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PubMed2001

Chiral Ansa metallocenes with Cp ring-fused to thiophenes and pyrroles: syntheses, crystal structures, and isotactic polypropylene catalysts.

Syntheses, crystal structures, and polymerization data for new isospecific metallocenes (heterocenes) having cyclopentenyl ligands b-fused to substituted thiophenes (Tp) and pyrroles (Pyr) are reported. The C2- and C1-symmetric heterocenes are dimethylsilyl bridged, have methyl groups adjacent to the bridgehead carbon atoms, and have aryl substituents protruding in the front. rac-Me2Si(2,5-Me2-3-Ph-6-Cp[b]Tp)2ZrCl2/MAO (MAO = methyl alumoxanes) is the most active metallocene catalyst for polypropylene reported to date. rac-Me2Si(2,5-Me2-3-Ph-6-Cp[b]Tp)2ZrCl2 and rac-Me2Si(2,5-Me2-1-Ph-4-Cp[b]Pyr)2ZrCl2 have the same structure, and the former is 6 times more active, produces half the total enantiofacial errors, and is 3.5 times less regiospecific in propylene polymerizations at the same conditions. rac-Me2Si(2-Me-4-Ph-1-Ind)2ZrCl2/MAO is 3.5 times lower in activity than rac-Me2Si(2,5-Me2-3-Ph-6-Cp[b]Tp)2ZrCl2 catalyst, and while the former is the more stereospecific and the less regiospecific, the sum of these two enantioface errors is the same for both species. Fine-tuning the heterocene sterics by changing selected hydrogen atoms on the ligands to methyl groups influenced their catalyst activities, stereospecificites, regiospecificites, and isotactic polypropylene (IPP) Mw. Thus, both substituting a hydrogen atom adjacent to the phenyl ring with a methyl group on an azapentalenyl ligand system and replacing one and then two hydrogens on the phenyl ring with methyls on thiopentalenyl ligands provided increased polymer Tm and Mw with increasing ligand bulk. Polymer molecular weights are sensitive to and inversely proportional to MAO concentration, and the catalyst activities increase when hydrogen is added for molecular weight control. The polymer Tm values with the thiopentalenyls as TIBAL/[Ph3C][B(C6F5)4] systems were higher than with MAO as catalyst activator. A racemic C1, pseudo-meso complex with a hybrid dimethylsilyl-bridged 2-Me-4-Ph-1-Ind/2,5-Me2-4-Ph-1-Cp[b]Pyr ligand produced the first sample of IPP with all the steric pentad intensities fitting the enantiomorphic site control model. Speculative mechanistic considerations are offered regarding electronic effects of the heteroatoms and steric effects of the ligand structures, the preferred phenyl torsion angles, and anion effects.

Journal Article↗
PubMed2002

67Zn solid-state and single-crystal NMR spectroscopy and X-ray crystal structure of zinc formate dihydrate.

The crystal structure, quadrupole coupling parameters, and the orientation of the electric field gradient tensors for each site of zinc formate dihydrate have been determined. There are two distinct sites in the asymmetric unit: one containing four in-plane waters with two bridging formats, the other containing six bridging formates. The solid-state NMR lineshapes have been assigned to their respective sites by using isotopic labeling and cross-polarization methods. The hydrated site corresponds to the lineshape having a quadrupole coupling constant (Cq) of 9.6 MHz and the anhydrous site has a Cq of 6.2 MHz. The absence of chemical shielding contributions to the observed lineshapes has been verified with a high-field solid-state NMR experiment performed at 18.8 T.

Crystallography, X-Ray↗
PubMed2004

Synthesis and X-ray single crystal structure of a bivalent glycocluster.

The crystal structure of a bivalent glycocluster containing aromatic amides reveals that alkylation of secondary amides alters amide configuration and thus carbohydrate presentation. This also facilitates non covalent interactions (azide-azide, carbonyl-pyranose and aromatic-pyranose) and thus carbohydrate-carbohydrate stacking.

Alkylation↗
PubMed1998

Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

The crystal structures of two ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I (Klentaq1) with a primer/template DNA and dideoxycytidine triphosphate, and that of a binary complex of the same enzyme with a primer/template DNA, were determined to a resolution of 2.3, 2.3 and 2.5 A, respectively. One ternary complex structure differs markedly from the two other structures by a large reorientation of the tip of the fingers domain. This structure, designated 'closed', represents the ternary polymerase complex caught in the act of incorporating a nucleotide. In the two other structures, the tip of the fingers domain is rotated outward by 46 degrees ('open') in an orientation similar to that of the apo form of Klentaq1. These structures provide the first direct evidence in DNA polymerase I enzymes of a large conformational change responsible for assembling an active ternary complex.

Amino Acid Sequence↗
PubMed1996

Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins.

The crystal structure of Escherichia coli B glutathione synthetase (GSHase) has been determined at the optimal catalytic condition pH 7.5. The most significant structural difference from the structure at pH 6.0 is the movement of the central domain towards the N-terminal domain almost as a rigid body. As a result of this movement, new interdomain and intersubunit polar interactions are formed which stabilize the dimeric structure further. The structure of GSHase at optimal pH was compared with 294 other known protein structures in terms of the spatial arrangements of secondary structural elements. Three enzymes (D-alanine: D-alanine ligase, succinyl-CoA synthetase and the biotin carboxylase subunit of acetyl-CoA carboxylase) were found to have structures similar to the ATP-binding site of GSHase, which extends across two domains. The ATP-binding sites in these four enzymes are composed of two antiparallel beta-sheets and are different from the classic mononucleotide-binding fold. Except for these proteins, no significant structural similarity was detected between GSHase and the other ATP-binding proteins. A structural motif in the N-terminal domain of GSHase has been found to be similar to the NAD-binding fold. This structural motif is shared by a number of other proteins that bind various negatively charged molecules.

Acetyl-CoA Carboxylase↗
PubMed2006

Considerations for the refinement of low-resolution crystal structures.

It is often assumed that crystal structures have to be obtained at sufficiently high resolution in order to perform macromolecular refinement. In several recent structures, the threshold of what is considered ;acceptable' has been pushed to lower diffraction resolutions. Here, considerations and modifications to standard refinement protocols are described that were used to solve and refine a particular set of low-resolution structures for the ATPase p97/VCP. It was found that reasonable R(free) values and good geometry can be achieved upon refinement that includes experimental phase information along with judicious use of restraints at diffraction limits as low as 4.7 A. At this resolution, the topology and the backbone-chain trace are mostly defined, some side-chain positions can be unambiguously assigned and ligands within known binding sites can be identified. Furthermore, large conformational changes can be discerned when structures in different states are available, information that is not easily obtainable by other means.

Adenosine Triphosphatases↗
PubMed1999

Disulfide engineering at the dimer interface of Lactobacillus casei thymidylate synthase: crystal structure of the T155C/E188C/C244T mutant.

The crystal structure of a covalently cross-linked Lactobacillus casei thymidylate synthase has been determined at 2.8 A resolution. The sites for mutation to achieve the bis-disulfide linked dimer were identified using the disulfide modeling program MODIP. The mutant so obtained was found to be remarkably thermostable. This increase in stability has been reasoned to be entirely a consequence of the covalent gluing between the two subunits.

Crystallography, X-Ray↗
PubMed1996

The crystal structure of transthyretin from chicken.

The crystal structure of chicken transthyretin has been solved at 290-pm resolution by molecular-replacement techniques. Transthyretin is the protein component of the amyloid fibrils found in patients suffering from either familial amyloidotic polyneuropathy or senile systemic amyloidosis. Familial amyloidotic polyneuropathy is an autosomal dominant hereditary type of amyloidosis which involves transthyretin with either one or two amino acid substitutions. The three-dimensional structure of chicken transthyretin was determined in order to compare a non-amyloidogenic, species-variant transthyretin with wild-type and mutant transthyretin molecules. Of the 31 chicken-to-human residue differences, 9 occur at positions which in human transthyretin give rise to amyloidogenic variants although none corresponds to the appropriate side-chain substitutions. The model of chicken transthyretin has been refined to an R-factor of 19.9%. The overall fold of the protein is that of an all-beta protein. Compared with wild-type human transthyretin the avian transthyretin shows quite large differences in the region known to be involved in binding to retinol-binding protein, it has a much shorter helical component than the human protein and some of the monomer-monomer interactions are different.

Animals↗
PubMed2005

Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.

The crystal structure of a subtilisin-like serine proteinase from the psychrotrophic marine bacterium, Vibrio sp. PA-44, was solved by means of molecular replacement and refined at 1.84 A. This is the first structure of a cold-adapted subtilase to be determined and its elucidation facilitates examination of the molecular principles underlying temperature adaptation in enzymes. The cold-adapted Vibrio proteinase was compared with known three-dimensional structures of homologous enzymes of meso- and thermophilic origin, proteinase K and thermitase, to which it has high structural resemblance. The main structural features emerging as plausible determinants of temperature adaptation in the enzymes compared involve the character of their exposed and buried surfaces, which may be related to temperature-dependent variation in the physical properties of water. Thus, the hydrophobic effect is found to play a significant role in the structural stability of the meso- and thermophile enzymes, whereas the cold-adapted enzyme has more of its apolar surface exposed. In addition, the cold-adapted Vibrio proteinase is distinguished from the more stable enzymes by its strong anionic character arising from the high occurrence of uncompensated negatively charged residues at its surface. Interestingly, both the cold-adapted and thermophile proteinases differ from the mesophile enzyme in having more extensive hydrogen- and ion pair interactions in their structures; this supports suggestions of a dual role of electrostatic interactions in the adaptation of enzymes to both high and low temperatures. The Vibrio proteinase has three calcium ions associated with its structure, one of which is in a calcium-binding site not described in other subtilases.

Adaptation, Physiological↗
PubMed1997

Three-dimensional models of interferon-alpha subtypes IFN-con1, IFN-alpha8, andIFN-alpha1 derived from the crystal structure of IFN-alpha2b.

The crystal structure of human interferon (Hu-IFN)-alpha2b has been determined at 2.9 A resolution. This experimentally derived model provides an accurate structural scaffold on which amino acid changes between the different human IFN-alpha subtypes may be compared. Accurate structural data are essential to identify structurally important residues buried in the hydrophobic core of the molecule from solvent accessible residues that may participate in receptor binding. Furthermore, the location and chemical composition of each amino acid substitution may be used to predict potential conformation changes that may occur in the different subtypes. The possible structural and surface effects of these amino acid changes on receptor binding and biologic activity are analyzed in the context of a proposed IFN-alpha receptor complex model. This model can be improved and corrected as additional biochemical and experimental structural data are obtained. These modeling techniques have been used to assess the structural and functional consequences of amino acid changes between Hu-IFN-alpha2b and consensus IFN (IFN-con1), Hu-IFN-alpha8, and Hu-IFN-alpha1, which each have distinct receptor-binding and biologic properties. Amino acids in IFN-alpha1 and IFN-alpha8 were identified that may explain the lower specific activities of these subtypes versus the activity of IFN-alpha2b. In contrast, a molecular explanation for the reported differences between IFN-alpha2b in receptor binding affinity of either IFN-alpha8 or IFN-con1 was not readily apparent. Notably, 15 of the 19 amino acid differences in IFN-con1 compared with IFN-alpha2b are located on the exterior surface, where they may enhance the antigenicity of this synthetic, nonnaturally occurring IFN. These modeling studies should assist in the design of further experiments to clarify these observations.

Amino Acid Sequence↗
PubMed2002

Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan.

Xanthan lyase, a member of polysaccharide lyase family 8, is a key enzyme for complete depolymerization of a bacterial heteropolysaccharide, xanthan, in Bacillus sp. GL1. The enzyme acts exolytically on the side chains of the polysaccharide. The x-ray crystallographic structure of xanthan lyase was determined by the multiple isomorphous replacement method. The crystal structures of xanthan lyase and its complex with the product (pyruvylated mannose) were refined at 2.3 and 2.4 A resolution with final R-factors of 17.5 and 16.9%, respectively. The refined structure of the product-free enzyme comprises 752 amino acid residues, 248 water molecules, and one calcium ion. The enzyme consists of N-terminal alpha-helical and C-terminal beta-sheet domains, which constitute incomplete alpha(5)/alpha(5)-barrel and anti-parallel beta-sheet structures, respectively. A deep cleft is located in the N-terminal alpha-helical domain facing the interface between the two domains. Although the overall structure of the enzyme is basically the same as that of the family 8 lyases for hyaluronate and chondroitin AC, significant differences were observed in the loop structure over the cleft. The crystal structure of the xanthan lyase complexed with pyruvylated mannose indicates that the sugar-binding site is located in the deep cleft, where aromatic and positively charged amino acid residues are involved in the binding. The Arg(313) and Tyr(315) residues in the loop from the N-terminal domain and the Arg(612) residue in the loop from the C-terminal domain directly bind to the pyruvate moiety of the product through the formation of hydrogen bonds, thus determining the substrate specificity of the enzyme.

Amino Acid Sequence↗
PubMed1998

The 2.3 A X-ray crystal structure of S. cerevisiae phosphoglycerate mutase.

The high resolution crystal structure of Saccharomyces cerevisiae phosphoglycerate mutase has been determined. This structure shows important differences from the lower resolution structure deposited in 1982. The crystal used to determine the new structure was of a different form, having spacegroup P2(1). The model was refined to a crystallographic R-factor of 18.9% and a free R-factor of 28.4% using all data between 25 and 2.3 A and employing a bulk solvent correction. The enzyme is a tetramer of identical, 246 amino acid subunits, whose structure is revealed to be a dimer of dimers, with four independent active sites located well away from the subunit contacts. Each subunit contains two domains, the larger with a typical nucleotide binding fold, although phosphoglycerate mutase has no physiological requirement to bind nucleotides. The catalytic-site histidine residues are no longer in a "clapping-hands" conformation, but more resemble the conformation seen in the distantly related enzymes prostatic acid phosphatase and fructose-2,6-bisphosphatase. However, the catalytic histidine residues in the mutase are found to be much closer to each other than in the phosphatase structures, perhaps due to the absence of bound ligands in the mutase crystal. An intricate web of H-bonds is found around the catalytic histidine residues, high-lighting residues probably important for maintaining their correct orientation and charge. The positions of certain other residues, including some found near the catalytic site and some lining the catalytic-site cleft, have been changed by the correction of registration errors between sequence and electron density in the original structure. Electron density was apparent for a portion of the functionally important C-terminal tail, which was absent from the earlier structure, showing it to adopt a mainly helical conformation.

Acid Phosphatase↗
PubMed2005

The effect of pressure on the crystal structure of hexagonal L-cystine.

The crystal structure of hexagonal L-cystine has been determined at room temperature at pressures between 0.4 and 3.7 GPa; unit-cell dimensions were measured up to 6.4 GPa. The structure of this phase consists of molecules in their zwitterionic form, and crystallizes in the hexagonal space group P6(1)22. The structure consists of hydrogen-bonded layers which are strongly reminiscent of those seen in alpha-glycine, and consist of R_4;4(16) hydrogen-bonded ring motifs. These layers are connected on one side by the disulfide bridges within the cystine molecules, and on the other by NH...O hydrogen bonds to other glycine-like layers. The most compressible unit-cell dimension, and the direction of greatest strain in the structure, is along the c-axis, and application of pressure pushes the layers closer together. The compression occurs approximately equally in the regions of the interlayer hydrogen bonds and the disulfide bridges; in the latter, changes in the C-S-S-C torsion angles allow the cystine molecules to act like springs. The effects of pressure can be interpreted in terms of closing-up of voids in the structure, and this leads to (i) a lessening of the N-C-C-O and C-S-S-C torsional angles, (ii) shortening of the N-H...O hydrogen bonds by 0.10-0.60 A and (iii) a further shortening of an already short S...S contact from 3.444 (4) A to 3.264 (4) A.

Crystallization↗
PubMed2006

Synthesis, crystal structures and magnetic behaviour of dimeric and tetrameric gadolinium carboxylates with trichloroacetic acid.

The novel gadolinium(III) containing compounds (CH3NH3)2[Gd2(CCl3COO)6(H2O)6](CCl3COO)2.2CCl3COOH (1) and (NH3CH3)2[Gd4(OH)4(CCl3COO)10(H2O)6].2H2O (2) were synthesized and structurally characterized by X-ray crystallography. In the crystal structure of 1 the gadolinium ions are bridged by carboxylate groups to dimers with a Gd3+ -Gd3+ distance of 420.2(3) pm. The compound crystallizes in the triclinic space group P1. In the crystal structure of the Gd3+ ions are bridged by hydroxide ions and carboxylate groups to tetramers with Gd3+ -Gd3+ distances between 380.3(1) and 388.0(1) pm. The compound crystallizes in the triclinic space group P1. The magnetic behaviour of these two compounds as well as of Gd2(CCl3COO)6(bipy)2(H2O)2.4bipy (3) (bipy = 2,2'-bipyridyl) was investigated in the temperature range 1.77-300 K. The magnetic data for these compounds indicate weak antiferromagnetic interactions.

Journal Article↗
PubMed2004

Synthesis, crystal structure, and spectroscopic characterization of trans-bis[(mu-1,3-bis(4-pyridyl)propane)(mu-(3-thiopheneacetate-O))(3-thiopheneacetate-O)]dicopper(II), [[Cu2(O2CCH2C4H3S)4mu-(BPP)2]]n: from a dinuclear paddle-wheel copper(II) unit to a 2-D coordination polymer involving monatomic carboxylate bridges.

From the reaction between a dinuclear paddle-wheel carboxylate, namely [Cu2mu-(O2CCH2C4H3S)4] (1), and the flexible ligand 1,3-bis(4-pyridyl)propane (BPP) a neutral 2-D coordination polymer [[Cu2(O2CCH2C4H3S)4mu-(BPP)2]]n (2) was obtained. Compounds 1 and 2 were characterized by means of elemental analysis, thermal analysis (TG/DSC), vibrational spectroscopy, and electron paramagnetic resonance (EPR). The crystal structure of 2 reveals that each Cu(II) is coordinated by two nitrogen atoms from different BPP ligands and two 3-thiopheneacetate groups within a distorted square planar geometry in a trans-[N, N, O, O] arrangement. The BPP ligand adopts a TG conformation bridging two copper centers giving rise to a 1-D sinusoidal polymeric chain along the crystallographic c axis. Adjacent 1-D chains are extended into a 2-D coordination network through pairs of monatomic carboxylate bridges in direction of the b axis. This bridging mode affords centrosymmetric dimeric units Cu2O2, and therefore, the copper ions are involved in a CuN2O2O' chromophore displaying a (4 + 1) square pyramidal coordination in the resultant 2-D polymeric network. The polycrystalline X-band EPR spectrum of 2 at room temperature is characteristic of a triplet state with nonnegligible zero-field splitting in agreement with the crystal structure. Crystal data for 2: monoclinic, space group P2(1)/c, a = 9.4253(10) A, b = 10.9373(10) A, c = 23.6378(10) A, beta = 98.733(4) degrees, Z = 2.

Journal Article↗
PubMed2003

The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism.

The membrane-bound glycoprotein dipeptidyl peptidase IV (DP IV, CD26) is a unique multifunctional protein, acting as receptor, binding and proteolytic molecule. We have determined the sequence and 1.8 A crystal structure of native DP IV prepared from porcine kidney. The crystal structure reveals a 2-2-2 symmetric tetrameric assembly which depends on the natively glycosylated beta-propeller blade IV. The crystal structure indicates that tetramerization of DP IV is a key mechanism to regulate its interaction with other components. Each subunit comprises two structural domains, the N-terminal eight-bladed beta-propeller with open Velcro topology and the C-terminal alpha/beta-hydrolase domain. Analogy with the structurally related POP and tricorn protease suggests that substrates access the buried active site through the beta-propeller tunnel while products leave the active site through a separate side exit. A dipeptide mimicking inhibitor complexed to the active site discloses key determinants for substrate recognition, including a Glu-Glu motif that distinguishes DP IV as an aminopeptidase and an oxyanion trap that binds and activates the P(2)-carbonyl oxygen necessary for efficient postproline cleavage. We discuss active and nonactive site-directed inhibition strategies of this pharmaceutical target protein.

Amino Acid Sequence↗
PubMed2002

[1.1](3,3')-azobenzenophane: novel crystal structure and cis-trans isomerization of distorted azobenzene.

[formula: see text] [1.1](3,3')-Azobenzenophane, in which two azobenzenes are cyclically connected by -CH2- chains at the meta positions, has been synthesized. The crystal structures of all isomers have been revealed. This is the first report on the crystal structure of the cis isomer of macrocyclic azobenzenes. The trans,trans isomer was slightly distorted, the trans,cis isomer highly deformed, and the cis,cis isomer unstrained. The thermal stability of cis isomers in solutions are deducible from the crystal structures.

Journal Article↗
PubMed1995

A homology model of the three-dimensional structure of human O6-alkylguanine-DNA alkyltransferase based on the crystal structure of the C-terminal domain of the Ada protein from Escherichia coli.

O6-Alkylguanine-DNA alkyltransferase (EC 2.1.1.63) repairs O6-alkylguanine lesions in DNA. A homology model of the human protein (hAT) was built, based on the crystal structure of the C-terminal domain of the Ada protein, which carries out a similar repair in Escherichia coli. Sequence alignments of known O6-alkylguanine-DNA alkyltransferases were used to aid the model building using QUANTA and CHARMm software. Despite low homology in the N-terminal half (hAT residues 1-85), a well-defined topology over this region in Ada permitted successful modelling. The C-terminal half of hAT (residues 92-207) was modelled almost entirely by residue-for-residue superposition onto the Ada structure up to residue hAT175. The model was solvated to a residue radius of 8.0 A [corrected] and then minimized using CHARMm. This structural model was used to rationalize findings from site-directed mutagenesis experiments on hAT, to make further predictions on the relationship between structure and function for the alkyltransferase family of proteins, and to explain the specificity towards known small-molecule inhibitors of the protein.

Amino Acid Sequence↗