Anionic charge is prioritized over geometry in aluminum and magnesium fluoride transition state analogs of phosphoryl transfer enzymes

Phosphoryl transfer reactions are ubiquitous in biology and metal fluoride complexes have played a central role in structural approaches to understanding how they are catalyzed. In particular, numerous structures of AlFx-containing complexes have been reported to be transition state analogs (TSAs). A survey of nucleotide kinases has proposed a correlation between the pH of the crystallization solution and the number of coordinated fluorides in the resulting aluminum fluoride TSA complexes formed. Enzyme ligands crystallized above pH 7.0 were attributed to AlF3, whereas those crystallized at or below pH 7.0 were assigned as AlF4-. We use 19F NMR to show that for beta-phosphoglucomutase from Lactococcus lactis, the pH-switch in fluoride coordination does not derive from an AlF4- moiety converting into AlF3. Instead, AlF4- is progressively replaced by MgF3- as the pH increases. Hence, the enzyme prioritizes anionic charge at the expense of preferred native trigonal geometry over a very broad range of pH. We demonstrate similar behavior for two phosphate transfer enzymes that represent typical biological phosphate transfer catalysts: an amino acid phosphatase, phosphoserine phosphatase from Methanococcus jannaschii and a nucleotide kinase, phosphoglycerate kinase from Geobacillus stearothermophilus. Finally, we establish that at near-physiological ratios of aluminum to magnesium, aluminum can dominate over magnesium in the enzyme-metal fluoride inhibitory TSA complexes, and hence is the more likely origin of some of the physiological effects of fluoride.     

Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR and molecular mechanics on a model peptide prepared as silk I and II

The influence of the bulky and H-bonding Tyr side-chain on its Ala- and Gly-rich environment in Bombyx mori silk fibroin was examined by (13)C cross-polarization magic angle spinning (CP/MAS), static (2)H and (19)F NMR and molecular mechanics calculations. Model peptides of the type (AG)(15) were synthesized with Tyr in a number of different positions, precipitated under conditions favoring either of the two characteristic protein conformations, and the resulting structures were assigned from their (13)C chemical shifts. Dialysis of native fibroin or the simple (AG)(15) peptide from a 9 M LiBr solution against water produces silk I (the structure of silk before spinning), whereas drying from formic acid yields silk II (fibrous structure after spinning). We found that the introduction one or more Tyr into (AG)(15) can have a dramatic effect not only on the local backbone conformation but also on the long-range intermolecular chain packing in the samples. The antiparallel beta-sheet conformation of silk II is able readily to accommodate a single Tyr residue. Interestingly, the beta-turn conformation of silk I only remains stable when Tyr is positioned near the chain terminus in (AG)(12)YG(AG)(2), but the conformation is driven towards silk II when Tyr is located in the central region of (AG)(7)YG(AG)(7). The role of H-bonding was tested by replacing Tyr with Phe or 4F-Phe, which are no longer compatible with silk I and fully induced a silk II conformation. In the presence of several Tyr residues a mixture of distorted beta-sheet and beta-turn conformations was obtained, regardless of the precipitation conditions. Static (2)H NMR of ring-deuterated [3',5'-(2)H(2)]Tyr located in the central region of (AG)(7)YG(AG)(7) showed that the side-chain is immobilized in both silk I and II, which was also observed by static (19)F NMR of the 4F-Phe analogue. To visualize the local packing around the Tyr side-chain, molecular mechanics calculations were performed on a mixture of (AG)(4) and AGAGYGAG, starting from either the beta-turn type II or the antiparallel beta-sheet structure. The resulting structures show that the intermolecular chain arrangement is significantly affected by Tyr, thus explaining the long-range packing effects in the semi-crystalline regions of silk fibers compared with the crystalline regions that are devoid of Tyr.     

Spectroscopic and thermal investigations of the fluoroaluminate complex formation in NaF-KF and LiF-NaF-KF eutectics

The dissolution and complex formation of fluoroaluminates in two eutectic alkalifluoride mixtures, NaF-KF (FNAK) and LiF-NaF-KF (FLINAK), have been investigated by Raman, NMR, and thermal analysis. Melting and dissolution took place stepwise. The eutectic alkalifluoride mixtures with minor amounts of dissolved fluoroaluminate salts started melting at around 460 and 740 degrees C for FLINAK and FNAK mixtures, respectively. Total melting/dissolution of mixtures with 9-11 mol % aluminum fluoro salts added took place near 780 degrees C in the FLINAK solvent and at approximately 900 degrees C for FNAK solutions. The solidified melts were characterized by Raman bands at 561 (nu(1)), 391 (nu(2)), and 328 cm(-1) (nu(5)) and a (27)Al NMR chemical shift near 0 ppm originating from isolated AlF(6)(3-) octahedral ions. The Raman and NMR signals due to AlF(6)(3-) were also observed at temperatures where the samples were only partly melted. Upon total melting, a pronounced dissociation of AlF(6)(3-) into AlF(5)(2-) and fluoride ions took place. At even higher temperatures, the equilibrium was displaced in favor of AlF(5)(2-) in the FNAK solvent. The AlF(5)(2-) ion was characterized by an intensive Raman band at 558 cm(-1) and an increasingly positive (27)Al chemical shift with raising temperature, e.g., of 16 ppm at 935 degrees C.     

Proof of innocence for the quintessential noninnocent ligand TCNQ in its tetranuclear complex with four [fac-Re(CO)3(bpy)]+ groups: unusually different reactivity of the TCNX ligands (TCNX = TCNE, TCNQ, TCNB)

The reactions of [fac-Re(CO)(3)(bpy)(MeOH)](PF(6)), bpy = 2.2'-bipyridine, with the TCNX ligands (TCNE = tetracyanoethene, TCNQ = 7,7,8,8-tetracyano-p-quinodimethane, and TCNB = 1,2,4,5-tetracyanobenzene) in CH(2)Cl(2) gave very different results. No reaction was observed with TCNB whereas TCNE produced very labile intermediates which converted under mild conditions to structurally characterized [(mu-CN)[fac-Re(CO)(3)(bpy)](2)](PF(6)) with an eclipsed conformation relative to the almost linear Re-CN-Re axis (Re-N(NC) 2.134(8) A, Re-C(CN) 2.098(8) A). With TCNQ, a stable tetranuclear complex [(mu(4)-TCNQ)[Re(CO)(3)(bpy)](4)](BF(4))(4) was obtained. Its structural, electrochemical, and spectroscopic analysis indicates only negligible charge transfer from the rhenium(I) centers to the extremely strong pi acceptor TCNQ. Evidence includes a calculated charge of only -0.09 for coordinated TCNQ according to the empirical structure/charge correlation of Kistenmacher, a high-energy nitrile stretching band nu(CN) = 2235 cm(-1), and unprecedented large anodic shifts >0.7 V of the reduction potentials. DFT calculations were used to confirm and explain the absence of electron delocalization from the electron-rich metals to the TCNQ acceptor bridge. Correspondingly, the X-band and high-frequency (285 GHz) EPR data (g = 2.007) as well as the IR and UV-vis-NIR spectroelectrochemical results (marginal nu(CO) shifts, TCNQ(*-) chromophore bands) support the almost exclusive confinement of the added electron in [(mu(4)-TCNQ)[Re(CO)(3)(bpy)](4)](3+) to the TCNQ bridge.     

Structure and Thermodynamics of NaF-AlF(3) Melts with Addition of CaF(2) and MgF(2)

The NaF-AlF(3) system with additions of CaF(2) and MgF(2) has been studied with Raman and vapor pressure measurements for 3 >/= CR (NaF/AlF(3) molar ratio) >/= 1 and up to 50 mol % additive. The results show that the binary melt can be described using the two equilibria AlF(6)(3)(-) = AlF(6)(2)(-) + F(-) and AlF(5)(2)(-) = AlF(4)(-) + F(-) with equilibrium constants 0.25 and 0.05, respectively, at 1293 K. Both reactions have positive reaction enthalpies. The first equilibrium is strongly shifted to the right resulting in a melt mixture with very low AlF(6)(3)(-) concentrations even at the Na(3)AlF(6) composition. Evidence for nonideal mixing of anions was found. For the ternaries, models based on Raman data are presented and compared with vapor pressure measurements. Good agreement is observed when association between the additives, CaF(2) or MgF(2), with the AlF(5)(2)(-) ions in the melt was considered. This association could be experimentally observed through a band broadening and a slight shift in the AlF(5)(2)(-) band frequency. Our vapor pressures and Raman data both indicate that MgF(2) clearly acts as an acid when added to NaF-AlF(3) melts of any composition. When CaF(2) is added, a slight decrease of vapor pressure occurs. Raman data indicate a decrease of AlF(4)(-) concentration, corresponding to a dissociation of CaF(2) with liberation of F(-) ions. All these results are, however, very much dependent on the initial melt composition. These data are explained in terms of acid-base, dilution, and association reactions of the solute with the solvent.     

Efficient light-driven carbon-free cobalt-based molecular catalyst for water oxidation

The abundant-metal-based polyoxometalate complex [Co(4)(H(2)O)(2)(PW(9)O(34))(2)](10-) is a hydrolytically and oxidatively stable, homogeneous, and efficient molecular catalyst for the visible-light-driven catalytic oxidation of water. Using a sacrificial electron acceptor and photosensitizer, it exhibits a high (30%) photon-to-O(2) yield and a large turnover number (>220, limited solely by depletion of the sacrificial electron acceptor) at pH 8. The photocatalytic performance of this catalyst is superior to that of the previously reported precious-metal-based polyoxometalate water oxidation catalyst [{Ru(4)O(4)(OH)(2)(H(2)O)(4)}(γ-SiW(10)O(36))(2)](10-).     

Amino acid selective cross-saturation method for identification of proximal residue pairs in a protein-protein complex

We describe an NMR-based approach, the amino acid selective cross-saturation (ASCS) method, to identify the pairs of the interface residues of protein-protein complexes. ASCS uses a "cross-saturation (CS)-donor" protein, in which only one amino acid is selectively (1)H-labeled in a (2)H-background, and a "CS-acceptor" protein with uniform (2)H, (15)N labeling. Irradiation of the (1)H-labeled amino acid, which exists only in the donor, decreases the intensity of the (1)H- (15)N HSQC signals of the acceptor residues proximal to the (1)H-labeled CS-source residue(s) through the CS phenomenon. Given the three-dimensional structure of each protein in the complex, but not the complex structure, the combinatorial analysis of multiple ASCS results specify the CS-source residue(s), based on the spatial complementarity between the CS-source residues on the CS donor and the cross-saturated amide protons on the acceptor. NMR investigations of the labeling selectivity and efficiency in an E. coli host, which are critical for ASCS, revealed that Ala, Arg, His, Ile, Leu, Lys, Met, Phe, Pro, Trp, and Tyr are selectively labeled with a high (1)H/(2)H ratio. The observation of the ASCS was then confirmed using the known structure of the yeast ubiquitin (Ub) and yeast ubiquitin hydrolase 1 (YUH1). Conversely, reasonable candidates for the CS-source residues were suggested by the analysis of the ASCS results, with reference to the individual structures of YUH1 and Ub. The pairwise distance information between the CS-source residues and the cross-saturated amide groups obtained by ASCS will be useful for modeling protein-protein complexes.     

Inhibitor scaffolds as new allele specific kinase substrates

The elucidation of protein kinase signaling networks is challenging due to the large size of the protein kinase superfamily (>500 human kinases). Here we describe a new class of orthogonal triphosphate substrate analogues for the direct labeling of analogue-specific kinase protein targets. These analogues were constructed as derivatives of the Src family kinase inhibitor PP1 and were designed based on the crystal structures of PP1 bound to HCK and N(6)-(benzyl)-ADP bound to c-Src (T338G). 3-Benzylpyrazolopyrimidine triphosphate (3-benzyl-PPTP) proved to be a substrate for a mutant of the MAP kinase p38 (p38-T106G/A157L/L167A). 3-Benzyl-PPTP was preferred by v-Src (T338G) (k(cat)/K(M) = 3.2 x 10(6) min(-)(1) M(-)(1)) over ATP or the previously described ATP analogue, N(6) (benzyl) ATP. For the kinase CDK2 (F80G)/cyclin E, 3-benzyl-PPTP demonstrated catalytic efficiency (k(cat)/K(M) = 2.6 x 10(4) min(-)(1) M(-)(1)) comparable to ATP (k(cat)/K(M) = 5.0 x 10(4) min(-)(1) M(-)(1)) largely due to a significantly better K(M) (6.4 microM vs 530 microM). In kinase protein substrate labeling experiments both 3-benzyl-PPTP and 3-phenyl-PPTP prove to be over 4 times more orthogonal than N(6)-(benzyl)-ATP with respect to the wild-type kinases found in murine spleenocyte cell lysates. These experiments also demonstrate that [gamma-(32)P]-3-benzyl-PPTP is an excellent phosphodonor for labeling the direct protein substrates of CDK2 (F80G)/E in murine spleenocyte cell lysates, even while competing with cellular levels (4 mM) of unlabeled ATP. The fact that this new more highly orthogonal nucleotide is accepted by three widely divergent kinases studied here suggests that it is likely to be generalizable across the entire kinase superfamily.     

Electron transfer through a prenucleated bimetalated alanine-based peptide helix

We have synthesized a 22 residue alanine-based peptide with a tris(bipyridyl)ruthenium(II) amino acid near the middle of the peptide which can act as a photoinducible electron donor. Two histidines spaced i, i + 4 near the C-terminus of the peptide were then cross-linked with a tetraammineruthenium(III) moiety to prenucleate the helix and provide an electron acceptor site. Introduction of the cross-link enhances the average helix content from 67% to 84% at 0 degrees C, as judged by circular dichroism spectroscopy. The temperature dependence of the mean molar residue ellipticity at 222 nm, [THETAV;](222), for the bimetalated peptide was fit to a modified Lifson-Roig helix-coil model to permit extraction of the population of helical conformation at each residue separating the electron donor and acceptor. On average, the residues between the donor and acceptor are 92% helical. Photoinduced electron transfer with a driving force of -1.0 eV and an estimated reorganization energy of 0.82 eV was measured by fluorescence quenching methods in H(2)O and D(2)O, yielding rate constants, k(ET), of 7 +/- 3 x 10(6) s(-)(1) and 5 +/- 1 x 10(6) s(-)(1) at 0 degrees C. Calculation of the electronic coupling matrix element, H(ab), with the Marcus equation yields a value of 0.19 +/- 0.4 cm(-)(1). Analysis in terms of the pathway model for electronic coupling indicates that this magnitude of H(ab) is consistent with the participation of hydrogen bonds in electronic coupling for an isolated alpha-helix.     

The chemoselective reactions of tyrosine-containing G-protein-coupled receptor peptides with [Cp*Rh(H2O)3](OTf)2, including 2D NMR structures and the biological consequences

The bioconjugation of organometallic complexes with peptides has proven to be a novel approach for drug discovery. We report the facile and chemoselective reaction of tyrosine-containing G-protein-coupled receptor (GPCR) peptides with [Cp*Rh(H(2)O)(3)](OTf)(2), in water, at room temperature, and at pH 5-6. We have focused on three important GPCR peptides; namely, [Tyr(1)]-leu-enkephalin, [Tyr(4)]-neurotensin(8-13), and [Tyr(3)]-octreotide, each of which has a different position for the tyrosine residue, together with competing functionalities. Importantly, all other functional groups present, i.e., amino, carboxyl, disulfide, phenyl, and indole, were not prominent sites of reactivity by the Cp*Rh tris aqua complex. Furthermore, the influence of the Cp*Rh moiety on the structure of [Tyr(3)]-octreotide was characterized by 2D NMR, resulting in the first representative structure of an organometallic-peptide complex. The biological consequences of these Cp*Rh-peptide complexes, with respect to GPCR binding and growth inhibition of MCF7 and HT29 cancer cells, will be presented for [(η(6)-Cp*Rh-Tyr(1))-leu-enkephalin](OTf)(2) and [(η(6)-Cp*Rh-Tyr(3))-octreotide](OTf)(2).     

A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): role of the active site cysteine-6 residue in the oxidative half-reaction

In the present DFT study, the catalytic mechanism of H2O2 formation in the oxidative half-reaction of NiSOD, E-Ni(II) + O2- + 2H+ --> E-Ni(III) + H2O2, has been investigated. The main objective of this study is to investigate the source of two protons required in this half-reaction. The proposed mechanism consists of two steps: superoxide coordination and H2O2 formation. The effect of protonation of Cys6 and the proton donating roles of side chains (S) and backbones (B) of His1, Asp3, Cys6, and Tyr9 residues in these two steps have been studied in detail. For protonated Cys6, superoxide binding generates a Ni(III)-O2H species in a process that is exothermic by 17.4 kcal/mol (in protein environment using the continuum model). From the Ni(III)-O2H species, H2O2 formation occurs through a proton donation by His1 via Tyr9, which relative to the resting position of the enzyme is exothermic by 4.9 kcal/mol. In this pathway, a proton donating role of His1 residue is proposed. However, for unprotonated Cys6, a Ni(II)-O2- species is generated in a process that is exothermic by 11.3 kcal/mol. From the Ni(II)-O2- species, the only feasible pathway for H2O2 formation is through donation of protons by the Tyr9(S)-Asp3(S) pair. The results discussed in this study elucidate the role of the active site residues in the catalytic cycle and provide intricate details of the complex functioning of this enzyme.     

New synthetic and structural aspects in the chemistry of alkylaluminum fluorides. The mutual influence of hard and soft ligands and the hybridization as rigorous structural criterion

A general synthetic strategy starting from metal alkyls is reported based on the hydrogen difluoride anion as a suitable reagent for obtaining organometallic fluorides. The newly prepared compounds are [Me(4)N][(i-Bu)(2)AlF(2)] (1), [Ph(4)P][(i-Bu)(2)AlF(2)] (2), and [Ph(4)P][AlF(4)] (3), containing the tetrahedral anions [(i-Bu)(2)AlF(2)](-) and [AlF(4)](-). The actual structures are prototypes that allowed a comparison of inorganic and organometallic fluorides in the frame of the hard and soft acid and base principle, by means of ab initio calculations. A new theoretical model is designed to put in equation form the qualitative statements of the Bent rule. The model allows the rationalization of the tendencies of bond angle variation in [R(2)MX(2)] systems containing a main group metal (M), in terms of hybridization of the central atom and the reciprocal influence of hard and soft ligands.     

A peptide dendrimer enzyme model with a single catalytic site at the core

Catalytic esterase peptide dendrimers with a core active site were discovered by functional screening of a 65,536-member combinatorial library of third-generation peptide dendrimers using fluorogenic 1-acyloxypyrene-3,6,8-trisulfonates as substrates. In the best catalyst, RMG3, ((AcTyrThr)(8)(DapTrpGly)(4)(DapArgSerGly)(2)DapHisSerNH2), ester hydrolysis is catalyzed by a single catalytic histidine residue at the dendrimer core. A pair of arginine residues in the first-generation branch assists substrate binding. The catalytic proficiency of dendrimer RMG3 (kcat/KM = 860 M(-1) min(-1) at pH 6.9) per catalytic site is comparable to that of the multivalent esterase dendrimer A3 ((AcHisSer)(8)(DapHisSer)(4)(DapHisSer)2DapHisSerNH2) which has fifteen histidines and five catalytic sites (Delort, E. et al. J. Am. Chem. Soc. 2004, 126, 15642-15643). Remarkably, catalysis in the single site dendrimer RMG3 is enhanced by the outer dendritic branches consisting of aromatic amino acids. These interactions take place in a relatively compact conformation similar to a molten globule protein as demonstrated by diffusion NMR. In another dendrimer, HG3 ((AcIlePro)(8)(DapIleThr)(4)(DapHisAla)(2)DapHisLeuNH2) by contrast, catalysis by a core of three histidine residues is unaffected by the outer dendritic layers. Dendrimer HG3 or its core HG1 exhibit comparable activity to the first-generation dendrimer A1 ((AcHisSer)(2)DapHisSerNH2). The compactness of dendrimer HG3 in solution is close to that a denatured peptide. These experiments document the first esterase peptide dendrimer enzyme models with a single catalytic site and suggest a possible relationship between packing and catalysis in these systems.     

The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains.

Cation-pi interactions between amino acid side chains are increasingly being recognized as important structural and functional features of proteins and other biomolecules. Although these interactions have been found in static protein structures, they have not yet been detected in dynamic biomolecular systems. We determined, by (1)H NMR spectroscopic titrations, the energies of cation-pi interactions of the amino acid derivative AcLysOMe (1) with AcPheOEt (2) and with AcTyrOEt (3) in aqueous and three organic solvents. The interaction energy is substantial; it ranges from -2.1 to -3.4 kcal/mol and depends only slightly on the dielectric constant of the solvent. To assess the effects of auxiliary interactions and structural preorganization on formation of cation-pi interactions, we studied these interactions in the association of pentapeptides. Upon binding of the positively-charged peptide AcLysLysLysLysLysNH(2) (5) to the negatively-charged partner AcAspAspXAspAspNH(2) (6), in which X is Leu (6a), Tyr (6b), and Phe (6c), multiple interactions occur. Association of the two pentapeptides is dynamic. Free peptides and their complex are in fast exchange on the NMR time-scale, and 2D (1)H ROESY spectra of the complex of the two pentapeptides do not show intermolecular ROESY peaks. Perturbations of the chemical shifts indicated that the aromatic groups in peptides 6b and 6c were affected by the association with 5. The association constants K(A) for 5 with 6a and with 6b are nearly equal, (4.0 +/- 0.7) x 10(3) and (5.0 +/- 1.0) x 10(3) M(-)(1), respectively, while K(A) for 5 with 6c is larger, (8.3 +/- 1.3) x 10(3) M(-)(1). Molecular-dynamics (MD) simulations of the pentapeptide pairs confirmed that their association is dynamic and showed that cation-pi contacts between the two peptides are stereochemically possible. A transient complex between 5 and 6 with a prominent cation-pi interaction, obtained from MD simulations, was used as a template to design cyclic peptides C(X) featuring persistent cation-pi interactions. The cyclic peptide C(X) had a sequence in which X is Tyr, Phe, and Leu. The first two peptides do, but the third does not, contain the aromatic residue capable of interacting with a cationic Lys residue. This covalent construct offered conformational stability over the noncovalent complexes and allowed thorough studies by 2D NMR spectroscopy. Multiple conformations of the cyclic peptides C(Tyr) and C(Phe) are in slow exchange on the NMR time-scale. In one of these conformations, cation-pi interaction between Lys3 and Tyr9/Phe9 is clearly evident. Multiple NOEs between the side chains of residues 3 and 9 are observed; chemical-shift changes are consistent with the placement of the side chain of Lys3 over the aromatic ring. In contrast, the cyclic peptide C(Leu) showed no evidence for close approach of the side chains of Lys3 and Leu9. The cation-pi interaction persists in both DMSO and aqueous solvents. When the disulfide bond in the cyclic peptide C(Phe) was removed, the cation-pi interaction in the acyclic peptide AC(Phe) remained. To test the reliability of the pK(a) criterion for the existence of cation-pi interactions, we determined residue-specific pK(a) values of all four Lys side chains in all three cyclic peptides C(X). While NOE cross-peaks and perturbations of the chemical shifts clearly show the existence of the cation-pi interaction, pK(a) values of Lys3 in C(Tyr) and in C(Phe) differ only marginally from those values of other lysines in these dynamic peptides. Our experimental results with dynamic peptide systems highlight the role of cation-pi interactions in both intermolecular recognition at the protein-protein interface and intramolecular processes such as protein folding.     

MgF(3)(-) as a transition state analog of phosphoryl transfer

The formation of complexes between small G proteins and certain of their effectors can be facilitated by aluminum fluorides. Solution studies suggest that magnesium may be able to replace aluminum in such complexes. We have determined the crystal structure of RhoA.GDP bound to RhoGAP in the presence of Mg(2+) and F(-) but without Al(3+). The metallofluoride adopts a trigonal planar arrangement instead of the square planar structure of AlF(4)(-). We have confirmed that these crystals contain magnesium and not aluminum by proton-induced X-ray emission spectroscopy. The structure adopted by GDP.MgF(-) possesses the stereochemistry and approximate charge expected for the transition state. We suggest that MgF3(-) may be the reagent of choice for studying phosphoryl transfer reactions.     

Nickel(III) oxidation of its glycylglycylhistamine complex

The doubly-deprotonated Ni(III) complex of Gly(2)Ha (where Ha is histamine) undergoes base-assisted oxidative self-decomposition of the peptide. At 相似文献   

Insight into the structural characteristics of core-links and flat-aluminum tridecamers: a density functional theory study

The structures of core-links Al(13) (C-Al(13)) and flat-Al(13) (F-Al(13)) complexes in aqueous solution have been investigated using density functional theory (DFT) at the level of B3LYP/6-31G(d). The present work focuses on the following three aspects: (1) C-Al(13)(9+) was optimized with the consideration of solvent effect and the (27)Al NMR chemical shifts using Hartree Fock GIAO and B3LYP GIAO methods were computed respectively; (2) the optimization of F-Al(13)(15+) was also performed and the (27)Al NMR chemical shifts were obtained using the same methods as above; (3) the structural parameters of a series of typical aluminum species (Al(3+), AlOH(2+), AlF(2+), Al(2)(4+), Al(6)(6+), K-Al(13)(7+), C-Al(13)(9+) and F-Al(13)(15+)) were compared.     

1H NMR study of the magnetic properties and electronic structure of the hydroxide complex of substrate-bound heme oxygenase from Neisseria meningitidis: influence of the axial water deprotonation on the distal H-bond network

The substrate and active site residues of the low-spin hydroxide complex of the protohemin complex of Neisseria meningitidis heme oxygenase (NmHO) have been assigned by saturation transfer between the hydroxide and previously characterized aquo complex. The available dipolar shifts allowed the quantitation of both the orientation and anisotropy of the paramagnetic susceptibility tensor. The resulting positive sign, and reduced magnitude of the axial anisotropy relative to the cyanide complex, dictate that the orbital ground state is the conventional "d(pi)" (d(2)(xy)(d(xz), d(yz))(3)); and not the unusual "d(xy)" (d(2)(xz)d(2)(yz)d(xy)) orbital ground state reported for the hydroxide complex of the homologous heme oxygenase (HO) from Pseudomonas aeruginosa (Caignan, G.; Deshmukh, R.; Zeng, Y.; Wilks, A.; Bunce, R. A.; Rivera, M. J. Am. Chem. Soc. 2003, 125, 11842-11852) and proposed as a signature of the HO distal cavity. The conservation of slow labile proton exchange with solvent from pH 7.0 to 10.8 confirms the extraordinary dynamic stability of NmHO complexes. Comparison of the diamagnetic contribution to the labile proton chemical shifts in the aquo and hydroxide complexes reveals strongly conserved bond strengths in the distal H-bond network, with the exception of the distal His53 N(epsilon)(1)H. The iron-ligated water is linked to His53 primarily by a pair of nonligated, ordered water molecules that transmit the conversion of the ligated H-bond donor (H(2)O) to a H-bond acceptor (OH(-)), thereby increasing the H-bond donor strength of the His53 side chain.     

Artificial metalloprotease with active site comprising aldehyde group and Cu(II)cyclen complex

To design artificial proteases that cleave peptide backbones of a wide range of proteins at selected sites, artificial active sites comprising the Cu(II) complex of cyclen (Cu(II)Cyc) and aldehyde group were synthesized on a cross-linked polystyrene. The aldehyde group was employed as the binding site in view of its ability of reversible formation of imine bonds with epsilon-amino groups of Lys residues exposed on the surface of proteins and Cu(II)Cyc as the catalytic group for peptide hydrolysis. The two polymeric artificial metalloproteases synthesized in the present study cleaved all of the protein substrates examined (myoglobin, gamma-globulin, bovine serum albumin, human serum albumin, lysozyme, and ovalbumin), manifesting saturation kinetic behavior. At 50 degrees C and pH 9.0 or 9.5, K(m) was (1.3-22) x 10(-)(4) M, comparable to those of natural proteases, and k(cat) was (6.0-25) x 10(-)(4) s(-)(1), corresponding to half-lives of 4.6-19 min. Intermediacy of the imine complexes formed between the aldehyde group of the catalyst and the epsilon-amino groups of Lys residues of the substrates was confirmed by the trapping experiment with NaB(OAc)(3)H. MALDI-TOF MS of the proteolytic reaction mixtures revealed formation of various cleavage products. Structures of some of the cleavage products were determined by using carboxypeptidase A and trypsin. Among various cleavage sites thus identified, Gln(91)-Ser(92) and Ala(94)-Thr(95) were the major initial cleavage sites in the degradation of myoglobin by the two catalysts. The selective cleavage of Gln(91)-Ser(92) and Ala(94)-Thr(95) was attributed to general acid assistance in peptide cleavage by Tyr(146) located in proximity to the two peptide bonds. Broad substrate selectivity, high cleavage-site selectivity, and high proteolytic rate are achieved, therefore, by positioning the aldehyde group in proximity to Cu(II)Cyc attached to a cross-linked polystyrene.     

Effect of the N-terminal basic residue on facile Cα-C bond cleavages of aromatic-containing peptide radical cations

Fragmentation of radical cationic peptides [R(G)(n-2)X(G)(7-n)]˙(+) and [R(G)(m-2)XG]˙(+) (X = Phe or Tyr; m = 2-5; n = 2-7) leads selectively to a(n)(+) product ions through in situ C(α)-C peptide backbone cleavage at the aromatic amino acid residues. In contrast, substituting the arginine residue with a less-basic lysine residue, forming [K(G)(n-2)X(G)(7-n)]˙(+) (X = Phe or Tyr; n = 2-7) analogs, generates abundant b-y product ions; no site-selective C(α)-C peptide bond cleavage was observed. Studying the prototypical radical cationic tripeptides [RFG]˙(+) and [KFG]˙(+) using low-energy collision-induced dissociation and density functional theory, we have examined the influence of the basicity of the N-terminal amino acid residue on the competition between the isomerization and dissociation channels, particularly the selective C(α)-C bond cleavage viaβ-hydrogen atom migration. The dissociation barriers for the formation of a(2)(+) ions from [RFG]˙(+) and [KFG]˙(+)via their β-radical isomers are comparable (33.1 and 35.0 kcal mol(-1), respectively); the dissociation barrier for the charge-induced formation of the [b(2)- H]˙(+) radical cation from [RFG]˙(+)via its α-radical isomer (39.8 kcal mol(-1)) was considerably higher than that from [KFG]˙(+) (27.2 kcal mol(-1)). Thus, the basic arginine residue sequesters the mobile proton to promote the charge-remote selective C(α)-C bond cleavage by energetically hindering the competing charge-induced pathways.