Search PubMed⌕ Search

Biomedical subjects

D W Banner

Publications and source records attributed to D W Banner.

16 recordsLinked to original sources
PubMed1995

Activation of blood coagulation factor VIIa with cleaved tissue factor extracellular domain and crystallization of the active complex.

Exposure of blood to tissue factor leads to the formation of a high affinity tissue factor/factor VIIa complex which initiates blood coagulation. As a first step toward obtaining structural information of this enzyme system, a complex of active-site inhibited factor VIIa (F.VIIai) and soluble tissue factor (sTF) was prepared for crystallization. Crystals were obtained, but only after long incubation times. Analysis by SDS-PAGE and mass spectrometry indicated the presence of sTF fragments similar to those formed by proteolytic digestion with subtilisin (Konigsberg, W., Nemerson, Y., Fang, C., Lin, T.-C. Thromb. Haemost. 69:1171, 1993). To test the hypothesis that limited proteolysis of sTF facilitated the crystallization of the complex, sTF fragments were generated by subtilisin digestion and purified. Analysis by tandem mass spectrometry showed the presence of nonoverlapping N- and C-terminal sTF fragments encompassing more than 90% of the tissue factor extracellular domain. Enzymatic assays and binding studies demonstrated that an equimolar mixture of N- and C-terminal fragments bound to factor VIIa and fully restored cofactor activity. A complex of F.VIIai and sTF fragments was prepared for crystallization. Crystals were obtained using microseeding techniques. The best crystals had maximum dimensions of 0.12 x 0.12 x 0.6 mm and showed diffraction to a resolution of 3 A.

Crystallization↗
PubMed1991

Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors.

The mode of binding of four active-site directed inhibitors to human thrombin has been determined by x-ray crystallographic analysis. The inhibitors studied are benzamidine, PPACK, NAPAP, and MD-805, of which the last three are compounds evolved specifically to inhibit thrombin. Crystal structures were determined in the presence of both the inhibitor and the undecapeptide [des-amino Asp55]hirudin(55-65) which binds distant from the active site. Despite having significantly different chemical structures, NAPAP and MD-805 bind to thrombin in a very similar "inhibitor binding mode" which is not that expected by direct analogy with the binding of substrate. Both inhibitors bind to thrombin in a similar way as to trypsin, but thrombin has an extra loop, the "Tyr-Pro-Pro-Trp loop," not present in trypsin, which gives further binding interactions and is seen to move somewhat to accommodate binding of the different inhibitors. The fact that NAPAP and MD-805 require different stereochemistry for potent inhibition is demonstrated, and its structural basis clarified. The wealth of data on analogs and variants of these lead compounds is shown to be compatible with this inhibitor binding mode.

Amino Acid Chloromethyl Ketones↗
PubMed1989

Genetic and structural analysis of the ColE1 Rop (Rom) protein.

Repressor of primer (Rop) is a small dimeric protein that participates in the mechanism that controls the copy number of plasmid of the ColE1 family by increasing the affinity between two complementary RNAs. The Rop dimer is a bundle of four tightly packed alpha-helices that are held together by hydrophobic interactions. We have systematically altered, by site directed mutagenesis, most of the solvent exposed amino acids of the Rop bundle and we have identified the alterations that cause a decrease of the activity of the regulatory molecule. We conclude that Rop folding is rather insensitive to amino acid substitutions and to other mutations as drastic as deletions and insertions. Looking along the 2-fold symmetry axis the amino acid side chains whose alterations affect the function of Rop are all located on one side of the molecule. Furthermore they are clustered at the extremities of the alpha-helix bundle, the only exception being the aromatic ring of Phe-14.

Amino Acid Sequence↗
PubMed1988

Control of ColE1 replication: low affinity specific binding of Rop (Rom) to RNAI and RNAII.

We have studied the interactions between the three molecules Rop, RNAI and RNAII that are involved in the regulatory mechanism controlling the replication of ColE1 plasmids. We show that it is possible to purify the two RNA molecules by passing an RNA mixture through an affinity column containing Rop immobilized to a solid support. The dissociation constants of the Rop-RNAI and Rop-RNAII complexes are of the order of 10(-4) M, several orders of magnitude higher than dissociation constants of stable protein-nucleic acid complexes (10(-10) M in the lambda repressor system). Although complete RNAI molecules have higher affinity, stem-and-loop I alone can also bind Rop, suggesting that this structure plays an important role in the interaction. Rop protects the stems of RNAI and RNAII from digestion by RNases while the sensitivity of the loops to digestion by RNase T1 is not affected by high concentrations of Rop. We propose a model for Rop-RNAI/RNAII interaction in which the dimeric protein acts as an adaptor between stem structures to position the two RNAs in the correct position for loop interaction.

Bacteriocin Plasmids↗
PubMed1987

Structure of the ColE1 rop protein at 1.7 A resolution.

Structural details of the Rop protein from plasmid ColE1 are presented, with a description of the X-ray crystal structure determination and refinement at a nominal resolution of 1.7 A. The 63 amino acid protein is a dimer. Each monomer consists almost entirely of two alpha helices, the whole molecule forming a highly regular four-alpha-helix bundle. This may be approximated by a four-stranded rope with a radius of 7.0 A, a left-handed helical twist and a pitch of 172.5 A. The packing constraints for this novel type of coiled-coil structure are given. The protein acts in the control of plasmid replication via regulation of an RNA-RNA interaction in a manner not yet understood in atomic detail.

Amino Acid Sequence↗
PubMed1987

The crystal structure of pseudoazurin from Alcaligenes faecalis S-6 determined at 2.9 A resolution.

The three-dimensional structure of pseudoazurin, a single copper-containing protein from Alcaligenes faecalis strain S-6, has been determined at 2.9 A resolution by X-ray crystallography. The sequences of two other pseudoazurins from Pseudomonas AM1 and Achromobacter cycloclastes may also be accommodated in this structure. The structure, an eight-stranded beta-barrel, resembles closely those of plastocyanin and azurin. It possesses two extra alpha-helices at the C-terminus, whereas azurins have an alpha-helical flap in the middle of their sequences.

Alcaligenes↗
PubMed1986

Crystal structure of L-Pro-L-Leu-Aib-Aib-L-Glu-L-Valol, the C-terminal hexapeptide fragment of trichotoxin.

The crystal structure of L-prolyl-L-leucyl-alpha-aminoisobutyryl-alpha- aminoiso-butyryl-alpha-L-glutamyl-L-valinol (L-Pro-L-Leu-Aib-Aib-L-Glu-L-Valol), the C-terminal hexapeptide fragment of trichotoxin, has been determined by X-ray crystallography. The hexapeptide forms a right-handed 3(10)-helix consisting of two 10-atom hydrogen-bonded beta-turns of type III and one beta-turn of type I. Two of the intramolecular hydrogen-bonds are particularly weak, thus suggesting that the title compound may adopt non-helical conformations in solution, as observed by circular dichroism. In the crystal the molecules are hydrogen-bonded head-to-tail, forming infinitely long helical columns.

Amino Acid Sequence↗
PubMed1984

How does Rop work?

Explore the source record for details and available documents.

DNA Replication↗
PubMed1984

Control of initiation of pMB1 replication: purified Rop protein and RNA I affect primer formation in vitro.

We show that a protein of 63 amino acids is the product of the rop gene, a gene which negatively regulates the copy number of plasmids of the ColE1 family. Rop protein purified to homogeneity inhibits ColE1 plasmid replication in a bacterial extract. Furthermore, we show that Rop inhibition requires RNA I. In a purified in vitro system that can support primer transcription and processing, Rop affects primer formation in two ways: first, it elicits transcription termination oat nucleotide 220, and second, it increases the ability of RNA I to inhibit RNAase H processing of the primer. The analysis of these data and the comparison with the results obtained in vivo with transcription fusion experiments allow us to propose a tentative model of the molecular mechanism underlying Rop-RNA I inhibition.

DNA Replication↗
PubMed1981

On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase.

Triose phosphate isomerase is a dimeric enzyme of molecular mass 56 000 which catalyses the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde-3-phosphate. The crystal structure of the enzyme from chicken muscle has been determined at a resolution of 2.5 A, and an independent determination of the structure of the yeast enzyme has just been completed at 3 A resolution. The conformation of the polypeptide chain is essentially identical in the two structures, and consists of an inner cylinder of eight strands of parallel beta-pleated sheet, with mostly helical segments connecting each strand. The active site is a pocket containing glutamic acid 165, which is believed to act as a base in the reaction. Crystallographic studies of the binding of DHAP to both the chicken and the yeast enzymes reveal a common mode of binding and suggest a mechanisms for catalysis involving polarization of the substrate carbonyl group.

Animals↗
PubMed1981

Structure of the protein and DNA in fd filamentous bacterial virus.

The virion of filamentous bacterial viruses comprises a cylindrical protein shell of o.d. approximately 60 A and i.d. 20A, containing a single-stranded circular DNA molecule which has two oppositely directed but not base-paired strands extending the length of the virion. The assembly of the virion involves an intracellular prepackaging of the DNA with a viral DNA-binding protein which is then displaced by the coat protein as the growing virion crosses the bacterial membrane. Studies of the virion by X-ray fibre diffraction show that the protein coat consists largely of alpha-helices oriented roughly parallel to the axis of the virion. As the normal to a planar peptide tends to align normal to a magnetic field, it is possible to improve significantly the orientation of virions in fibres using a strong magnet. The success of this technique with the Pf1 strain of virus led us to apply it to the better-known fd (f1, M13) strain. We report here new information about the arrangement of protein and DNA in the fd virion obtained from the improved diffraction pattern (Fig. 1).

Bacteriophages↗