Biomedical subjects

G D Brayer

Publications and source records attributed to G D Brayer.

At least 73 records · Page 4Linked to original sources

PubMed1985

Characterization of human blood coagulation factor XII cDNA. Prediction of the primary structure of factor XII and the tertiary structure of beta-factor XIIa.

A human liver cDNA library was screened by colony hybridization with two mixtures of synthetic oligodeoxyribonucleotides as probes. These oligonucleotides encoded regions of beta-factor XIIa as predicted from the amino acid sequence. Four positive clones were isolated that contained DNA coding for most of factor XII mRNA. DNA sequence analysis of these overlapping clones showed that they contained DNA coding for part of an amino-terminal extension, the complete amino acid sequence of plasma factor XII, a TGA stop codon, a 3' untranslated region of 150 nucleotides, and a poly(A)+ tail. The cDNA sequence predicts that plasma factor XII consists of 596 amino acid residues. Within the predicted amino acid sequence of factor XII, we have identified three peptide bonds that are cleaved by kallikrein during the formation of beta-factor XIIa. Comparison of the structure of factor XII with other proteins revealed extensive sequence identity with regions of tissue-type plasminogen activator (the epidermal growth factor-like region and the kringle region) and fibronectin (type I and type II homologies). As the type II region of fibronectin contains a collagen-binding site, the homologous region in factor XII may be responsible for the binding of factor XII to collagen. The carboxyl-terminal region of factor XII shares considerable amino acid sequence homology with other serine proteases including trypsin and many clotting factors. A preliminary structural model of beta-factor XIIa is proposed based on the known high resolution x-ray diffraction structures of trypsin, chymotrypsin, and elastase.

Amino Acid Sequence↗

PubMed1985

Crystallization and preliminary diffraction data for iso-1-cytochrome c from yeast.

Deep red crystals of the electron transfer protein, iso-1-cytochrome c from yeast (Saccharomyces cerevisiae), have been obtained from a 90% saturated solution of (NH4)2SO4 containing 2 mg protein/ml, 0.1 M-sodium phosphate and adjusted to pH 6.7. The space group is P4(1)2(1)2 (or P4(3)2(1)2) with a = b = 36.4 A, c = 136.8 A and Z = 8. Crystals are stable for at least ten days in the X-ray beam and diffract to better than 2.0 A resolution. Comparable and morphologically similar crystal forms of three iso-1-cytochrome c mutants at Phe87, a pivotal residue in the electron transport chain, have also been obtained.

Crystallography↗

PubMed1985

Refined structure of alpha-lytic protease at 1.7 A resolution. Analysis of hydrogen bonding and solvent structure.

The structure of alpha-lytic protease, a serine protease produced by the bacterium Lysobacter enzymogenes, has been refined at 1.7 A resolution. The conventional R-factor is 0.131 for the 14,996 reflections between 8 and 1.7 A resolution with I greater than or equal to 2 sigma (I). The model consists of 1391 protein atoms, two sulfate ions and 156 water molecules. The overall root-meansquare error is estimated to be about 0.14 A. The refined structure was compared with homologous enzymes alpha-chymotrypsin and Streptomyces griseus protease A and B. A new sequence numbering was derived based on the alignment of these structures. The comparison showed that the greatest structural homology is around the active site residues Asp102, His57 and Ser195, and that basic folding pathways are maintained despite chemical changes in the hydrophobic cores. The hydrogen bonds in the structure were tabulated and the distances and angles of interaction are similar to those found in small molecules. The analysis also revealed the presence of close intraresidue interactions. There are only a few direct intermolecular hydrogen bonds. Most intermolecular interactions involve bridging solvent molecules. The structural importance of hydrogen bonds involving the side-chain of Asx residues is discussed. All the negatively charged groups have a counterion nearby, while the excess positively charged groups are exposed to the solvent. One of the sulfate ions is located near the active site, whereas the other is close to the N terminus. Of the 156 water molecules, only seven are not involved in a hydrogen bond. Six of these have polar groups nearby, while the remaining one is in very weak density. There are nine internal water molecules, consisting of two monomers, two dimers and one trimer. No significant second shell of solvent is observed.

Amino Acid Sequence↗

PubMed1985

A model for intracellular complexation between gene-5 protein and bacteriophage fd DNA.

A structural model for the helical intracellular complex formed between the gene-5 DNA-binding protein (G 5 BP; approximately 1274 copies) and bacteriophage fd DNA has been derived by an atomic-contact analysis approach. These studies depended in large part on the recently determined high-resolution structure of the G 5 BP dimer and cross-correlations with physical-chemical data available from other techniques. The approach was to systematically scan the full set of helical complexation parameters involved, based upon observed structural and orientational constraints, to determine those compatible with both the structure of the G 5 BP dimer and the overall dimensions of the full complex. This process was monitored throughout by close scrutiny of dimer-dimer contacts and the use of hard-copy and interactive graphics devices. Instead of the wide variety of possibilities that had been expected from such an approach, only one satisfactory assembly of DNA and G 5 BP dimers could be found. The results indicate that phage DNA will be wound to the outside of the helical protein ribbon that forms the core of intracellular complex at a density of five nucleotides per G 5 BP monomer. Bound DNA strands are positioned in two contiguous binding channels, which form as a consequence of the interactions of complexed G 5 BP dimers. These channels run just inside the outer extended beta loops, composed of residue 20-30, and are separated by approximately 3.2 nm. The DNA phosphate backbone is bound at a substantially smaller radial distance (approximately 3.5 nm) than the maximum radius of the intracellular complex as a whole (approximately 4.5 nm) since bound DNA is embedded within these well-defined binding channels. Our studies also indicate that a number of sterically unacceptable contacts, involving residues 38-42, prevent complexation of otherwise complementary dimer surfaces in the absence of nucleic acids. In the process of binding DNA, these residues change conformation thereby allowing self-assembly of dimer units into a helical structure. We propose that these residues act as a two-position stereochemical switch that allows or disallows complex formation in response to the absence or presence of DNA.

Bacteriophages↗

PubMed1985

The 1.8 A structure of the complex between chymostatin and Streptomyces griseus protease A. A model for serine protease catalytic tetrahedral intermediates.

The naturally occurring serine protease inhibitor, chymostatin, forms a hemiacetal adduct with the catalytic Ser195 residue of Streptomyces griseus protease A. Restrained parameter least-squares refinement of this complex to 1.8 A resolution has produced an R index of 0 X 123 for the 11,755 observed reflections. The refined distance of the carbonyl carbon atom of the aldehyde to O gamma of Ser195 is 1 X 62 A. Both the R and S configurations of the hemiacetal occur in equal populations, with the end result resembling the expected configuration for a covalent tetrahedral product intermediate of a true substrate. This study strengthens the concept that serine proteases stabilize a covalent, tetrahedrally co-ordinated species and elaborates those features of the enzyme responsible for this effect. We propose that a major driving force for the hydrolysis of peptide bonds by serine proteases is the non-planar distortion of the scissile bond by the enzyme, which thereby lowers the activation energy barrier to hydrolysis by eliminating the resonance stabilization energy of the peptide bond.

Amino Acid Sequence↗

PubMed1985

Topological comparison of two helix destabilizing proteins: ribonuclease A and the gene 5 DNA binding protein.

A topological comparison of the two helix destabilizing proteins, pancreatic ribonuclease A and the gene 5 DNA binding protein of bacteriophage fd has been completed utilizing the available high resolution tertiary structures of each protein. The results indicate these two proteins are structurally if not also evolutionarily related. Regions of closet topological equivalence occur between beta loops directly involved in nucleotide binding or are required for the maintenance of their respective oligonucleotide binding channels. In addition, there is a similar placement of critical amino acid side chains about the binding site. Further evidence for this structural relationship is obtained by comparison of structural data for the mode of complexation of polynucleotides to each protein. The results of topological comparison suggest the essential property shared by helix destabilizing proteins, whether specialized DNA binding proteins such as G5BP or proteins with other primary functional roles, like ribonuclease A, is the presence of an elongated oligonucleotide binding channel. Although ribonuclease A and G5BP are structurally related, it seems likely any protein with this structural feature will exhibit a helix destabilizing capacity. This conclusion is supported by the diversity of molecular characteristics shown by other proteins having this activity.

DNA Helicases↗

PubMed1985

Structural model for the trialkyltin binding site on cat hemoglobin.

The binding site for trialkyltin complexes on the alpha- chain of cat oxyhemoglobins is proposed to involve the SG and NE2 atoms of Cys-13 and His-113 respectively. On deoxygenation, the conformation of this region changes substantially, allowing complexation only through the ND1 nitrogen atom of His-113, a much less favorable interaction. Thus the model presented explains the preferential binding of trialkyltin complexes to R-state cat hemoglobin and suggests the type of interaction that is likely to occur between these compounds and a variety of less well-characterized enzymes to produce the metabolic effects that trialkyltin complexes are known to produce in vivo.

Animals↗

PubMed1984

Critical evaluation of comparative model building of Streptomyces griseus trypsin.

The X-ray crystal structure of Streptomyces griseus trypsin has been solved and refined at 1.7-A resolution. The structure of this protein had been predicted in two models on the basis of its expected homology to structures of bovine trypsin and other pancreatic serine proteases [Jurásek, L., Olafson, R.W., Johnson, P., & Smillie, L.B. (1976) Miami Winter Symp. 11, 93-123; Greer, J. (1981) J. Mol. Biol. 153, 1027-1042]. An evaluation of these models in light of the known structure demonstrates the effect of several sources of error on such comparative model building. The objective of comparative model building is often to explain substrate specificity, or to suggest potential highly specific drugs. The unique parts of modeled proteins that are most important for such purposes are, however, the most poorly determined by the model-building procedure.

Animals↗

PubMed1984

Mechanism of DNA binding to the gene 5 protein of bacteriophage fd.

A model for the bimolecular complex arising from the interaction of single-stranded DNA with the gene 5 DNA binding protein (G5BP) of bacteriophage fd is proposed on the basis of difference Fourier analyses and the correlation between structural and physicochemical data. The essential DNA binding element is the G5BP dimer which provides two antiparallel DNA binding channels, each constructed from amino acid contributions of both monomers within the pair. These channels display identical bonding environments but opposite polarities as a consequence of the inherent dyad symmetry within each dimer unit. The two channels are separated by 30 A, and each is 10 A wide and 40 A long. We propose that DNA binding is a consequence of two general sets of interactions. Aromatic side chains of G5BP stack upon nucleic acid bases, and the DNA phosphate backbone is bound by a series of appropriately positioned lysyl and arginyl side chains. The DNA conformation is fully extended, and each binding channel can accommodate up to five nucleotides. Only minor conformational changes in the native G5BP structure are required to optimize the binding of DNA. The G5BP-DNA complexation model presented here serves to explain some of the mechanistic features associated with the role this protein plays in the formation of a nucleoprotein helix during the bacteriophage fd life cycle.

Coliphages↗

PubMed1983

Refined structure of the gene 5 DNA binding protein from bacteriophage fd.

The three-dimensional structure of the gene 5 DNA binding protein (G5BP) from bacteriophage fd has been determined from a combination of multiple isomorphous replacement techniques, partial refinements and deleted fragment difference Fourier syntheses. The structure was refined using restrained parameter least-squares and difference Fourier methods to a final residual of R = 0.217 for the 3528 statistically significant reflections present to 2.3 A resolution. In addition to the 682 atoms of the protein, 12 solvent molecules were included. We describe here the dispositions and orientations of the amino acid side-chains and their interactions as visualized in the G5BP structure. The G5BP monomer of 87 peptide units is almost entirely in the beta-conformation, organized as a three-stranded sheet, a two-stranded beta-ribbon and a broad connecting loop. There is no alpha-helix present in the molecule. Two G5BP monomers are tightly interlocked about an intermolecular dyad axis to form a compact dimer unit of about 55 A X 45 A X 36 A. The dimer is characterized by two symmetry-related antiparallel clefts that traverse the monomer surfaces essentially perpendicular to the dyad axis. From the three-stranded antiparallel beta-sheet, formed from the first two-thirds of the sequence, extend three tyrosine residues (26, 34, 41), a lysine (46) and two arginine residues (16, 21) that, as indicated by other physical and chemical experiments, are directly involved in DNA binding. Other residues likely to share binding responsibility are arginine 80 extending from the beta-ribbon and phenylalanine 73 from the tip of this loop, but as provided, however, by the opposite monomer within each G5BP dimer pair. Thus, both symmetry-related DNA binding sites have a composite nature and include contributions from both elements of the dimer. The gene 5 dimer is clearly the active binding species, and the two monomers within the dyad-related pair are so structurally contiguous that one cannot be certain whether the isolated monomer would maintain its observed crystal structure. This linkage is manifested primarily as a skeletal core of hydrophobic residues that extends from the center of each monomer continuously through an intermolecular beta-barrel that joins the pair. Protruding from the major area of density of each monomer is an elongated wing of tenuous structure comprising residues 15 through 32, which is, we believe, intimately involved in DNA binding. This wing appears to be dynamic and mobile, even in the crystal and, therefore, is likely to undergo conformational change in the presence of the ligand.

Amino Acid Sequence↗

PubMed1982

Preliminary diffraction data for crystals of ribonucleases A and B and their complexes with deoxy(pA)4 and deoxy(pA)6.

Crystals suitable for three-dimensional x-ray diffraction analysis have been reproducibly grown of both pancreatic ribonuclease A and B, and also of their complexes with deoxy-(pA)4 and deoxy-(pA)6. The crystals, all of which are grown from polyethylene glycol 4000 at low ionic strength, diffract to high resolution and would seem to provide another opportunity for the direct visualization of a protein-nucleic acid interaction.

Crystallization↗

PubMed1981

Active site of alpha-lytic protease: enzyme-substrate interactions.

The active site of alpha-lytic protease has been studied with a number of synthetic peptides and compared with similar data published for elastase. The kinetic data indicate that the active site of alpha-lytic protease extends over at least six subsites (S4--S2'). This extended active site has the effect of increasing kcat/Km by more than 10(6)-fold on going from an N-acetylated amino acid amide to a hexapeptide, due mainly to increases in kcat. There are major differences between alpha-lytic protease and elastase, both in terms of the kinetic parameters for a number of substrates and in terms of the tertiary structure of the active site. The ability of the S1 subsite to interact with various P1 amino acid side chains differs markedly between the two enzymes, and can be rationalized in terms of the tertiary structural differences. For alpha-lytic protease, enzyme-substrate interactions made in subsite S2 appears to be of primary importance, whereas subsite S4 is most important for elastase. The tertiary structural homology of alpha-lytic protease with another bacterial serine protease, Streptomyces griseus protease A, has allowed detailed model building of a tetrapeptide Ac-Pro-Ala-Pro-Ala-OH at the active site. In this way, the subsites S1--S4 have been examined for alpha-lytic protease and compared to other serine proteases.

Binding Sites↗

PubMed1980