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PubMed2003

Noble gas-actinide complexes of the CUO molecule with multiple Ar, Kr, and Xe atoms in noble-gas matrices.

Laser-ablated U atoms react with CO in excess argon to produce CUO, which is trapped in a triplet state in solid argon at 7 K, based on agreement between observed and relativistic density functional theory (DFT) calculated isotopic frequencies ((12)C(16)O, (13)C(16)O, (12)C(18)O). This observation contrasts a recent neon matrix investigation, which trapped CUO in a linear singlet state calculated to be about 1 kcal/mol lower in energy. Experiments with krypton and xenon give results analogous to those with argon. Similar work with dilute Kr and Xe in argon finds small frequency shifts in new four-band progressions for CUO in the same triplet states trapped in solid argon and provides evidence for four distinct CUO(Ar)(4-n)(Ng)(n) (Ng = Kr, Xe, n = 1, 2, 3, 4) complexes for each Ng. DFT calculations show that successively higher Ng complexes are responsible for the observed frequency progressions. This work provides the first evidence for noble gas-actinide complexes, and the first example of neutral complexes with four noble gas atoms bonded to one metal center.

Journal Article↗

PubMed1994

11-fold symmetry of the trp RNA-binding attenuation protein (TRAP) from Bacillus subtilis determined by X-ray analysis.

The trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis has been crystallized and examined by crystallography using X-ray synchrotron radiation diffraction data. Crystals of TRAP complexed with L-tryptophan belong to space group C2 with a = 156.8 A, b = 114.05 A, c = 105.9 A, beta = 118.2 degrees. Crystals of a potential heavy-atom derivative of TRAP complexed with 5-bromo-L-tryptophan grow in the same space group with similar cell dimensions. X-ray data for the native crystals and for the derivative have been collected to 2.9 A and 2.2 A resolution, respectively. Peaks in the self-rotation function and in the Patterson synthesis could only be explained by two 11-subunit oligomers (each formed by an 11-fold axis of symmetry) in the asymmetric unit lying with the 11-fold rotation axes parallel to each other. The consequence is that the TRAP molecule has 11-fold symmetry and contains 11 subunits.

Bacillus subtilis↗

PubMed2004

A 1,3,2-oxazaborolidine dimer derived from (S)-alpha,alpha-diphenylprolinol.

The reaction of (S)-alpha,alpha-diphenylprolinol with an excess of borane-tetrahydrofuran complex yields a stable crystalline material with the composition C34H38B2N2O2, which features a borane adduct of a spirocyclic structure with two oxazaborolidine rings joined by a central tetrahedral B atom. This dimeric oxazaborolidine complex, viz. 3,3,3',3'-tetraphenyl-1,1'-spirobi(3a,4,5,6-tetrahydro-3H-pyrrolo[1,2-c][1,3,2]oxazaborole)-7-borane, is the dominant product under various reaction conditions; its crystal structure is consistent with 11B, 1H and 13C NMR and IR analyses.

Biphenyl Compounds↗

PubMed2003

Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution.

The atomic resolution structure of Leishmania mexicana triosephosphate isomerase complexed with 2-phosphoglycolate shows that this transition state analogue is bound in two conformations. Also for the side chain of the catalytic glutamate, Glu(167), two conformations are observed. In both conformations, a very short hydrogen bond exists between the carboxylate group of the ligand and the catalytic glutamate. The distance between O11 of PGA and Oepsilon2 of Glu(167) is 2.61 and 2.55 A for the major and minor conformations, respectively. In either conformation, Oepsilon1 of Glu(167) is hydrogen-bonded to a water network connecting the side chain with bulk solvent. This network also occurs in two mutually exclusive arrangements. Despite the structural disorder in the active site, the C termini of the beta strands that construct the active site display the least anisotropy compared with the rest of the protein. The loops following these beta strands display various degrees of anisotropy, with the tip of the dimer interface loop 3 having very low anisotropy and the C-terminal region of the active site loop 6 having the highest anisotropy. The pyrrolidine ring of Pro(168) at the N-terminal region of loop 6 is in a strained planar conformation to facilitate loop opening and product release.

Animals↗

PubMed2003

Unusual complex chemistry of rare-Earth elements: large ionic radii-small coordination numbers.

Because of their large ionic radii and relatively low oxidation states rare-earth elements generally form complexes which have high coordination numbers and weak metal-ligand bonds. They are often not suitable for homogeneous catalysis on account of their instability of configuration in solution. Complexes of the corresponding metal atoms with low coordination numbers may be an improvement. This type of complex can be obtained in the classical way by the introduction of bulky ligands, and recently, they were also prepared in reactions with ligand groups which offer remarkable metal-ligand bond features. This concept is demonstrated for complexes with bulky bis(trimethylsilyl)amido ligands [N(SiMe(3))(2)](-) and "slim" phosphoraneiminato ligands (NPR(3)(-)). Their suitability as catalysts for the ring-opening polymerization of lactones is reported as well.

Journal Article↗

PubMed2002

Identification and structural analysis of a zebrafish apo and holo cellular retinol-binding protein.

Cellular retinol-binding proteins (CRBPs) are cytoplasmic retinol-specific binding proteins. Mammalian CRBPs have been thoroughly characterised previously. Here we report on the identification and X-ray structural analysis of the apo (1.7A resolution) and holo (1.4A resolution) forms of a zebrafish CRBP. According to amino acid sequence and structure analyses, the zebrafish CRBP that we have identified resembles closely mammalian CRBP II, suggesting that it is the zebrafish orthologue of this mammalian CRBP type. Zebrafish CRBP forms a tight complex with all-trans retinol, producing an absorption spectrum similar to those of mammalian holo-CRBPs, albeit slightly blue-shifted. The superposition of the alpha-carbon atoms of the liganded (complexed with retinol) and unliganded forms of zebrafish CRBP shows significant differences in correspondence of the betaC-betaD (residues 55-58) and betaE-betaF (residues 74-77) turns, providing evidence for the occurrence of conformational changes accompanying retinol binding/release. Remarkable and well-defined ligand-dependent conformational changes in the protein region comprising the two beta-turns affect both the main chain and the side-chains of several residues. The two beta-turns project towards the interior of the cavity devoid of ligand of the apoprotein. The side-chains of F57, Y60 and L77 change substantially their orientation and position in the apoprotein relative to the holoprotein. In the beta-barrel internal cavity of apo-CRBP they occupy some of the space that is otherwise occupied by bound retinol in holo-CRBP, and are displaced from these positions on ligand binding. These results indicate that a flexible area encompassing the betaC-betaD and betaE-betaF turns may serve as the ligand portal and that these turns undergo conformational changes associated with the not yet clarified mechanism of retinol binding and release in CRBPs.

Amino Acid Sequence↗

PubMed2001

Structural bases for inhibitor binding and catalysis in polyamine oxidase.

Polyamine oxidase (PAO) carries out the FAD-dependent oxidation of the secondary amino groups of spermidine and spermine, a key reaction in the polyamine catabolism. The active site of PAO consists of a 30 A long U-shaped catalytic tunnel, whose innermost part is located in front of the flavin ring. To provide insight into the PAO substrate specificity and amine oxidation mechanism, we have investigated the crystal structure of maize PAO in the reduced state and in complex with three different inhibitors, guazatine, 1,8-diaminooctane, and N(1)-ethyl-N(11)-[(cycloheptyl)methyl]-4,8-diazaundecane (CHENSpm). In the reduced state, the conformation of the isoalloxazine ring and the surrounding residues is identical to that of the oxidized enzyme. Only Lys300 moves away from the flavin to compensate for the change in cofactor protonation occurring upon reduction. The structure of the PAO.inhibitor complexes reveals an exact match between the inhibitors and the PAO catalytic tunnel. Inhibitor binding does not involve any protein conformational change. Such lock-and-key binding occurs also in the complex with CHENSpm, which forms a covalent adduct with the flavin N5 atom. Comparison of the enzyme complexes hints at an "out-of-register" mechanism of inhibition, in which the inhibitor secondary amino groups are not properly aligned with respect to the flavin to allow oxidation. Except for the Glu62-Glu170 pair, no negatively charged residues are involved in the recognition of substrate and inhibitor amino groups, which is in contrast to other polyamine binding proteins. This feature may be exploited in the design of drugs specifically targeting PAO.

Binding, Competitive↗

PubMed2005

Synthesis and characterization of manganese(II) and iron(III) d5 tripodal imidazole complexes. Effect of oxidation state, protonation state and ligand conformation on coordination number and spin state.

The 1 : 3 Schiff base condensates of tris(2-aminoethyl)amine (tren) or tris(3-aminopropyl)amine (trpn) with 4-methyl-5-imidazolecarboxaldehyde, H3L1 and H3L2, respectively, were generated in situ and used to prepare complexes with manganese(II) and iron(III). The resultant complexes, [MnH3L1](ClO4)2, [MnH3L1](ClO4)2.EtOH.H2O, [MnH3L2](ClO4)2, [FeH3L1](ClO4)3.1.5(EtOH) and [FeHL1](I3) (0.525)(I)(0.475).2.625H2O, have been characterized by EA, IR, ES MS, variable temperature magnetic susceptibility, X-ray crystallography, and Mössbauer spectroscopy for the iron complexes. The three manganese(II) complexes are high spin with [MnH3L2](ClO4)2 exhibiting coordination number seven while the others are six coordinate. [FeH3L1](ClO4)3.1.5(EtOH) has two iron sites, a seven coordinate and a pseudo seven coordinate site. The complex is high spin at room temperature but exhibits a magnetic moment that decreases with temperature corresponding to conversion of one of the sites to low spin. [FeHL1](I3) (0.525)(I)(0.475).2.625H2O is low spin even at room temperature. In the present complexes the apical nitrogen atom, N(ap), of the tripodal ligand is pyramidal and directed toward the metal atom. The data show that the M-N(ap) distance decreases as the oxidation state of the metal increases, as the number of bound imidazole protons on the ligand increases, and as the number of carbon atoms in the backbone of the ligand (tren vs. trpn) increases. In a limiting sense, short M-N(ap) distances result in high spin seven coordinate mono capped octahedral complexes and long M-N(ap) distances result in low spin six coordinate octahedral complexes.

Crystallography, X-Ray↗

PubMed2006

A new twist in anion binding: metallo-helicate hosts for anionic guests.

The condensation of 5-chlorocarbonyl-2,2'-bipyridine with a variety of rigid aromatic diamines, L, gave a series of new bisamido-2,2'-bipyridine based ligands (L = 4,4'-methylenediamine, L1; L = 1,1-bis(4-aminophenyl)cyclohexane, L2; L = 1,1-bis(4-amino-3,5-dimethylphenyl)cyclohexane, L3) capable of forming dinuclear triple helicate complexes on coordination to Fe(II). The reaction of various Fe(II) salts with gave: {[Fe2(L1)3](BF4)4, 1; [Fe2(L1)3](ClO4)4, 2; [Fe2(L1)3]Cl4, 3; [Fe2(L1)3](SO4)2, 4; [Fe2(L2)3](BF4)4, 5; [Fe2(L2)3]Cl4, 6; [Fe2(L3)3](BF4)4; 7; [Fe2(L3)3]Cl4, 8; and [Fe2(L3)3](SO4)2, 9, as determined by UV-Vis, IR and 1H NMR spectroscopy, electrospray mass spectrometry (ESMS) and elemental analyses. A UV-Vis complexometric titration experiment between L3 and Fe(BF4)2 established conclusively a [Fe2(L3)3]4+ product species. 1H NMR spectroscopy showed that the complexes exist as both rac-(helical) and meso-(non-helical) isomers in DMSO-d6 solution at 298 K. L1-L3 were designed such that following complexation, six amide hydrogen atoms would line an inter-strand intrahelical cavity of sufficient size to facilitate the binding of guest species within it. Indeed, ESMS studies showed characteristic peaks typical of complex-anion species in solution. Furthermore, 1H NMR titration experiments showed that anions bind within the intrahelical cavity as titration of 1, 5 and 7 with Bu4NCl showed significant downfield shifts in the amide and bipyridyl H6 proton resonances to yield a species of 1 : 2 host to guest stoichiometry. Moreover, addition of Bu4NCl to 1, 5 and 7 shifted the rac-/meso-species distribution from 1 : 2 in favour of the meso- to 100% in favour of the rac-isomer, showing that Cl- ions favour the formation of the triple helicate species in DMSO-d6 solution.

Journal Article↗

PubMed1997

Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex.

As an extension of our recent X-ray crystallographic determination of the tertiary structure of D-amino acid oxidase (DAO) [Mizutani, H. et al. (1996) J. Biochem. 120, 14-17], we solved the crystal structure of the complex of DAO with a substrate analog, o-aminobenzoate (OAB). The alignment between flavin and OAB in the crystal structure of the complex is consistent with charge-transfer interaction through the overlap between the highest occupied molecular orbital of OAB and the lowest unoccupied molecular orbital of flavin. Starting with the atomic coordinates of this complex as the initial model, we carried out molecular mechanics simulation for the DAO-D-leucine complex and thus obtained a model for the enzyme-substrate complex. According to the enzyme-substrate complex model, the alpha-proton is pointed toward N(5) of flavin while the lone-pair of the substrate amino group can approach C(4a) of flavin within an interacting distance. This model as well as DAO-OAB complex enables the evaluation of the substrate-flavin interaction prior to electron transfer from the substrate to flavin and provides two possible mechanisms for the reductive-half reaction of DAO, i.e., the electron-proton-electron transfer mechanism and the ionic mechanism.

Amino Acid Oxidoreductases↗

PubMed2006

Influence of DNA condensation state on transfection efficiency in DNA/polymer complexes: an AFM and DLS comparative study.

Atomic force microscopy (AFM) is used to describe the formation process of polymer/DNA complexes. Two main objectives of this research are presented. The first one is to apply AFM as an effective tool to analyse DNA molecules and different polycation/DNA complexes in order to evaluate their degree of condensation (size and shape). The other one is to search for a relationship between the condensation state of DNA and its transfection efficiency. In this study, linear methacrylate based polymers and globular SuperFect polymers are used in order to induce DNA condensation. Ternary complexes, composed of methacrylate based polymers and polyethylene glycol (PEG)-based copolymers, are also investigated. AFM allows us to confirm good condensation conditions and relate them (or not) to transfection efficiencies. These AFM results (obtained after drying in air) are compared with measurements deduced from Dynamic Light Scattering (DLS) experiments performed in water. This comparison allowed us to identify the structural modifications resulting from deposition on the mica surface.

Animals↗

PubMed2003

Hydrothermal syntheses, crystal structures, and magnetic properties of inorganic-organic hybrid vanadium selenites with zero- to three-dimensional structures: (1,10-phenanthroline)(2)V(2)SeO(7), (2,2'-bipyridine)VSeO(4), (4,4'-bipyridine)V(2)Se(2)O(8), and (4,4'-bipyridine)(2)V(4)Se(3)O(15).H(2)O.

A family of inorganic-organic hybrid vanadium selenites with zero-, one-, two-, and three-dimensional structures, (1,10-phen)(2)V(2)SeO(7), (2,2'-bipy)VSeO(4), (4,4'-bipy)V(2)Se(2)O(8), and (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O (where phen = phenanthroline and bipy = bipyridine), were hydrothermally synthesized and characterized by single-crystal X-ray diffraction. Different bidentate organodiamine ligands and reactant concentrations were used in the four reaction systems, which are responsible for the variety of structural dimensions of the compounds. (1,10-phen)(2)V(2)SeO(7) crystallizes in a monoclinic system with space group P2(1)/n and cell parameters a = 8.6509(3) A,( )b = 7.8379(2) A, c = 34.0998(13) A, beta = 91.503(2) degrees, and Z = 4. (2,2'-bipy)VSeO(4) crystallizes in a monoclinic system with space group C2/c and cell parameters a = 17.0895(12) A, b = 14.7707(10) A, c = 11.7657(8) A, beta = 131.354(3) degrees, and Z = 8. (4,4'-bipy)V(2)Se(2)O(8) crystallizes in a triclinic system with space group Ponemacr; and cell parameters a = 7.1810(10) A, b = 10.8937(13) A, c = 11.1811(15) A, alpha = 115.455(3) degrees, beta = 107.582(3) degrees, gamma = 91.957(4) degrees, and Z = 2. (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O crystallizes in a monoclinic system with space group Pc and cell parameters a = 7.9889(9) A, b = 7.8448 A, c = 23.048(3) A, beta = 99.389(4) degrees, and Z = 2. (1,10-phen)(2)V(2)SeO(7) has an isolated structure, (2,2'-bipy)VSeO(4) has a chain structure, (4,4'-bipy)V(2)Se(2)O(8) has a layered structure, and (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O has a framework structure. The chains are constructed from VO(4)N(2) octahedra and SeO(3) pyramids, laced by organic ligands (2,2'-bipy). The layers consist of vanadium selenite chains [(VO)(2)(SeO(3))(2)]( infinity ), linked by 4,4'-bipy molecules. The framework is composed of vanadium selenite sheets [V(4)Se(3)O(16)]( infinity ), pillared by 4,4'-bipy molecules. All of the compounds are thermally stable to 300 degrees C, and the magnetic susceptibilities confirm the existence of tetravalent V atoms in the antiferromagnetic (4,4'-bipy)V(2)Se(2)O(8) complex and mixed tetravalent and pentavalent V atoms in the paramagnetic complex (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O.

Journal Article↗

PubMed2003

Chloro(L-glutamato-kappa 2N,O)(1,10-phenanthroline-kappa 2,N')copper(II) monohydrate.

The crystal structure of the title compound, [CuCl(C(5)H(8)NO(4))(C(12)H(8)N(2))].H(2)O or [CuCl(L-Glu)(phen)].H(2)O (where phen is 1,10-phenanthroline and L-Glu is L-glutamate), shows that the ternary complex consists of two neutral molecules, in which the Cu(II) ions each have a distorted square-pyramidal coordination geometry comprised of one bidentate phenanthroline ligand, one O,N-bidentate L-glutamate anion and an apical Cl(-) anion. The angles between the planes of the Cu-phenanthroline and the Cu-aminocarboxylate chelate rings are 6.1 (5) and 11.8 (5) degrees in the two molecules. The Cu-Cl bond lengths are 2.608 (3) and 2.590 (3) A in the two molecules, slightly longer than the value of 2.546 A observed for the Cu-Cl bond in the analogous chloro(L-glycinato)(1,10-phenanthroline)copper complex [Solans, Ruiz-Ramírez, Martinez, Gasque & Briansó (1983). Acta Cryst. C44, 628-631]. Additionally, the Cu ion is weakly coordinated at a sixth position by an alpha-carboxyl O atom from a neighbouring complex. A number of intra- and intermolecular hydrogen bonds stabilize the crystal structure.

Journal Article↗

PubMed2003

DFT calculations of isomer shifts and quadrupole splitting parameters in synthetic iron-oxo complexes: applications to methane monooxygenase and ribonucleotide reductase.

To predict isomer shifts and quadrupole splitting parameters of Fe atoms in the protein active sites of methane monooxygenase and ribonucleotide reductase, a correlation between experimental isomer shifts ranging 0.1-1.5 mm s(-)(1) for Fe atoms in a training set with the corresponding density functional theory (DFT) calculated electron densities at the Fe nuclei in those complexes is established. The geometries of the species in the training set, consisting of synthetic polar monomeric and dimeric iron complexes, are taken from the Cambridge structural database. A comparison of calculated Mössbauer parameters for Fe atoms from complexes in the training set with their corresponding experimental values shows very good agreement (standard deviation of 0.11 mm/s, correlation coefficient of -0.94). However, for the Fe atoms in the active sites of the structurally characterized proteins of methane monooxygenase and ribonucleotide reductase, the calculated Mössbauer parameters deviate more from their experimentally measured values. The high correlation that exists between calculated and observed quadrupole splitting and isomer shift parameters for the synthetic complexes leads us to conclude that the main source of the error arising for the protein active sites is due to the differing degrees of atomic-level resolution for the protein structural data, compared to the synthetic complexes in the training set. Much lower X-ray resolutions associated with the former introduce uncertainty in the accuracy of several bond lengths. This is ultimately reflected in the calculated isomer shifts and quadrupole splitting parameters of the Fe sites in the proteins. For the proteins, the closest correspondence between predicted and observed Mössbauer isomer shifts follows the order MMOH(red), RNR(red), MMOH(ox), and RNR(ox), with average deviations from experiment of 0.17, 0.17, 0.17-0.20, and 0.32 mm/s, but this requires DFT geometry optimization of the iron-oxo dimer complexes.

Chemical Phenomena↗

PubMed1987

Optically detected magnetic resonance of tryptophan residues in complexes formed between a bacterial single-stranded DNA binding protein and heavy atom modified poly(uridylic acid).

Optically detected magnetic resonance (ODMR) methods were employed to study three single-stranded DNA binding (SSB) proteins encoded by plasmids of enteric bacteria: pIP71a, R64, and F. Equilibrium binding isotherms obtained by fluorescence titrations reveal that the complexes of the plasmid SSB proteins with heavy atom modified polynucleotides are readily disrupted by salt. Since all the plasmid SSB proteins show limited solubility at low ionic strength (pIP71a greater than R64 greater than F), we were able to bind only the pIP71a protein to mercurated poly(uridylic acid) [poly(5-HgU)] and brominated poly(uridylic acid) [poly(5-BrU)]. ODMR results reveal the existence of at least one heavy atom perturbed, red-shifted, stacked Trp residue in these complexes. Amplitude-modulated phosphorescence microwave double resonance spectra display selectively the phosphorescence associated with Hg-perturbed Trp residue(s) in the pIP71a SSB protein-poly(5-HgU) complex, which has a broad, red-shifted 0,0-band. Our results suggest that Trp-135 in Escherichia coli SSB, which is absent in the plasmid-encoded SSB proteins, is located in a polar environment and is not involved in stacking interactions with the nucleotide bases. Phosphorescence spectra and lifetime measurements of the pIP71a SSB protein-poly (5-BrU) complex show that at least one Trp residue in the complex does not undergo stacking. This sets a higher limit of two stacking interactions of Trp residues with nucleotide bases in complexes of pIP71a SSB with single-stranded polynucleotides.

DNA-Binding Proteins↗

PubMed1994

Crystallographic studies of isosteric NAD analogues bound to alcohol dehydrogenase: specificity and substrate binding in two ternary complexes.

CNAD (5-beta-D-ribofuranosylnicotinamide adenine dinucleotide) is an isosteric C-glycosidic analogue of NAD(H) containing a neutral pyridine ring. CPAD (5-beta-D-ribofuranosylpicolinamide adenine dinucleotide) is a closely related pyridine-containing analogue with the pyridine nitrogen on the opposite side of the ring. CNAD is a potent and specific inhibitor of horse liver alcohol dehydrogenase (LADH), binding with a dissociation constant in the nanomolar range. CPAD binds LADH with an affinity comparable to that of NAD. Crystal structures of CNAD and CPAD bound to LADH are presented at 2.4 and 2.7 A, respectively. The two complexes are isomorphous, crystallizing in the triclinic system with cell dimensions different from those seen in previous ternary LADH complexes. Structures were solved using the molecular replacement method and refined to crystallographic R values of 18% (CNAD) and 17% (CPAD). Both inhibitors bind to the "closed" form of LADH in the normal cofactor-binding cleft. The conformation of LADH-bound CPAD closely mimics that of LADH-bound NAD(H). The data suggest that alcohol substrate binds directly to the catalytic zinc atom. In the CNAD complex, the pyridine nitrogen replaces alcohol as the fourth coordination ligand to the active site zinc atom, while all other polar interactions remain the same as those of bound NAD(H). The zinc-nitrogen ligand explains the high affinity of CNAD for LADH.

Alcohol Dehydrogenase↗

PubMed1995

Crystal structure of human alpha-thrombin complexed with hirugen and p-amidinophenylpyruvate at 1.6 A resolution.

Crystals of human alpha-thrombin complexed with hirugen and the alpha-keto acid thrombin inhibitor APPA (p-amidinophenylpyruvate) that diffract to 1.6 A resolution were obtained by soaking an alpha-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier method and refined to an R factor of 18.7% at 1.6 A resolution. This structure is the highest resolution structure of the thrombin molecule that is currently available. With the exception of the region near Arg77A-Asn78, the structures of the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex. As previously determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms a covalent bond with O gamma of Ser195 of thrombin to yield a "transition-state" analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombin and trypsin reveals differences in hydrogen bonding and shows for the first time that the S1 site of thrombin is larger than that of trypsin and as a result thrombin may be able to accommodate a bulkier P1 group than trypsin.

Amino Acid Sequence↗

PubMed2003

Electron and hydrogen-atom self-exchange reactions of iron and cobalt coordination complexes.

Reported here are self-exchange reactions between iron 2,2'-bi(tetrahydro)pyrimidine (H(2)bip) complexes and between cobalt 2,2'-biimidazoline (H(2)bim) complexes. The (1)H NMR resonances of [Fe(II)(H(2)bip)(3)](2+) are broadened upon addition of [Fe(III)(H(2)bip)(3)](3+), indicating that electron self-exchange occurs with k(Fe,e)(-) = (1.1 +/- 0.2) x 10(5) M(-1) s(-1) at 298 K in CD(3)CN. Similar studies of [Fe(II)(H(2)bip)(3)](2+) plus [Fe(III)(Hbip)(H(2)bip)(2)](2+) indicate that hydrogen-atom self-exchange (proton-coupled electron transfer) occurs with k(Fe,H.) = (1.1 +/- 0.2) x 10(4) M(-1) s(-1) under the same conditions. Both self-exchange reactions are faster at lower temperatures, showing small negative enthalpies of activation: DeltaH++(e(-)) = -2.1 +/- 0.5 kcal mol(-1) (288-320 K) and DeltaH++(H.) = -1.5 +/- 0.5 kcal mol(-1) (260-300 K). This behavior is concluded to be due to the faster reaction of the low-spin states of the iron complexes, which are depopulated as the temperature is raised. Below about 290 K, rate constants for electron self-exchange show the more normal decrease with temperature. There is a modest kinetic isotope effect on H-atom self-exchange of 1.6 +/- 0.5 at 298 K that is close to that seen previously for the fully high-spin iron biimidazoline complexes.(12) The difference in the measured activation parameters, E(a)(D) - E(a)(H), is -1.2 +/- 0.8 kcal mol(-1), appears to be inconsistent with a semiclassical view of the isotope effect, and suggests extensive tunneling. Reactions of [Co(H(2)bim)(3)](2+)-d(24) with [Co(H(2)bim)(3)](3+) or [Co(Hbim)(H(2)bim)(2)](2+) occur with scrambling of ligands indicating inner-sphere processes. The self-exchange rate constant for outer-sphere electron transfer between [Co(H(2)bim)(3)](2+) and [Co(H(2)bim)(3)](3+) is estimated to be 10(-)(6) M(-1) s(-1) by application of the Marcus cross relation. Similar application of the cross relation to H-atom transfer reactions indicates that self-exchange between [Co(H(2)bim)(3)](2+) and [Co(Hbim)(H(2)bim)(2)](2+) is also slow, < or =10(-3) M(-1) s(-1). The slow self-exchange rates for the cobalt complexes are apparently due to their interconverting high-spin [Co(II)(H(2)bim)(3)](2+) with low-spin Co(III) derivatives.

Cobalt↗