Thiol Proton Research Articles

Kinetic and structural details of urease inactivation by thiuram disulphides

This paper reports on the molecular details of the reactivity of urease, a nickel-dependent enzyme that catalyses the last step of organic nitrogen mineralization, with thiuram disulphides, a class of molecules known to inactivate the enzyme with high efficacy but for which the mechanism of action had not been yet established. IC50 values of tetramethylthiuram disulphide (TMTD or Thiram) and tetraethylthiuram disulphide (TETD or Disulfiram) in the low micromolar range were determined for plant and bacterial ureases. The X-ray crystal structure of Sporosarcina pasteurii urease inactivated by Thiram, determined at 1.68 Å resolution, revealed the presence of a covalent modification of the catalytically essential cysteine residue. This is located on the flexible flap that modulates the size of the active site channel and cavity. Formation of a Cys-S-S-C(S)-N(CH3)2 functionality responsible for enzyme inactivation was observed. Quantum-mechanical calculations carried out to rationalise the large reactivity of the active site cysteine support the view that a conserved histidine residue, adjacent to the cysteine in the active site flap, modulates the charge and electron density along the thiol SH bond by shifting electrons towards the sulphur atom and rendering the thiol proton more reactive. We speculate that this proton could be transferred to the nickel-coordinated urea amide group to yield a molecule of ammonia from the generated Curea-NH3+ functionality during catalysis.

Turn on the luminescence channel by the suppression of conical intersection process for the sulfur-containing hydrogen-bonded molecules

The sulfur-containing hydrogen bonds exhibit notable potential in gene and protein engineering. As an important research direction of sulfur-containing hydrogen bonding dynamics, the excited-state intramolecular proton transfer (ESIPT) reaction of the thiol proton has garnered significant interest. Recently, Chou et al. synthesized a series of sulfur-containing H-bonded molecules, inclusive of 3-thiolflavone (3 TF), its trifluoromethyl derivative (3FTF), and its diethylamino derivative (3NTF), thereby inaugurating a new chapter in the ESIPT reaction of the thiol proton. Nevertheless, many open issues cannot be answered solely by experimental means and call for a detailed theoretical investigation, especially the relationship between the molecular excited-state properties and different luminescence properties of the three molecules. Herein, we validate that the molecules undergo the ESIPT reaction of the thiol proton and identify the time scale through the time-dependent density functional theory (TDDFT) calculation. Moreover, employing the spin-flip TDDFT approach, the analysis of the non-radiative transition process reveals that difference in Gibbs free energy of activation (ΔG⧧) for the transition from Frank-Condon point to minimum energy conical intersection (MECI) point primarily accounts for the different luminescence properties of the three molecules. Besides, we also reveal the reason for the abnormal blue-shifted fluorescence of the 3NTF in the aggregated state by the ONIOM (TDDFT: UFF) strategy. These findings are favorable to understanding the luminescence mechanism of sulfur-containing H-bonded molecules and provide a reference for the synthesis and design of the luminescent materials based on the molecules with thiol proton transfer properties.

Molecular Principles of the Excited-State Intramolecular Thiol Proton Transfers in 3-thiolflavone Derivatives.

The excited-state intramolecular proton transfer (ESIPT) effect has attracted considerable attention due to its potential applications in photoluminescent materials. However, only a few theoretical reports have investigated the ESIPT process involving sulfur-hydrogen bonds. Herein, we systematically investigated the ESIPT effect of three 3-thiolflavone derivatives containing sulfur-hydrogen bonds with M06-2X functional combined Def2-TZVP basis set. The intramolecular sulfur-hydrogen bonds were confirmed in the ground and excited states via analyzing the bond lengths, interaction energies, and infrared vibrational spectra. Besides, we demonstrated that the electron-withdrawing group led to a more stable tautomer compared to the electron-donating group. Conversely, the electron-donating group played a crucial role in reducing the energy barrier of the ESIPT reaction due to the strengthening of the hydrogen bond in the excited state. Interestingly, the substituent group can determine the excited-state electronic properties of keto tautomers. Specifically, the electron-withdrawing group caused significant improvement in the nπ* transition configuration, significantly reducing the radiation rate. The electron-donating group increased the proportion of the ππ* transition configuration, thus, the keto tautomer had bright emission. We expect these findings to open new avenues for designing potential luminescent materials.

Triplet state generation followed by the excited-state intramolecular proton transfer in 3-sulfanylchromen-4-one

We theoretically study the triplet formation dynamics of tautomers associated with the excited-state intramolecular proton transfer of 3-sulfanylchromen-4-one (3-SC). The S1-T3 intersystem crossing pathway is expected to compete with the intramolecular thiol proton transfer upon photoexciting the normal tautomer (parent molecule) to its S1 state. The triplet formation via the S1′-T2′ intersystem crossing tends to be the dominant nonradiative process in the proton-transferred tautomer. The wavepacket transfer to the respective accessible receiver triplet state is more pronounced in the proton-transferred tautomer than its parent tautomer, implying an efficient triplet formation followed by the proton transfer via S1 in 3-SC.

Effects of solvent polarity on the novel excited-state intramolecular thiol proton transfer and photophysical property compared with the oxygen proton transfer

Recently, the dual-fluorescent phenomena of excited state intramolecular thiol proton transfer (ESIPT) for 3-thiolflavone derivative (3NTF) were reported by Chou and coworkers for the first time [J. Am. Chem. Soc. 143 (2021) 12715–12724], which opened a new chapter in the field of ESIPT. Based on density functional theory (DFT) and time-dependent density functional theory (TDDFT), the proton transfer processes of 3NTF in toluene, dichloromethane and acetonitrile were studied. By optimizing the structure of the ground (S0) state and first excited (S1) state of 3NTF in different solvents, the hydrogen-bond parameters and proton-transfer potential energy curves were calculated. It was shown that although photo-excitation enhanced the intramolecular hydrogen bonding strength and thus promoted the occurrence of ESIPT, the solvent polarities inhibited the enhancement of the hydrogen bond of S1 state, which was not conducive to ESIPT. The electron spectra analyses were consistent with experimental data, which confirmed the rationality of molecular configurations. The time-evolved excited state dynamics simulation was performed based on the optimized structure of 3NTF, indicating that the ESIPT was an ultrafast photochemical reaction less than 180 fs. Moreover, we compared the potential energy surfaces of ESIPT, electronic structures based on natural transition orbitals (NTOs) method and electron-hole isosurfaces for the 3NTF and the traditional flavone molecule (3NHF), concluded that the unusually large Stokes shift fluorescence of 3NTF was mainly caused by the coupling of ESIPT and twisting intramolecular charge transfer (TICT), and the 3NTF isomer had the more nπ* character in the electron transition process. The nπ* ICT significantly increased with the decrease of solvent polarities, affecting the molecular photophysical properties, this made it more widely used in biomedical, photochemical, materials science and other fields.

MRI Detection of Hepatic N-Acetylcysteine Uptake in Mice.

This proof-of-concept study looked at the feasibility of using a thiol–water proton exchange (i.e., CEST) MRI contrast to detect in vivo hepatic N-acetylcysteine (NAC) uptake. The feasibility of detecting NAC-induced glutathione (GSH) biosynthesis using CEST MRI was also investigated. The detectability of the GSH amide and NAC thiol CEST effect at B0 = 7 T was determined in phantom experiments and simulations. C57BL/6 mice were injected intravenously (IV) with 50 g L−1 NAC in PBS (pH 7) during MRI acquisition. The dynamic magnetisation transfer ratio (MTR) and partial Z-spectral data were generated from the acquisition of measurements of the upfield NAC thiol and downfield GSH amide CEST effects in the liver. The 1H-NMR spectroscopy on aqueous mouse liver extracts, post-NAC-injection, was performed to verify hepatic NAC uptake. The dynamic MTR and partial Z-spectral data revealed a significant attenuation of the mouse liver MR signal when a saturation pulse was applied at −2.7 ppm (i.e., NAC thiol proton resonance) after the IV injection of the NAC solution. The 1H-NMR data revealed the presence of hepatic NAC, which coincided strongly with the increased upfield MTR in the dynamic CEST data, providing strong evidence that hepatic NAC uptake was detected. However, this MTR enhancement was attributed to a combination of NAC thiol CEST and some other upfield MT-generating mechanism(s) to be identified in future studies. The detection of hepatic GSH via its amide CEST MRI contrast was inconclusive based on the current results.

Chapter Open for the Excited-State Intramolecular Thiol Proton Transfer in the Room-Temperature Solution.

We report here, for the first time, the experimental observation on the excited-state intramolecular proton transfer (ESIPT) reaction of the thiol proton in room-temperature solution. This phenomenon is demonstrated by a derivative of 3-thiolflavone (3TF), namely, 2-(4-(diethylamino)phenyl)-3-mercapto-4H-chromen-4-one (3NTF), which possesses an -S-H···O═ intramolecular H-bond (denoted by the dashed line) and has an S1 absorption at 383 nm. Upon photoexcitation, 3NTF exhibits a distinctly red emission maximized at 710 nm in cyclohexane with an anomalously large Stokes shift of 12 230 cm-1. Upon methylation on the thiol group, 3MeNTF, lacking the thiol proton, exhibits a normal Stokes-shifted emission at 472 nm. These, in combination with the computational approaches, lead to the conclusion of thiol-type ESIPT unambiguously. Further time-resolved study renders an unresolvable (<180 fs) ESIPT rate for 3NTF, followed by a tautomer emission lifetime of 120 ps. In sharp contrast to 3NTF, both 3TF and 3-mercapto-2-(4-(trifluoromethyl)phenyl)-4H-chromen-4-one (3FTF) are non-emissive. Detailed computational approaches indicate that all studied thiols undergo thermally favorable ESIPT. However, once forming the proton-transferred tautomer, the lone-pair electrons on the sulfur atom brings non-negligible nπ* contribution to the S1' state (prime indicates the proton-transferred tautomer), for which the relaxation is dominated by the non-radiative deactivation. For 3NTF, the extension of π-electron delocalization by the diethylamino electron-donating group endows the S1' state primarily in the ππ* configuration, exhibiting the prominent tautomer emission. The results open a new chapter in the field of ESIPT, covering the non-canonical sulfur intramolecular H-bond and its associated ESIPT at ambient temperature.

Kinetic Isotope Effects on Electron Transfer Across Self-Assembled Monolayers on Gold.

Reactions requiring controlled delivery of protons and electrons are important in storage of energy in small molecules. While control over proton transfer can be achieved by installing appropriate chemical functionality in the catalyst, control of electron-transfer (ET) rates can be achieved by utilizing self-assembled monolayers (SAMs) on electrodes. Thus, a deeper understanding of the ET through SAM to an immobilized or covalently attached redox-active species is desirable. Long-range ET across several SAM-covered Au electrodes to covalently attached ferrocene is investigated using protonated and deuterated thiols (R-SH/R-SD). The rate of tunneling is measured using both chronoamperometry and cyclic voltammetry, and it shows a prominent kinetic isotope effect (KIE). The KIE is ∼2 (normal) for medium-chain-length thiols but ∼0.47 (inverse) for long-chain thiols. These results imply substantial contribution from the classical modes at the Au-(H)SR interface, which shifts substantially upon deuteration of the thiols, to the ET process. The underlying H/D KIE of these exchangeable thiol protons should be considered when analyzing solvent isotope effects in catalysis utilizing SAM.

Photoinduced NO and HNO Production from Mononuclear {FeNO}6 Complex Bearing a Pendant Thiol.

Light triggers the formation of HNO from a metal-nitrosyl species, facilitated by an intramolecular pendant thiol proton. Two {FeNO}6 complexes (the Enemark-Felthan notation), [Fe(NO)(TMSPS2)(TMSPS2H)] (1, TMSPS2H2 = 2,2'-dimercapto-3,3'-bis(trimethylsilyl)diphenyl)phenylphosphine; H is a dissociable proton) with a pendant thiol and [Fe(NO)(TMSPS2)(TMSPS2CH3)] (2) bearing a pendant thioether, are spectroscopically and structurally characterized. Both complexes are highly sensitive to visible light. Upon photolysis, complex 2 undergoes NO dissociation to yield a mononuclear Fe(III) complex, [Fe(TMSPS2)(TMSPS2CH3)] (3). In contrast, the pendant SH of 1 can act as a trap for the departing NO radical upon irradiation, resulting in the formation of an intermediate A with an intramolecular [SH···ON-Fe] interaction. As suggested by computational results (density functional theory), the NO stretching frequency (νNO) is sensitive to the intramolecular interaction between the pendant ligand and the iron-bound NO, and a shift of νNO from 1833 (1) to 1823 cm-1 (A) is observed experimentally. Subsequent photolysis of the intermediate A results in HNO production and a thiyl group that then coordinates to the Fe center for the formation of [Fe(TMSPS2)2] (4). In contrast with the common acid-base coupling pathway, the HNO is not voluntarily yielded from 1 but rather is generated by the photopromoted pathway. The photogenerated HNO can further react with [MnIII(TMSPS3)(DABCO)] (TMSPS3H3 = (2,2'2''-trimercapto-3,3',3''-tris(trimethylsilyl)triphenylphosphine; DABCO = 1,4-diazabicyclo[2.2.2]octane) in organic media to yield anionic [Mn(NO)(TMSPS3)]- (5-) with a {MnNO}6 electronic configuration, whereas [MnIII(TMSPS3)(DABCO)] reacts with NO gas for the formation of a {MnNO}5 species, [Mn(NO)(TMSPS3)] (6). Effective differentiation of the formation of HNO from complex 1 with the pendant SH versus NO from 2 with the pendant SMe is achieved by the employment of [MnIII(TMSPS3)(DABCO)].

Thiol-water proton exchange of glutathione, cysteine, and N-acetylcysteine: Implications for CEST MRI.

Amide-, amine-, and hydroxyl-water proton exchange can generate MRI contrast through chemical exchange saturation transfer (CEST). In this study, we show that thiol-water proton exchange can also generate quantifiable CEST effects under near-physiological conditions (pH = 7.2 and 37°C) through the characterization of the pH dependence of thiol proton exchange in phosphate-buffered solutions of glutathione, cysteine, and N-acetylcysteine. The spontaneous, base-catalyzed, and buffer-catalyzed exchange contributions to the thiol exchange were analyzed. The thiol-water proton exchange of glutathione and cysteine was found to be too fast to generate a CEST effect around neutral pH due to significant base catalysis. The thiol-water proton exchange of N-acetylcysteine was found to be much slower, yet still in the fast-exchange regime with significant base and buffer catalysis, resulting in a 9.5% attenuation of the water signal at pH 7.2 in a slice-selective CEST NMR experiment. Furthermore, the N-acetylcysteine thiol CEST was also detectable in human serum albumin and agarose phantoms.

Electrophilic additions of nitrated fatty acids with biological thiols: comparison with type-2 alkenes

We investigated the adduct formations of cysteine and glutathione with electrophilic substrates. Density functional theory with a continuum model was applied to explore the reactions that serve as models for cell signaling proteins and electrophiles. Biological electrophilic species including nitrated fatty acids (NO2-FAs), 15-deoxy-delta12,14-prostaglandin J2 (15d-PGJ2) and neurotoxic type-2 alkenes were included in our investigation. The reaction sequence begins with a thiol proton transfer with the base, followed by nucleophilic attack, and ends with a second proton transfer to accomplish thiol additions to the substrates. It was observed that adduct formations between the thiols and type-2 alkenes are comparatively more exergonic than those with NO2-FAs and 15d-PGJ2. The type-2 alkenes that were most exergonic in adduct formations were experimentally identified to be the most toxic. The computational approach presented in this work may serve as a convenient method to predict the degree of neurotoxicity.

\u201cCarboranyl-cysteine\u201d\u2014Synthesis, Structure and Self-Assembly Behavior of a Novel \u03b1-Amino Acid

Substitution of the thiol proton in cysteine with m-carborane furnished 2-amino-3-(1,7-dicarba-closo-dodecacarboranyl-1-thio)propanoic acid (3), a boron cluster amino acid that exhibits self-assembly to form micron-sized constructs. Field emission scanning electron microscopy revealed that ethanol solutions of 3 form floret-shaped constructs, while fibrillar architectures are formed in water. Furthermore, slow evaporation of methanol solutions of 3 produced crystals whose structure was revealed by X-ray crystallography. The crystal structure shows that the hydrogen bonding interactions between pairs of 3 result in the formation of bilayers of 174 Å in length. The orientation of the clusters is not random in the crystal structure, such that the side-by-side aligned polyhedra are offset by 158 degrees. The material was characterized by FT-IR, NMR, high resolution mass spectrometry and dynamic light scattering. Circular dichroism studies indicated that self-assembly occurs at concentrations as low as 0.01 μM. This represents the first demonstration of self-assembly of a carborane-based molecule in the absence of metals. The amino acid motif provides opportunities for the controlled synthesis of extended multimeric units with tunable properties and the potential for applications in biology, medicine and materials chemistry.

Modifying methionine on proteins

Thanks to the chemistry of its thiol group, cysteine has long been the go-to amino acid when researchers want to modify a protein. It’s easy to pluck off cysteine’s thiol proton and replace it with something else, such as a drug molecule or a dye. But this chemistry can cause problems, explains Christopher J. Chang, a chemical biologist at the University of California, Berkeley. Those cysteine residues are often involved in catalysis or play a role in stabilizing the protein via formation of disulfide bonds. If scientists could find a different amino acid to modify, they’d be less likely to disrupt protein function when making antibody-drug conjugates or preparing covalent protein probes. Teaming up with synthetic chemists in F. Dean Toste’s lab at UC Berkeley, Chang’s lab has managed to do just that: develop a bioconjugation method that selectively modifies methionine residues (Science 2017, DOI: 10.1126/science.aal3316). The method is based

H2S Reactivity on Oxygen-Deficient Heterotrimetallic Cores: Cluster Fluxionality Simulates Dynamic Aspects of Surface Chemical Reactions.

Understanding the mechanistic aspects of heterogeneous reactions on supported metal catalysts is challenging due to several disparate factors, among which the dynamic nature of the surface is a major contributor. In this study, the dynamic aspect of a surface has been probed by choosing small metal clusters as illustrative models. Two anionic hetero-trimetallic clusters, namely, W2TcO6(-) and W2OsO6(-), were reacted with H2S gas to exhibit splitting of the gas molecule and complete oxygen-sulfur exchange in the metal core. During this atom-exchange process, the core exhibits remarkable fluxionality to augment a thiol proton migration from one metal center to another, as well as a rapid interchange of the terminal and bridging oxygens. The fluxional nature of the core is further evidenced by two oppositely oriented oxo groups working in concert to accomplish the proton transfer, upon introduction of sulfur inside the core. These fluxional processes in the small hetero-trimetallic cores closely resemble the dynamic nature of the surface in a heterogeneous reaction. Throughout the fluxional processes investigated in this study, two-state reactivity and multiple instances of spin crossover are observed in our computational studies. Interestingly, the neutral hetero-trimetallic cores can also undergo complete oxygen-sulfur exchange reaction with H2S. The investigated metal clusters are promising materials, since they not only can liberate dihydrogen from water (reported in J. Phys. Chem. A, 2014, 118, 11047) but also can completely strip the sulfur from environmentally hazardous H2S gas.

Oxidation of Gold Clusters by Thiols

The formation of gold-thiolate nanoparticles via oxidation of gold clusters by thiols is examined in this work. Using the BP86 density functional with a triple ζ basis set, the adsorption of methylthiol onto various gold clusters Aun(Z) (n = 1-8, 12, 13, 20; Z = 0, -1, +1) and Au38(4+) is investigated. The rate-limiting step for the reaction of one thiol with the gold cluster is the dissociation of the thiol proton; the resulting hydrogen atom can move around the gold cluster relatively freely. The addition of a second thiol can lead to H2 formation and the generation of a gold-thiolate staple motif.

Staple Motifs, Initial Steps in the Formation of Thiolate-Protected Gold Nanoparticles: How Do They Form?

Recent structural determinations have shown that thiolate-protected gold nanoparticles are not as regular and symmetric as initially thought, but characteristic substructures (staple motifs) are formed on their surface. However, their mechanism of formation, especially the fate of the sulfur protons upon thiol binding, remains one of the most intriguing unanswered questions in gold cluster chemistry. By means of ab initio molecular dynamics (AIMD), we monitor the trajectory of thiol protons reacting with a gold cluster, demonstrating that the staple motif forms in a multiple-pathway chemical reaction, releasing molecular hydrogen. The results obtained also reconcile the conclusions of structural determinations with the interpretations of spectroscopic experiments on solution, suggesting the presence of intact thiols or chemisorbed hydrogen.

Synthesis and characterization of an unsymmetrical cobalt(III) active site analogue of nitrile hydratase

The design, synthesis, and characterization of an unsymmetrical diamidato-dithiol ligand (H(4) 1, where the hydrogen atoms represent deprotonatable amide and thiol protons) and its cobalt(III) complex, a synthetic analogue of the cobalt-containing nitrile hydratase enzyme family, are reported. The ligand was prepared in 24% yield from an overall eight-step synthetic pathway following a modified protocol established in our laboratory that includes two peptide couples using O-(1H-benzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate as the coupling agent. The ligand and all precursors were characterized by NMR spectroscopy and elemental analysis. The cobalt nitrile hydratase synthetic analogue complex [NBu(4)][Co(1)] was prepared on deprotonating ligand H(4) 1 to [1](4-) on addition of 5equiv of NaH in N,N-dimethylformamide and adding 1equiv of CoCl(2) at -40°C under a N(2) atmosphere followed by oxidizing the complex by stirring it overnight open to dry air. The complex [NBu(4)][Co(1)] was isolated after counterion exchange with 1equiv of NBu(4)Cl followed by crystallization from MeCN/Et(2)O in 71% yield. The structure of the complex was confirmed by X-ray diffraction analysis. Cyclic voltammetry studies on [NBu(4)][Co(1)] in a 0.1M [NBu(4)][PF(6)]/MeCN solution showed a quasi-reversible reduction potential at -1.1V (vs. Ag/AgCl), and magnetic susceptibility investigations indicated the complex is paramagnetic in both the solid and the solution states as determined from inverse-Gouy and Evans NMR methods, respectively.

Critical Role of Water and the Structure of Inverse Micelles in the Brust–Schiffrin Synthesis of Metal Nanoparticles

Although Brust-Schiffrin two-phase synthesis is a popular method for synthesizing ligand-protected metal nanoparticles with an average size of less than 5 nm, the details on how the reactions can be controlled from a mechanistic point of view are still unclear, therefore hindering efforts to synthesize monodisperse metal nanoparticles. It was recently discovered that this method is basically an inverse-micelle-based synthesis (Li, Y.; Zaluzhna, O.; Xu, B.; Gao, Y.; Modest, J. M.; Tong, Y. Y. J. J. Am. Chem. Soc.2011, 133, 2092). In this letter, the critical role of water and the structure of inverse micelles in typical synthesis of gold nanoparticles were further investigated. We found that (1) water encapsulated in the inverse micelles of [TOA](+) that also hosted metal ions formed a hydrophilic microenvironment that acted as a reaction-enabling proton-accepting medium for the thiol protons (RS-H) and (2) not only the presence but also the amount of water in the reaction medium has a profound effect on the Au(I) precursor species (a pure [TOA][AuX(2)] complex or a mixture of a [TOA][AuX(2)] complex and polymeric [Au(I)SR](n) species), the reduction of Au(III) by thiols, and the formation of uniform small metal nanoparticles. A quantitative analysis of the (1)H NMR of the encapsulated water enabled an estimation of the size and composition of the involved inverse micelles.

Mononuclear [NiII(L)(P-(o-C6H4S)2(o-C6H4SH))]0/1- (L = Thiolate, Selenolate, PPh3, and Cl) Complexes with Intramolecular [Ni···S···H···S]/[Ni···H···S] Interactions Modulated by the Coordinated Ligand L: Relevance to the [NiFe] Hydrogenases

The shift of the IR nu(S)(-)(H) frequency to lower wavenumbers for the series of complexes [Ni(II)(L)(P-(o-C6H4S)2(o-C6H4SH))]0/1- (L = PPh3 (1), Cl (6), Se-p-C6H4-Cl (5), S-C4H3S (7), SePh (4)) indicates that a trend of increasing electronic donation of the L ligands coordinated to the Ni(II) center promotes intramolecular [Ni-S...H-S] interactions. Compared to the Ni...S(H) distance, in the range of 3.609-3.802 A in complexes 1 and 4-7, the Ni...S(CH3) distances of 2.540 and 2.914 A observed in the [Ni(II)(PPh3)(P(o-C6H4S)2(o-C6H4-SCH3))] complexes (8a and 8b, two conformational isomers with the chemical shift of the thioether methyl group at delta 1.820 (-60 degrees C) and 2.109 ppm (60 degrees C) (C4D8O)) and the Ni...S(CH3) distances of 3.258 and 3.229 A found in the [Ni(II)(L)(P(o-C6H4S)2(o-C6H4-SCH3))]1- complexes (L = SPh (9), SePh (10)) also support the idea that the pendant thiol protons of the Ni(II)-thiol complexes 1/4-7 were attracted by both the sulfur of thiolate and the nickel. The increased basicity (electronic density) of the nickel center regulated by the monodentate ligand attracted the proton of the pendant thiol effectively and caused the weaker S...H bond. In addition, the pendant thiol interaction modes in the solid state (complexes 1a and 1b, Scheme 1) may be controlled by the solvent of crystallization. Compared to complex 1a, the stronger intramolecular [Ni-S...H-S] interaction (or a combination of [Ni-S...H-S]/[Ni...H-S] interactions) found in complexes 4-7 led to the weaker S-H bond strength and accelerated the oxidation (by O2) of complexes 4-7 to produce the [Ni(Y)(L)(P(o-C6H4S)3)]1- (L = Se-p-C6H4-Cl (11), SePh (12), S-C4H3S (13)) complexes.

Structural and Functional Studies Suggest a Catalytic Mechanism for the Phosphotransacetylase from Methanosarcina thermophila

Phosphotransacetylase (EC 2.3.1.8) catalyzes reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. Two crystal structures of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila in complex with the substrate CoA revealed one CoA (CoA1) bound in the proposed active site cleft and an additional CoA (CoA2) bound at the periphery of the cleft. The results of isothermal titration calorimetry experiments are described, and they support the hypothesis that there are distinct high-affinity (equilibrium dissociation constant [KD], 20 microM) and low-affinity (KD, 2 mM) CoA binding sites. The crystal structures indicated that binding of CoA1 is mediated by a series of hydrogen bonds and extensive van der Waals interactions with the enzyme and that there are fewer of these interactions between CoA2 and the enzyme. Different conformations of the protein observed in the crystal structures suggest that domain movements which alter the geometry of the active site cleft may contribute to catalysis. Kinetic and calorimetric analyses of site-specific replacement variants indicated that there are catalytic roles for Ser309 and Arg310, which are proximal to the reactive sulfhydryl of CoA1. The reaction is hypothesized to proceed through base-catalyzed abstraction of the thiol proton of CoA by the adjacent and invariant residue Asp316, followed by nucleophilic attack of the thiolate anion of CoA on the carbonyl carbon of acetyl phosphate. We propose that Arg310 binds acetyl phosphate and orients it for optimal nucleophilic attack. The hypothesized mechanism proceeds through a negatively charged transition state stabilized by hydrogen bond donation from Ser309.