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At least 811 records · Page 45Linked to original sources
PubMed2006

Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex reveals the structural basis of broad spectrum indomethacin efficacy.

The crystal structure of the ternary complex of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin (15-oxo-PG) 13-reductase (LTB4 12HD/PGR), an essential enzyme for eicosanoid inactivation pathways, with indomethacin and NADP+ has been solved. An indomethacin molecule bound in the anti-configuration at one of the two active site clefts of the homo-dimer interface in the LTB4 12HD/PGR and was confirmed by a binding calorimetry. The chlorobenzene ring is buried in the hydrophobic pore used as a binding site by the omega-chain of 15-oxo-PGE2. The carboxyl group interacts with the guanidino group of Arg56 and the phenolic hydroxyl group of Tyr262. Indomethacin shows a broad spectrum of efficacy against lipid-mediator related proteins including cyclooxygenase-2, phospholipase A2, PGF synthase and PGE synthase-2 but in the syn-configuration as well as LTB4 12HD/PGR in the anti-configuration. Indomethacin does not necessarily mimic the binding mode of the lipid-mediator substrates in the active sites of these complex structures. Thus, the broad spectrum of indomethacin efficacy can be attributed to its ability to adopt a range of different stable conformations. This allows the indomethacin to adapt to the distinct binding site features of each protein whilst maintaining favorable interactions between the carboxyl group and a counter charged functional group.

15-Oxoprostaglandin 13-Reductase↗
PubMed1998

Contribution of cytogenetics and FISH in the diagnosis of meningiomas. A study of 189 tumors.

The correlation between cytogenetic and histopathological findings were analysed in 189 meningiomas. The tumors were classified according to increasing degrees of anaplasia. We observed normal karyotype or only monosomy 22 in grade 1 (benign) tumors, while in grade 3 (anaplastic) only 1.5% of karyotypes were normal. Grade 2 (atypical) and 3 (anaplastic) tumors showed complex structural abnormalities. Loss of chromosome 14 were only found in grade 3. In cases with complex structural rearrangements, fluorescence in situ hybridization technique (FISH) has been realized and permitted a best identification of abnormalities. In our series, five patients recurred. They presented chromosomal abnormalities. These complex karyotypes in recurrent meningiomas might indicate aggressive tumor characteristics. Our results indicate histolopathological and cytogenetics correlations might represent a prognostic factor in meningiomas.

Adult↗
PubMed2004

Perceptual or motor learning in SRT tasks with complex sequence structures.

We investigated under which conditions sequence learning in a serial reaction time task can be based on perceptual learning. A replication of the study of Mayr (1996) confirmed perceptual and motor learning when sequences were learned concurrently. However, between-participants manipulations of the motor and perceptual sequences only supported motor learning in cases of more complex deterministic and probabilistic sequence structures. Perceptual learning using a between-participants design could only be established with a simple deterministic sequence structure. The results seem to imply that perceptual learning can be facilitated by a concurrently learned motor sequence. Possibly, concurrent learning releases necessary attentional resources or induces a structured learning condition under which perceptual learning can take place. Alternatively, the underlying mechanism may rely on binding between the perceptual and motor sequences.

Adult↗
PubMed2000

Structure and function of the fourth subunit (Dpb4p) of DNA polymerase epsilon in Saccharomyces cerevisiae.

DNA polymerase epsilon (Polepsilon) of Saccharomyces cerevisiae is purified as a complex of four polypeptides with molecular masses of >250, 80, 34 (and 31) and 29 kDa as determined by SDS-PAGE. The genes POL2, DPB2 and DPB3, encoding the catalytic Pol2p, the second (Dpb2p) and the third largest subunits (Dpb3p) of the complex, respectively, were previously cloned and characterised. This paper reports the partial amino acid sequence of the fourth subunit (Dpb4p) of Polepsilon. This protein sequence matches parts of the predicted amino acid sequence from the YDR121w open reading frame on S.cerevisiae chromosome IV. Thus, YDR121w was renamed DPB4. A deletion mutant of DPB4 (Deltadpb4) is not lethal, but chromosomal DNA replication is slightly disturbed in this mutant. A double mutant haploid strain carrying the Deltadpb4 deletion and either pol2-11 or dpb11-1 is lethal at all temperatures tested. Furthermore, the restrictive temperature of double mutants carrying Deltadpb4 and dpb2-1, rad53-1 or rad53-21 is lower than in the corresponding single mutants. These results strongly suggest that Dpb4p plays an important role in maintaining the complex structure of Polepsilon in S.cerevisiae, even if it is not essential for cell growth. Structural homologues of DPB4 are present in other eukaryotic genomes, suggesting that the complex structure of S. cerevisiae Polepsilon is conserved in eukaryotes.

Amino Acid Motifs↗
PubMed1997

Acenaphthenequinone thiosemicarbazone and its transition metal complexes: synthesis, structure, and biological activity.

The reaction of iron, nickel, copper, and zinc chlorides or acetates with acenaphthenequinone thiosemicarbazone, Haqtsc leads to the formation of novel complexes that have been characterized by spectroscopic studies (NMR, IR) and biological properties. The crystal structures of the free ligand Haqtsc 1 and of the compound [Ni(aqtsc)2].DMF 2, have also been determined by X-ray methods from diffractometer data. In 1, the conformation of the two nonequivalent molecules is governed by intramolecular hydrogen bonds, while an intermolecular hydrogen bond is responsible for dimer-like groups formation. In 2, the coordination geometry about nickel is distorted octahedral, and the two ligand molecules are terdentate monodeprotonated. Biological studies have shown that, for the first time at least up the used doses, a free ligand is active both in the inhibition of cell proliferation and in the induced differentiation on Friend erythroleukemia cells (FLC).

Acenaphthenes↗
PubMed2001

A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes.

Mass spectrometric structural analysis of crosslinked peptides is a powerful method to elucidate the spatial arrangement of polypeptides in protein complexes. Our aim is to develop bifunctional crosslinkers that, after crosslinking protein complexes followed by proteolytic digestion, give rise to crosslinked peptides that can be readily tracked down by mass spectrometry. To this end we synthesized the crosslinker N-benzyliminodiacetoyloxysuccinimid (BID), which yields stable benzyl cation marker ions upon low-energy collision-induced dissociation (CID) tandem mass spectrometry. Sensitive detection of the marker ion upon low-energy CID is demonstrated with different BID-crosslinked peptide preparations. With BID it becomes possible to retrieve crosslinked and crosslinker-adducted peptides, without the necessity of purifying crosslinked peptides prior to identification. The basic design of this crosslinker can be varied upon, in order to meet specific crosslinking needs.

Bradykinin↗
PubMed1993

Identification of an immunodominant linear neutralization domain on the S2 portion of the murine coronavirus spike glycoprotein and evidence that it forms part of complex tridimensional structure.

Numerous studies have demonstrated that the spike glycoprotein of coronaviruses bears major determinants of pathogenesis. To elucidate the antigenic structure of the protein, a panel of monoclonal antibodies was studied by competitive ELISA, and their reactivities were assayed against fragments of the murine coronavirus murine hepatitis virus strain A59 S gene expressed in prokaryotic vectors. An immunodominant linear domain was localized within the predicted stalk, S2, of the peplomer. It is recognized by several neutralizing antibodies. Other domains were also identified near the proteolytic cleavage site, in the predicted globular head, S1, and in another part of the stalk. Furthermore, competition results suggest that the immunodominant functional domain forms part of a complex three-dimensional structure. Surprisingly, some antibodies which have no antiviral biological activities were shown to bind the immunodominant neutralization domain.

Amino Acid Sequence↗
PubMed1997

DNA-lipid complexes: stability of honeycomb-like and spaghetti-like structures.

A molecular level theory is presented for the thermodynamic stability of two (similar) types of structural complexes formed by (either single strand or supercoiled) DNA and cationic liposomes, both involving a monolayer-coated DNA as the central structural unit. In the "spaghetti" complex the central unit is surrounded by another, oppositely curved, monolayer, thus forming a bilayer mantle. The "honeycomb" complex is a bundle of hexagonally packed DNA-monolayer units. The formation free energy of these complexes, starting from a planar cationic/neutral lipid bilayer and bare DNA, is expressed as a sum of electrostatic, bending, mixing, and (for the honeycomb) chain frustration contributions. The electrostatic free energy is calculated using the Poisson-Boltzmann equation. The bending energy of the mixed lipid layers is treated in the quadratic curvature approximation with composition-dependent bending rigidity and spontaneous curvature. Ideal lipid mixing is assumed within each lipid monolayer. We found that the most stable monolayer-coated DNA units are formed when the charged/neutral lipid composition corresponds (nearly) to charge neutralization; the optimal monolayer radius corresponds to close DNA-monolayer contact. These conclusions are also valid for the honeycomb complex, as the chain frustration energy is found to be negligible. Typically, the stabilization energies for these structures are on the order of 1 k(B)T/A of DNA length, reflecting mainly the balance between the electrostatic and bending energies. The spaghetti complexes are less stable due to the additional bending energy of the external monolayer. A thermodynamic analysis is presented for calculating the equilibrium lipid compositions when the complexes coexist with excess bilayer.

Computer Simulation↗
PubMed2003

Catalytic oxidation of 3,5-Di-tert-butylcatechol by a series of mononuclear manganese complexes: synthesis, structure, and kinetic investigation.

The manganese compounds [Mn(bpia)(OAc)(OCH(3))](PF(6)) (1), [Mn(bipa)(OAc)(OCH(3))](PF(6)) (2), [Mn(bpia)(Cl)(2)](ClO(4)) (3), [Mn(bipa)(Cl)(2)](ClO(4)) (4), [Mn(Hmimppa)(Cl)(2)] x CH(3)OH (5), and [Mn(mimppa)(TCC)] x 2CHCl(3) (6) (bpia = bis(picolyl)(N-methylimidazole-2-yl)amine; bipa = bis(N-methylimidazole-2-yl)(picolyl)amine; Hmimppa = ((1-methylimidazole-2-yl)methyl)((2-pyridyl)methyl)(2-hydroxyphenyl)amine; TCC = tetrachlorocatechol) were synthesized and characterized by various techniques such as X-ray crystallography, mass spectrometry, IR, EPR, and UV/vis spectroscopy, cyclic voltammetry, and elemental analysis. 1 and 2 crystallize in the triclinic space group Ponemacr; (No. 2), 4 and 6 crystallize in the monoclinic space group P2(1)/n (No. 14), and 5 crystallizes in the orthorhombic space group Pna2(1). Complexes 1-4 are structurally related to the proposed active site of the manganese-dependent extradiol-cleaving catechol dioxygenase exhibiting an N(4)O(2) donor set (1 and 2) or N(4)Cl(2) donor set (3 and 4). Cyclic voltammetric data show that the substitution of oxygen donor atoms with chloride causes a shift of redox potentials to more positive values. These compounds show high catalytic activity regarding the oxidation of 3,5-di-tert-butylcatechol to 3,5-di-tert-butylquinone exhibiting saturation kinetics at high substrate concentrations. The turnover numbers k(cat) = (86 +/- 7) h(-1) (1), k(cat) = (101 +/- 4) h(-1) (2), k(cat) = (230 +/- 4) h(-1) (3), and k(cat) = (130 +/- 4) h(-1) (4) were determined from the double reciprocal Lineweaver-Burk plot. Compounds 5 and 6 can be regarded as structural and electronic Mn analogues for substituted forms of Fe-containing intradiol-cleaving catechol dioxygenases. To our knowledge 5 is the first mononuclear Mn(II) compound featuring an N(3)OCl(2) donor set.

Catalysis↗
PubMed2003

Studies on the nitroreductase prodrug-activating system. Crystal structures of complexes with the inhibitor dicoumarol and dinitrobenzamide prodrugs and of the enzyme active form.

The E. coli nitroreductase enzyme (NTR) has been widely used in suicide gene therapy (GDEPT and ADEPT) applications as a activating enzyme for nitroaromatic prodrugs of the dinitrobenzamide class. NTR has been previously shown to be a homodimeric enzyme with two active sites. We present here the crystal structures of the reduced form of NTR and its complexes with the inhibitor dicoumarol and three dinitrobenzamide prodrugs. Comparison of the structures of the oxidized and reduced forms of the native enzyme shows that the principal structural changes occur in the FMN cofactor and indicate that the enzyme itself is a relatively rigid structure that primarily provides a rigid structural framework on which hydride transfer occurs. The aziridinyldinitrobenzamide prodrug CB 1954 binds in nonidentical ways in both of the two active sites of the homodimeric enzyme, employing both hydrophobic and (in active site B) a direct H-bond contact to the side chain of Lys14. In active site A the 2-nitro group stacks above the FMN, and in active site B the 4-nitro group does, explaining why reduction of either nitro group is observed. In contrast, the larger mustard group of the dinitrobenzamide mustard compound SN 23862 forces the prodrug to bind at both active sites with only the 2-nitro group able to participate in hydride transfer from the FMN, explaining why only the 2-hydroxylamine reduction product is observed. In each site, the nitro groups of the prodrug make direct H-bond contacts with the enzyme; in active Site A the 2-nitro to Ser40 and the 4-nitro to Asn71, while in active Site B the 2-nitro contacts the main chain nitrogen of Thr41 and the 4-nitro group the Lys14 side chain. The related amide-substituted mustard SN 27217 binds in a broadly similar fashion, but with the larger amide group substituent able to reach and contact the side chain of Arg107, further restricting the prodrug conformations in the binding site. The inhibitor dicoumarol appears to bind primarily by pi-stacking interactions and hydrophobic contacts, with no conformational changes in the enzyme. One of the hydroxycoumarin subunits stacks above the plane of the FMN via pi-overlap with the isoalloxazine ring, penetrating deep into the groove, with the other less well-defined. These studies suggest guidelines for further prodrug design. Steric bulk (e.g., mustard rather than aziridine) on the ring can limit the possible binding orientations, and the reducible nitro group must be located para to the mustard. Substitution on the carboxamide side chain still allows the prodrugs to bind, but also limits their orientation in the binding site. Finally, modulating substrate specificity by alteration of the structure of the enzyme rather than the prodrug might usefully focus on modifying the Phe124 residue and those surrounding it.

Aniline Mustard↗
PubMed1998

Structural differences of the enteric nervous system in the cattle forestomach revealed by whole mount immunohistochemistry.

The specific motility patterns of the forestomach of ruminants, composed of three structurally distinct compartments (rumen, reticulum, omasum), require an elaborate intramural innervation. To demonstrate the complex structure of the enteric nervous system (ENS), whole mount preparations obtained from different sites of the bovine forestomach were submitted to immunohistochemical procedures in which neuronal (protein gene product 9.5, neurofilament 200) and glial (protein S-100, glial fibrillary acid protein) markers were applied. Immunohistochemistry performed on whole mounts allowed a detailed two-dimensional assessment of the architecture of the intramural nerve networks. Generally, the myenteric and submucosal plexus layers were composed of ganglia and interconnecting nerve fiber strands, whereas the mucosal plexus consisted of an aganglionated nerve network. However, the texture of the ENS showed considerable regional differences concerning the ganglionic size, shape and density and the arrangement of nerve fiber strands. The myenteric plexus of the ruminal wall, showing a low ganglionic density and wide polygonal meshes, contrasted with the nerve network within the ruminal pillar which consisted of ropeladder-like nerve fiber strands and parallel orientated ganglia. The highest ganglionic density was observed at the reticular groove, the most prominent ganglia were found within the omasal wall. Branches of the vagal nerve frequently ramified within the myenteric plexus layers. The submucosal plexus of the rumen was divided into an external and internal layer; the reticular submucosal plexus followed the cristae and cellulae reticuli, the omasal submucosal (sublaminar) plexus showed intra- and parafascicular ganglia apart from ganglia located at the junctions of the nerve network. The mucosal plexus of the rumen consisted of thin nerve fascicles ramifying between the ruminal papillae, and reticular mucosal nerve fibers passed throughout the base of the cellulae reticuli. The highly specialised nerve network of the intralaminar omasal plexus showed radial and transverse trajectories reflecting the spatial arrangement of the intralaminar musculature. The demonstrated structural complexity of the ENS reflects the functional complexity of the ruminant forestomach and indicates the relatively high degree of autonomy in coordinating the different motility patterns required for the processing of the ingesta.

Animals↗
PubMed2004

The parsley plastocyanin-turnip cytochrome f complex: a structurally distorted but kinetically functional acidic patch.

In general, inter-protein electron transfer proceeds via the formation of transient complexes. The initial stage of the interaction between plastocyanin (PCu) and cytochrome f (cyt f ) from plants is mediated by complementary electrostatics. Given the diffuse nature of its acidic patch, parsley PCu is an atypical example of a plant PCu. The interaction of this PCu with turnip cyt f was investigated by stopped-flow kinetics, NMR spectroscopy and protein-docking simulations. We show that, despite the altered acidic patch, parsley PCu is as efficient as spinach PCu in accepting electrons from cyt f, over the physiological range of ionic strength. At high ionic strength, the rate constant for the reaction of cyt f with parsley PCu is twice that of the spinach protein. This difference in reactivity is attributed to variations in the hydrophobic patch of parsley PCu. The results of NMR studies and protein-docking simulations indicate that parsley PCu and its spinach analogue adopt different orientations in their complexes with cyt f.

Amino Acid Sequence↗
PubMed2001

Distinct roles for dystroglycan, beta1 integrin and perlecan in cell surface laminin organization.

Dystroglycan (DG) is a cell surface receptor for several extracellular matrix (ECM) molecules including laminins, agrin and perlecan. Recent data indicate that DG function is required for the formation of basement membranes in early development and the organization of laminin on the cell surface. Here we show that DG-mediated laminin clustering on mouse embryonic stem (ES) cells is a dynamic process in which clusters are consolidated over time into increasingly more complex structures. Utilizing various null-mutant ES cell lines, we define roles for other molecules in this process. In beta1 integrin-deficient ES cells, laminin-1 binds to the cell surface, but fails to organize into more morphologically complex structures. This result indicates that beta1 integrin function is required after DG function in the cell surface-mediated laminin assembly process. In perlecan-deficient ES cells, the formation of complex laminin-1 structures is defective, implicating perlecan in the laminin matrix assembly process. Moreover, laminin and perlecan reciprocally modulate the organization of the other on the cell surface. Taken together, the data support a model whereby DG serves as a receptor essential for the initial binding of laminin on the cell surface, whereas beta1 integrins and perlecan are required for laminin matrix assembly processes after it binds to the cell.

Animals↗
PubMed2005

Use of structure-based drug design approaches to obtain novel anthranilic acid acyl carrier protein synthase inhibitors.

Acyl carrier protein synthase (AcpS) catalyzes the transfer of the 4'-phosphopantetheinyl group from the coenzyme A to a serine residue in acyl carrier protein (ACP), thereby activating ACP, an important step in cell wall biosynthesis. The structure-based design of novel anthranilic acid inhibitors of AcpS, a potential antibacterial target, is presented. An initial high-throughput screening lead and numerous analogues were modeled into the available AcpS X-ray structure, opportunities for synthetic modification were identified, and an iterative process of synthetic modification, X-ray complex structure determination with AcpS, biological testing, and further modeling ultimately led to potent inhibitors of the enzyme. Four X-ray complex structures of representative anthranilic acid ligands bound to AcpS are described in detail.

Anti-Bacterial Agents↗
PubMedDate not supplied

Chemical probes for water-oxidation: synthetic manganese complexes in photoactivation of water splitting complex and as exogenous electron donors to photosystem II.

Photoactivation of the water splitting enzyme was performed with 13 different synthetic manganese complexes and characterized by oxygen evolution yield, thermoluminescence and chlorophyll fluorescence induction kinetics. The efficiency of different compounds in photoactivation correlated with the rate of linear electron transport in the presence of these compounds. The organic ligands, associated with the manganese ions, do not prevent the photoactivation of the water splitting complex (WOC). Photoactivation with different manganese complexes depended on the number of the Mn-ions in the complex, their valence state and the nature of their donor atoms. The most efficient restorations were achieved by using tetrameric complexes having a dimer+dimer structure, complexes containing Mn(II) ions, and having 4-6 oxygen and 0-2 nitrogen atoms as donor atoms. Further, the effectiveness of photoactivation depended largely on the structure of the complexes. Our data support the notion that WOC in intact thylakoids requires the cooperation and well determined arrangement of all four manganese ions, and argue against the hypothesis that two manganese ions are sufficient for water splitting. Photoactivation by some complexes led to anomalous flash-oxygen patterns, which are explained by a modified/perturbed water splitting complex.

Chlorides↗
PubMed2004

Excitement in f block: structure, dynamics and function of nine-coordinate chiral lanthanide complexes in aqueous media.

Lanthanide complexation chemistry has been studied intensively over the past 15 years and progress has been stimulated by the advent of well-defined, kinetically robust systems tailored to applications as bioactive probes for magnetic resonance and luminescence. In this tutorial review, the extent to which an enhanced understanding of the relationship between complex structure and spectral properties is emerging is discussed, together with an examination of the mechanism of ligand exchange processes. Such issues are aiding the development of responsive probes, ranging from simple sensors to more complex studies defining water structure and exchange dynamics.

Animals↗
PubMed1996

The crystal structures of complexes formed between lysozyme and antibody fragments.

Type c lysozymes, and hen egg lysozyme in particular, have been extensively used to study the immune response because of their strong immunogenicity, the availability of many natural variants to study cross-reactivity, and the possibility to correlate these results with the known three-dimensional structure of lysozymes from several species. To date, the structure of six different murine monoclonal anti-lysozyme antibodies has been studied as a complex between the Fab fragment and antigen. In some cases, the structure of the uncomplexed Fab is also available, giving detail at the atomic level of the changes which take place during the formation of the antibody-antigen complex. The bacterially-expressed Fv molecule, the simplest fragment of an immunoglobulin retaining an intact antigen-binding site, has been studied for three of the monoclonal anti-lysozyme antibodies. Recombinant Fv fragments have opened up the possibility of using site-directed mutagenesis to study the effect of amino acid changes at the antibody-antigen interface. The six monoclonal antibodies appear to recognize epitopes which are localised on three different regions of the lysozyme surface.

Amino Acid Sequence↗
PubMed2003

Theory of diffraction from D019 ordered c.p.h structures containing complex stacking faults on basal planes.

Antiphase boundaries and stacking faults affect the deformation behaviour of intermetallics. In an ordered c.p.h. (close-packed hexagonal) structure of D0(19) type (e.g. Mg(3)Cd, Ti(3)Al-based alloys), stable planar faults of two types are possible on the basal plane. These are antiphase boundaries (APBs) and complex stacking faults (CSFs), which are a combination of an APB and a stacking fault. The latter can be either of shear or of climb type. If the bounding partial dislocations of a CSF lie in its plane, then it is designated as a shear CSF, otherwise it is called a climb CSF. A mathematical formulation of the theory of diffraction from a D0(19) structure having a shear or climb type of CSF has been carried out. The diffraction effects owing to the presence of these CSFs have been found. Integrated intensities and widths of the reflections are affected. These have been evaluated in terms of the probability of the occurrence of these faults.

Journal Article↗