxyl radical adds predominantly to the sulfanilic acid ring of the different sulfa drugs based on similar hydroxyl radical rate constants and transient absorption spectra. In contrast, the variation in the rate constants for hydrated electrons with the sulfa drugs suggests the reaction occurs at different reaction sites, likely the different heterocyclic rings. The results of this study provide fundamental mechanistic parameters, hydroxyl radical and hydrated electron rate constants, and degradation efficiencies that are critical for the evaluation and implementation of advanced oxidation processes (AOPs).