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W Bode

Publications and source records attributed to W Bode.

At least 217 records · Page 12Linked to original sources
PubMed1985

Determination of the protein content of crystals formed by Mastigocladus laminosus C-phycocyanin, Chroomonas spec. phycocyanin-645 and modified human fibrinogen using an improved Ficoll density gradient method.

We demonstrated for several protein crystals of known protein content that the simple Ficoll density gradient method for crystal density determination as described by Westbrook (1976) often leads to quite erroneous results. In particular, the apparent density of loosely packed crystals can show a tremendous change within the first minutes of measurement. In order to derive the correct protein content the apparent crystal density must be followed as a function of time and has to be extrapolated back to the time of insertion of the crystal into the gradient. The packing densities of four novel protein crystals, formed by Mastigocladus laminosus C-phycocyanin, Chroomonas spec. phycocyanin-645 (two forms), and modified human fibrinogen have been determined and that of proteinase II of Crotalus adamanteus has been corrected. The C-phycocyanin crystals were found to contain (in contrast to earlier results reported by others) only one (alpha beta)-monomer, the phycocyanin-645 crystals two and three (alpha alpha' beta 2)-monomers, respectively, and the fibrinogen crystals one fibrinogen molecule per asymmetric unit.

Centrifugation, Density Gradient↗
PubMed1984

The refined 2.2-A (0.22-nm) X-ray crystal structure of the ternary complex formed by bovine trypsinogen, valine-valine and the Arg15 analogue of bovine pancreatic trypsin inhibitor.

Large orthorhombic crystals of the complex formed by bovine trypsinogen and a semisynthetic homologous bovine pancreatic trypsin inhibitor with the reactive-site lysine residue replaced by an arginine residue [( Arg15]PTI) have been obtained which are isomorphous with the crystals of PTI-trypsinogen [Bode, W., Schwager, P. and Huber, R. (1978) J. Mol. Biol. 118, 99-112]. The X-ray crystal structure of the ternary complex of trypsinogen-[Arg15]PTI with the dipeptide Val-Val has been determined by X-ray data to 2.2-A (0.22-nm) resolution by means of difference Fourier methods and has been crystallographically refined to a final R-value of 0.17. Replacement of the reactive-site Lys15 by an arginine residue is accompanied in the complex by small movements of polar side groups of trypsin and enclosed solvent molecules within the specificity pocket. Only solvent molecule 414 OH which mediates the hydrogen bond interactions between Lys15 NZ and Asp189 carboxylate is expelled, thus allowing the bulkier guanidyl group to approach this carboxylate. The dipeptide Val-Val binds in the pocket accepting the Ile-Val N-terminus in trypsin. The cavity left by the CD-methyl group of Ile16 upon replacement by a valine residue is only partially filled by slight rearrangements of neighbouring peptide side chains. Part of the positive free energy change observed upon replacement of Ile-Val may allow for the maintenance of this cavity.

Animals↗
PubMed1983

The X-ray crystal structure analysis of the refined complex formed by bovine trypsin and p-amidinophenylpyruvate at 1.4 A resolution.

The X-ray crystal structure of the complex formed by bovine beta-trypsin and the potent small inhibitor p-amidinophenylpyruvate at pH 7.6, has been determined by difference Fourier methods at 1.4 A resolution and subsequently refined to a crystallographic R value of 0.191, applying diagonal matrix least-squares procedures including energy constraints. The amidino and the phenyl group of this inhibitor are bound to the specificity pocket, essentially as previously observed in benzamidine-trypsin. The reactive Ser195 O gamma of trypsin forms a covalent bond of length 1.7 A to the carbonyl carbon of the pyruvate group. The hybridization of this carbonyl carbon is just between trigonal and tetrahedral. The imidazole ring of His57 is in a correct orientation to form bonds via its N epsilon 2 hydrogen to one of the carboxylate oxygens of p-amidinophenylpyruvate and to Ser195 O gamma. The probable proton shift makes Ser195 O gamma more nucleophilic and the attacked carbonyl carbon of p-amidinophenylpyruvate more electrophilic and thus facilitates bond formation. These specific interactions offer a qualitative explanation for the unique binding properties of p-amidinophenylpyruvate and for the applicability of the quantitative structure-activity relations previously found by Markwardt and coworkers for three series of p-amidinophenylalkanone compounds with carbonyl groups in alpha-, beta- and gamma-position to the phenyl ring.

Animals↗
PubMed1983

On the aggregation of fibrinogen molecules.

Aggregates of human and bovine fibrinogen were obtained under various conditions, ranging from segment-like precipitates to highly ordered paracrystals and crystals. Their biochemical characterization and the interpretation of their banding pattern by electron optical means was attempted. The observed extra vivum aggregation of fibrinogen without thrombin action, i.e. without cleavage of fibrino-peptides A and B is of particular interest with regard to Copley's theory of the endoendothelial fibrin lining. The in vivo formation of such fibrinogen gels is discussed.

Adenosine Triphosphate↗
PubMed1983

On the aggregation of fibrinogen molecules.

Aggregates of human and bovine fibrinogen were obtained under various conditions, ranging from segment-like precipitates to highly ordered paracrystals and crystals. Their biochemical characterization and the interpretation of their banding pattern by electron optical means was attempted. The observed extra vivum aggregation of fibrinogen without thrombin action, i.e. without cleavage of fibrino-peptides A and B is of particular interest with regard to Copley's theory of the endoendothelial fibrin lining. The in vivo formation of such fibrinogen gels is discussed.

Animals↗
PubMed1982

Interaction of human alpha 1-proteinase inhibitor with chymotrypsinogen A and crystallization of a proteolytically modified alpha 1-proteinase inhibitor.

Human alpha 1-proteinase inhibitor (alpha 1-PI) can form very stable complexes with chymotrypsinogen A or chymotrypsin if limited proteolysis by a contaminant proteinase is prevented with diisopropyl fluorophosphate. The contaminant proteinase cleaves the alpha 1-PI component in the alpha 1-PI-chymotrypsinogen A complex close to its N-terminus, between threonine-11 and aspartate-12 and the chymotrypsinogen A part between tyrosine-146 and threonine-147. By this modification the complex becomes unstable and dissociates into modified alpha 1-PI and neo-chymotrypsinogen A. A tritium labelling experiment shows that the contaminant proteinase is present in a 0.5-1.0% (w/w) ratio in the inhibitor preparation. These experiments indicate that alpha 1-PI is not a temporary inhibitor for these enzymes, as assumed by other authors. Isolated modified alpha 1-PI can be crystallized as tetragonal bipyramides from 2.6M sodium potassium phosphate pH 8.0. The crystals are suitable for three dimensional X-ray structure analysis. In spite of the cleavage of the susceptible peptide bond by chymotrypsinogen A, the C-terminal 3.6 kDa cleavage peptide remains tightly bound to the inhibitor by means of non-covalent interactions. In accordance with the result of the known complete amino-acid sequence of the inhibitor this finding offers an alternative explanation to the suggestion of alpha 1-PI being a double headed inhibitor. Isolated neo-chymotrypsinogen A can be activated to active chymotrypsin and can form a very labile 1 : 1 complex with alpha 1-PI, which dissociates rapidly into inactive inhibitor and neo-chymotrypsinogen.

Amino Acid Sequence↗
PubMed1982

[Concentrically layered microconcrements in the renal medulla of nephrolithiasis patients. A contribution to the renal stone pathogenesis (author's transl)].

The electron microscopic investigation of the renal medulla in calcium oxalate stone patients has shown the frequent occurrence of globoid microconcrements in the basal laminae of the collecting ducts and of the thin limbs in Henle's loop. They have a concentrically layered structure, the diameter is usually below 1.5 microns, rarely more than 3 microns. Some of these objects were also seen in the interstitial connective tissue. Tissue of stone-free patients exhibited either no or only few such microconcrements which were usually located in the interstitial space. Histochemical tests and energy dispersive microprobe analysis suggest that calcium phosphate and acid mucopolysaccharides are principal components of the microconcrements. There are indications that some microconcrements might be expelled from the basal laminae into the urinary space and may form agglomerations. They might then furnish nuclei for heterogeneous crystallization especially in cases without hypercalciuria or hyperoxaluria.

Calcium Oxalate↗
PubMed1979

[Activation, activity and inhibition of bovine trypsin].

Trypsin is a prototype of a large group of enzymes belonging to serine proteinases. The X-ray crystal-structure analyses of its proenzyme trypsinogen, of the active trypsin and of their complexes formed with the pancreatic trypsin inhibitor (PTI) have considerably enhanced our understanding of the mechanisms of activitation, action and inhibition. The trypsinogen is an incompletely folded molecule. Its substrate-binding site becomes only completely fixed upon the enzymatic cleavage of an N-terminal peptide. The contact regions of trypsin and PTI are almost complementary. The complex formed is a (stable) intermediate in the normal tryptic substrate-cleavage reaction.

Animals↗
PubMed1979

Regulation of late functions in Salmonella bacteriophages P22 and L studied by assaying endolysin synthesis.

The rate of endolysin synthesis in Salmonella typhimurium cells infected by bacteriophage P22 or L was taken as a measure for the activity of 23 gene product (the positive regulator for the "late" genes of P22 and L). Endolysin in coded for by gene 19. The amber mutations in gene 23 of P22 and L, used in this study, reduced the rate of endolysin synthesis by a factor of ca. 90 for P22 and of ca. 20 for L. In mixed infections with 19- and 23- mutants the 23 gene products of P22 and L ACT As positive regulators for the respective gene 19 in cis and in trans. Cross-specificity of the 23 gene products, i.e., turning on expression of gene 19 on a chromosome of the other species, could not be demonstrated.

Crosses, Genetic↗