Ground term splitting of high-spin cobalt(2+) ion as a probe of coordination structure. 2. The ligand environment of the active site metal ion of carboxypeptidase A in ester hydrolysis

The influence of solvent composition on the coordination environment of the Co/Mn/Br based para-xylene oxidation catalyst as revealed by EPR and ESEEM spectroscopy

The industrially important para-xylene oxidation reaction, based on a Co/Mn/Br catalyst, operates in a water/acetic acid (H2O/AcOH) solvent system.

Applying Unconventional Spectroscopies to the Single-Molecule Magnets, Co(PPh3 )2 X2 (X=Cl, Br, I): Unveiling Magnetic Transitions and Spin-Phonon Coupling

Large separation of magnetic levels and slow relaxation in metal complexes are desirable properties of single-molecule magnets (SMMs). Spin-phonon coupling (interactions of magnetic levels with phonons) is ubiquitous, leading to magnetic relaxation and loss of memory in SMMs and quantum coherence in qubits. Direct observation of magnetic transitions and spin-phonon coupling in molecules is challenging. We have found that far-IR magnetic spectra (FIRMS) of Co(PPh₃ )₂ X₂ (Co-X; X=Cl, Br, I) reveal rarely observed spin-phonon coupling as avoided crossings between magnetic and u-symmetry phonon transitions. Inelastic neutron scattering (INS) gives phonon spectra. Calculations using VASP and phonopy programs gave phonon symmetries and movies. Magnetic transitions among zero-field split (ZFS) levels of the S=3/2 electronic ground state were probed by INS, high-frequency and -field EPR (HFEPR), FIRMS, and frequency-domain FT terahertz EPR (FD-FT THz-EPR), giving magnetic excitation spectra and determining ZFS parameters (D, E) and g values. Ligand-field theory (LFT) was used to analyze earlier electronic absorption spectra and give calculated ZFS parameters matching those from the experiments. DFT calculations also gave spin densities in Co-X, showing that the larger Co(II) spin density in a molecule, the larger its ZFS magnitude. The current work reveals dynamics of magnetic and phonon excitations in SMMs. Studies of such couplings in the future would help to understand how spin-phonon coupling may lead to magnetic relaxation and develop guidance to control such coupling.

Probing the generality of spin crossover complex T½vs. ligand 15N NMR chemical shift correlations: towards predictable tuning

A study of 6 families (42 members) demonstrates that within a family the easily calculated 15N-NMR values of ligands enable predictable tuning of T1/2 in the corresponding complexes, except for 2 families with weakly influencing meta-substituents.

Quantitative and Chemically Intuitive Evaluation of the Nature of M-L Bonds in Paramagnetic Compounds: Application of EDA-NOCV Theory to Spin Crossover Complexes

To improve understanding of M-L bonds in 3d transition metal complexes, analysis by energy decomposition analysis and natural orbital for chemical valence model (EDA-NOCV) is desirable as it provides a full, quantitative and chemically intuitive ab initio description of the M-L interactions. In this study, a generally applicable fragmentation and computational protocol was established and validated by using octahedral spin crossover (SCO) complexes, as the transition temperature (T1/2 ) is sensitive to subtle changes in M-L bonding. Specifically, EDA-NOCV analysis of Fe-N bonds in five [FeII (Lazine )2 (NCBH3 )2 ], in both low-spin (LS) and paramagnetic high-spin (HS) states led to: 1) development of a general, widely applicable, corrected M+L6 fragmentation, tested against a family of five LS [FeII (Lazine )3 ](BF4 )2 complexes; this confirmed that three Lazine are stronger ligands (ΔEorb,σ+π =-370 kcal mol-1 ) than 2 Lazine +2 NCBH3 (=-335 kcal mol-1 ), as observed. 2) Analysis of Fe-L bonding on LS→HS, reveals more ionic (ΔEelstat ) and less covalent (ΔEorb ) character (ΔEelstat :ΔEorb 55:45 LS→64:36 HS), mostly due to a big drop in σ (ΔEorb,σ ↓50 %; -310→-145 kcal mol-1 ), and a drop in π contributions (ΔEorb,π ↓90 %; -30→-3 kcal mol-1 ). 3) Strong correlation of observed T1/2 and ΔEorb,σ+π , for both LS and HS families (R2 =0.99 LS, R2 =0.95 HS), but no correlation of T1/2 and ΔΔEorb,σ+π (LS-HS) (R2 =0.11). Overall, this study has established and validated an EDA-NOCV protocol for M-L bonding analysis of any diamagnetic or paramagnetic, homoleptic or heteroleptic, octahedral transition metal complex. This new and widely applicable EDA-NOCV protocol holds great promise as a predictive tool.

Solvent water interactions within the active site of the membrane type I matrix metalloproteinase

Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters. Here we report a novel crystal structure of membrane type I MMP (MT1-MMP or MMP-14), which includes a small peptide bound at the catalytic Zn site via its C-terminus. This structure models the initial product state formed immediately after peptide cleavage but before the final proton transfer to the bound amine; the amine is not present in our system and as such proton transfer cannot occur. Modeling of the protein, including earlier structural data of Bertini and coworkers [I. Bertini, et al., Angew. Chem., Int. Ed., 2006, 45, 7952-7955], suggests that the C-terminus of the peptide is positioned to form an H-bond network to the amine site, which is mediated by a single oxygen of the functionally important Glu240 residue, facilitating efficient proton transfer. Additional quantum chemical calculations complemented with magneto-optical and magnetic resonance spectroscopies clarify the role of two additional, non-catalytic first coordination sphere waters identified in the crystal structure. One of these auxiliary waters acts to stabilize key intermediates of the reaction, while the second is proposed to facilitate C-fragment release, triggered by protonation of the amine. Together these results complete the enzymatic cycle of MMPs and provide new design criteria for inhibitors with improved efficacy.

Spectroscopic Studies of the EutT Adenosyltransferase from Salmonella enterica: Evidence of a Tetrahedrally Coordinated Divalent Transition Metal Cofactor with Cysteine Ligation

The EutT enzyme from Salmonella enterica, a member of the family of ATP:cobalt(I) corrinoid adenosyltransferase (ACAT) enzymes, requires a divalent transition metal ion for catalysis, with Fe(II) yielding the highest activity. EutT contains a unique cysteine-rich HX₁₁CCX₂C(83) motif (where H and the last C occupy the 67th and 83rd positions, respectively, in the amino acid sequence) not found in other ACATs and employs an unprecedented mechanism for the formation of adenosylcobalamin. Recent kinetic and spectroscopic studies of this enzyme revealed that residues in the HX₁₁CCX₂C(83) motif are required for the tight binding of the divalent metal ion and are critical for the formation of a four-coordinate (4c) cob(II)alamin [Co(II)Cbl] intermediate in the catalytic cycle. However, it remained unknown which, if any, of the residues in the HX₁₁CCX₂C(83) motif bind the divalent metal ion. To address this issue, we have characterized Co(II)-substituted wild-type EutT (EutT^WT/Co) by using electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism (MCD) spectroscopies. Our results indicate that the reduced catalytic activity of EutT^WT/Co relative to that of the Fe(II)-containing enzyme arises from the incomplete incorporation of Co(II) ions and, thus, a decrease in the relative population of 4c Co(II)Cbl. Our MCD data for EutT^WT/Co also reveal that the Co(II) ions reside in a distorted tetrahedral coordination environment with direct cysteine sulfur ligation. Additional spectroscopic studies of EutT/Co variants possessing a single alanine substitution of either His67, His75, Cys79, Cys80, or Cys83 indicate that Cys80 coordinates to the Co(II) ion, while the additional residues are important for maintaining the structural integrity and/or high affinity of the metal binding site.

A role for hydrogen bonding in DNA recognition by the non-classical CCHHC type zinc finger, NZF-1

The non-classical zinc finger protein, Neural Zinc Finger Factor-1, contains six Cys2His2Cys domains. All three cysteines and the second histidine directly bind Zn(II). Using a combination of mutagenesis, metal coordination and DNA binding studies, we report that the first histidine is involved in a functionally important hydrogen bonding interaction.

Multireference ab initio studies of zero-field splitting and magnetic circular dichroism spectra of tetrahedral Co(II) complexes

A newly developed multireference (MR) ab initio method for the calculation of magnetic circular dichroism (MCD) spectra was calibrated through the calculation of the ground- and excited state properties of seven high-spin (S = 3/2) Co(II) complexes. The MCD spectra were computed by the explicit treatment of spin-orbit coupled (SOC) and spin-spin coupled (SSC) N-electron states. For the complexes studied in this work, we found that the SOC is more important than the SSC for determining the ground state zero field splitting (ZFS). Our computed ZFS parameter D for the [Co(PPh(3))(2)Cl(2)] model complex is -17.6 cm(-1), which is reasonably close to the experimental value of -14.8 cm(-1). Generally, the computed absorption and MCD spectra are in fair agreement with experiment for all investigated complexes. Thus, reliable electronic structure and spectroscopic predictions for medium sized transition metal complexes are feasible on the basis of this methodology. This characterizes the presented method as a promising tool for MCD spectra interpretations of transition metal complexes in a variety of areas of chemistry and biology.

Syntheses and kinetic evaluation of racemic and optically active 2-benzyl-2-methyl-3,4-epoxybutanoic acids as irreversible inactivators for carboxypeptidase A

Racemic and optically active 2-benzyl-2-methyl-3,4-epoxybutanoic acids were synthesized and evaluated as inactivators for carboxypeptidase A, a representative zinc-containing proteolytic enzyme. Only the threo-form of the inactivator is effective and its potency in terms of k(inact)/K(I) value is lower by 42-fold compared with 2-benzyl-3,4-epoxybutanoic acid, indicating that the alpha-methyl group affects adversely in the inactivation contrary to the expectation that it would enhance the inactivation activity of the inhibitor through additional interactions of the methyl group with a small cavity (alpha-methyl hole) present next to the S1' hydrophobic pocket. Of the enantiomeric pair, the inactivator having the (2S,3R)-configuration is more potent than its enantiomer by 44-fold. The observed kinetic results may be rationalized on the basis that the methyl group in the inactivator having the (2R,3S)-configuration experiences the van der Waals repulsive interactions with the bottom of the active site crevice in binding to CPA, casting a doubt on the presence of the so-called alpha-methyl hole at the active site of carboxypeptidase A.

A novel strategy for designing irreversible inhibitors of metalloproteases: acetals as latent electrophiles that interact with catalytic nucleophile at the active site

A new strategy for design of irreversible inactivators for carboxypeptidase A (CPA), a prototypic zinc protease, has been developed by exploiting the property of acetals to generate an oxacarbenium ion intermediate in the conversion into the corresponding carbonyl compounds. The design strategy is exemplified by 2-benzyl-5-alkyl-3,5-dioxapentanoic acids (1a-c). Interestingly, (R)-1b is slightly more potent than an (S)-1b as an inactivator of CPA.

Hippuryl-alpha-methylphenylalanine and hippuryl-alpha-methylphenyllactic acid as substrates for carboxypeptidase A. Syntheses, kinetic evaluation and mechanistic implication

(R)- and (S)-Hippuryl-alpha-methylphenylalanine [(R)- and (S)-Hipp-alpha-MePhe] and (S)-hippuryl-alpha-methylphenyllactic acid [(S)-Hipp-alpha-MeOPhe] were synthesized and evaluated as substrates for carboxypeptidase A (CPA) in an effort to shed further light on the catalytic mechanism of the enzyme. The rate of CPA-catalyzed hydrolysis of (S)-Hipp-alpha-MePhe was reduced by 105-fold compared with that of (S)-Hipp-Phe, but the hydrolysis rate of (S)-Hipp-OPhe was lowered by only 6.8-fold by the introduction of a methyl group at the alpha-position. (R)-Hipp-alpha-MePhe failed to be hydrolyzed initially, then started to undergo hydrolysis in about 2 h at a much reduced rate. The results of present study may be envisioned on the basis of the proposition that while peptide substrate is hydrolyzed via a tetrahedral transition state formed by the attack of the zinc-bound water molecule at the peptide carbonyl carbon, ester hydrolysis takes the path that involves an anhydride intermediate generated by the attack of the carboxylate of Glu-270 at the ester carbonyl carbon.

Detection of an anhydride intermediate in the carboxypeptidase A catalyzed hydrolysis of a peptide substrate by solid state NMR spectroscopy and its mechanistic implication

We have detected an anhydride intermediate in the CPA catalyzed proteolytic reaction of Gly-Tyr. It appears that since the zinc-bound water molecule which is believed to attack the scissile amide carbonyl carbon in the hydrolysis reaction is excluded by the N-terminal amino group of Gly-Tyr, the carboxylate of Glu-270 becomes to attack the amide bond to generate the anhydride intermediate.

Zn2+ regulation of ornithine transcarbamoylase. II. Metal binding site

Two types of conformational changes are mediated in Escherichia coli ornithine transcarbamoylase by the metal ion zinc. Upon binding of zinc in rapid equilibrium, the enzyme undergoes an allosteric transition. In the absence of substrates, the zinc-bound enzyme further undergoes a slow isomerization with a concomitant activity loss. Three metal ions are tightly complexed in the isomerized enzyme as determined by gel chromatography and atomic absorption spectroscopy. Since the enzyme is a trimer composed of identical subunits, one zinc ion is bound per enzyme monomer. With the application of site-directed mutagenesis, the cysteinyl residue at position 273 of the enzyme has been identified as a metal ligand. When this residue is replaced by an alanine, zinc is no longer a tight-binding inhibitor and does not promote isomerization. The alteration in the action of zinc on the mutant enzyme is attributed to a reduced metal affinity. The mutant enzyme, when saturated by the metal, displays an intrinsic allostery unchanged from that of the wild-type; an identical Hill coefficient of 1.5 is found for zinc binding to the Ala273 and wild-type enzymes. Cys273 is also a binding site of L-ornithine. At pH 8.5, the Ala273 enzyme binds the substrate analog L-norvaline ten times more weakly and exhibits a kcat/Kmorn that is 27 times less than that of the wild-type enzyme. This finding supports our earlier interpretation that the zinc-induced ornithine co-operativity of ornithine transcarbamoylase is caused by direct competition between L-ornithine and the metal for the same site. As controls, each of the remaining three cysteinyl residues of the bacterial ornithine transcarbamoylase has also been replaced with alanine. These sulfhydryl groups are found not to be related to zinc complexation, ornithine binding or enzyme allostery.

How do enzymes work?

The principle of transition-state stabilization asserts that the occurrence of enzymic catalysis is equivalent to saying that an enzyme binds the transition state much more strongly than it binds the ground-state reactants. An outline of the origin and gradual acceptance of this idea is presented, and elementary transition-state theory is reviewed. It is pointed out that a misconception about the theory has led to oversimplification of the accepted expression relating catalysis and binding, and an amended expression is given. Some implications of the transition-state binding principle are then explored. The amended expression suggests that internal molecular dynamics may also play a role in enzymic catalysis. Although such effects probably do not make a major contribution, their magnitude is completely unknown. Two examples of recent advances due to application of the transition-state binding principle are reviewed, one pertaining to the zinc protease mechanism and the other to the generation of catalytic antibodies.