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Biomedical subjects

A McPherson

Publications and source records attributed to A McPherson.

At least 163 records · Page 9Linked to original sources
PubMed1986

Crystal structure of RNase A complexed with d(pA)4.

Co-crystals of pancreatic RNase A complexed with oligomers of d(pA)4 were grown from polyethylene glycol 4000 at low ionic strength and the X-ray diffraction data were collected to 2.5 A resolution. From a series of heavy-atom derivatives a multiple isomorphous replacement-phased electron density map of the RNase-d(pA)4 complex was calculated to 3.5 A. By inspection, the disposition of the known structure of RNase in the unit cell was determined and this was confirmed by calculation of a standard crystallographic residual, R. Refinement of the protein alone in the unit cell as a strictly rigid body yielded an R factor of 0.32 at 2.8 A resolution. From difference Fourier syntheses DNA fragments were elucidated and incorporated into a model of the complex. The entire asymmetric unit was refined using a restrained-constrained least-squares procedure (CORELS) interspersed with difference Fourier syntheses. At the present time the crystal structure has been refined to an overall R value of 0.215 at 2.5 A resolution. The asymmetric unit of the complex crystals contains four oligomers of d(pA)4 associated with each molecule of RNase. In addition, there may also be partially ordered fragments of DNA at low occupancy present in the unit cell, but these have not, at this time, been incorporated into the model. One tetramer of d(pA)4 is entirely bound by a single protein molecule and occupies a portion of the active site cleft, filling the purine binding site and the phosphate site at the catalytic center with its 5' nucleotide. Two other tetramers are partly intermolecular. One passes from near the pyrimidine binding site over the surface of the protein toward arginine 39 and into a solvent region. A third tetramer is anchored at its 5' terminus by a salt link to lysine 98, passes near arginine and then through a solvent region to terminate with its 3' end near the surface of another protein molecule in the lattice. The fourth tetramer of d(pA)4 is bound at its 5' end on the opposite side of the protein from the active site in an electropositive anion trap that includes lysines 31 and 91 as well as arginine 33. There may be a DNA-DNA interaction involving the 5' phosphate of one tetramer and the 3' bases of two other tetramers and this may help to stabilize the crystalline complex.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1986

The mechanism of binding of a polynucleotide chain to pancreatic ribonuclease.

The crystalline complex of pancreatic ribonuclease (RNase) with oligomers of d(pA)4 has been solved by x-ray diffraction methods and refined by standard procedures to a conventional crystallographic R factor of 0.22 at 2.5 angstrom resolution. The asymmetric unit is a complex of one RNase molecule associated with four d(pA)4 oligomers. Although the DNA in this complex is segmented, and therefore shows some discontinuities, it nevertheless traces a continuous path 12 nucleotides in length that passes through the active site cleft of the enzyme and over the surface of the protein. The DNA makes a series of eight to nine electrostatic bonds between its phosphate groups and lysine and arginine residues on the protein, as well as specific chemical interactions at the active site. The path described by the sequence of nucleotides is likely to be that taken by an extended polynucleotide chain when it is bound by the enzyme.

Animals↗
PubMed1986

X-ray studies of nucleotide binding and pyridoxal phosphate labeling of the gene 5 DNA unwinding protein.

X-ray diffraction studies have been carried out using difference Fourier methods to evaluate the reaction or interaction of an affinity label and 5'-phosphate nucleotides with the gene 5 DNA binding protein in the crystalline state. In the first case the crystalline protein was reacted with pyridoxal phosphate. Pyridoxal phosphate, which has served as an affinity label for nucleotide binding sites on other enzymes, demonstrated a major site of substitution at the center of the protein's DNA binding cleft adjacent to lysine 46 as well as two other reaction sites near residues implicated in DNA binding. Difference Fourier maps of crystals exposed to 5'-dAMP, 5'-dCMP and 5'-dTMP indicated that phosphate groups were associated with most lysine and arginine side-chains on the surface of the protein but that the nucleoside portion of the ligands were generally disordered. In several cases, however, more specific binding of the nucleotides appeared to have occurred and these sites were primarily within the proposed DNA binding cleft of the protein. In particular, binding was observed near tyrosine 34, phenylalanine 73 and within the curl of the DNA binding loop containing tyrosine 26.

Adamantane↗
PubMed1986

Isolation, characterization, and preliminary X-ray diffraction data for a serine protease from Penicillium cyclopium.

The major extracellular protein of Penicillium cyclopium has been isolated from its culture media and purified by ammonium sulfate fractionation, gel, and ion-exchange chromatography. We show this secreted protein to be endopeptidase. The molecular weight is approximately 32,000, the pI is 5.0, and the pH optimum using a variety of protein and synthetic substrates is around 7.0. Inhibition studies show that the protease is not inhibited by pepstatin nor by p-chloromercuribenzoic acid, indicating, respectively, that it is not an aspartyl protease nor a thiol protease. Complete inhibition is observed, however, with phenylmethanesulfonyl fluoride. Three crystal forms suitable for high resolution x-ray diffraction studies have been obtained from this purified protease with reflections being observed to well beyond 3.0 A resolution. One form having a needle morphology is of the orthorhombic crystal class and has space group P2(1)2(1)2(1). The unit cell dimensions are a = 41.9 A, b = 43.2 A, and c = 111.5 A with 1 molecule of the protease occurring in the asymmetric unit. The second form grown at pH values less than 6.0 has a plate morphology, is of orthorhombic space group P2(1)2(1)2(1), and has unit cell dimensions a = 59.12 A, b = 62.33 A, and c = 70.62 A. The third form is polyhedral in habit, is also of space group P2(1)2(1)2(1), and appears when the pH of the mother liquor is greater than 7.0. The cell dimensions of this crystal form are a = 57.07 A, b = 58.82 A, c = 70.79 A, and again there is 1 molecule/asymmetric unit. Three-dimensional structural analysis by x-ray diffraction is now underway. All crystal forms are somewhat denser than the norm having mass to volume ratios of 1.58, 2.00, and 1.85 A3/dalton, respectively.

Chromatography, Gel↗
PubMed1986

An experiment regarding crystallization of soluble proteins in the presence of beta-octyl glucoside.

Twenty-one soluble proteins, five tRNAs, and three protein-nucleic acid complexes were studied in a systematic manner with regard to their crystallization behavior from polyethylene glycol and ammonium sulfate solutions in the presence of 0 to 1.5% beta-octyl glucoside. Our observations suggest that this neutral detergent does influence in a very positive way the growth characteristics of the macromolecules included in this experiment. In general, more reproducible and rapid growth was noted with an increased number of large individual crystals at the expense of microcrystals. In several cases, new crystal forms were discovered. Selected x-ray diffraction analyses imply that crystals grown in the presence of beta-octyl glucoside diffract as well or better than those grown in its absence. In addition, a screen of two proteins grown in the presence of 14 different common detergents suggested that a general detergent effect may be beneficial for the growth of crystals of biological macromolecules.

Crystallization↗
PubMed1986

Structure of the crystalline complex between ribonuclease A and D(pA)4.

Crystals of a complex formed between ribonuclease A and d(pA)4 were grown and their structure determined by a combination of multiple isomorphous replacement (MIR) and molecular replacement techniques. The known structure of ribonuclease A in the correct orientation in the unit cell yielded a conventional crystallographic R factor of 0.32 at 2.8 A resolution when refined as a rigid body. Difference Fourier syntheses permitted determination of the disposition of the DNA in the unit cell. Refinement of both protein and DNA by constrained-restrained least squares procedures resulted in an R factor of 0.22 at 2.5 A resolution. The structure of the crystalline complex is comprised of four ordered oligomers of d(pA)4 associated with each molecule of RNAse. If the sites of interaction between protein and d(pA)4 fragments are mapped on the surface of the protein, they describe an essentially continuous path into and through the active site, across the surface of the enzyme and finally into the basic amino acid cluster on the opposite side of the protein.

Crystallization↗
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

Crystallization and preliminary X-ray analysis of the vitamin D-binding protein from human serum.

The vitamin D-binding protein from human serum has been crystallized from polyethylene glycol as a complex with 25-hydroxyvitamin D3 and examined by X-ray diffraction photography. The space group of the crystals is C2 with a = 203.0 A, b = 75.8 A, c = 90.9 A and beta = 109.5 degrees. There are two molecules of 56,000 dalton in the asymmetric unit. The crystals diffract to about 3.0 A resolution but the patterns exhibit a substantial level of diffuse scatter.

Crystallization↗
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↗
PubMed1984

Crystallization of alpha 1-acid glycoprotein.

Crystals of alpha 1-acid glycoprotein have been grown reproducibly from delipidated protein in the presence of chlorpromazine. The crystals are large hexagonal prisms of space group either P622 or P6(2)22 and the unit cell dimensions are a = b = 101 A and C = 201 A. The unit cell is very highly hydrated and is nearly 80% solvent. It contains one molecule of protein per asymmetric unit. The crystals diffract only to low resolution, presumably reflecting the extensive hydration and accompanying disorder.

Chlorpromazine↗
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↗
PubMed1984

Radiolabelled peanut lectin for the scintigraphic detection of cancer.

To investigate the role of intravenously administered, radioiodinated peanut lectin (131I-PNA) in the non-invasive detection of cancer, the pharmacokinetics and scintigraphic distribution of this novel tumor-seeking compound were studied in 8 patients with metastatic cancer of the colon, breast or lung. Scintigraphic localization of 131I-PNA was apparent at certain anatomical sites of known metastases in 2 patients and in a further 2 patients an adjacent malignant pleural effusion was visualized. The rapid clearance of radioactivity from the whole body and plasma with marked renal concentration and rapid urinary excretion of significant amounts of intact 131I-PNA (mol. wt. 107,000, pI 5.95) implied that this molecule was excreted selectively by the renal tubules. PNA or other lectins may find a role in the scintigraphic detection of selected types of cancer.

Arachis↗
PubMed1984

Cooperative interactions of the gene 5 protein.

Using the refined molecular structure of the Gene 5 DNA Binding Protein (G5BP) and the mechanism of DNA binding deduced from a variety of experimental techniques (G. D. Brayer and A. McPherson, J. Mol. Biol. 169, 565, 1983; G. D. Brayer and A. McPherson, Biochemistry 23, 340, 1984), we have modeled the contiguous, linear aggregation of G5BP dimers along two opposing single strands of DNA. Using both automated graphics systems and systematic calculations of intermolecular contacts between adjacent units, we have optimized the fit of complementary protein surfaces in the presence of DNA. We propose that a minor conformational change involving residues 38-43, triggered by the binding of nucleic acid, relieves several critical steric contacts and permits otherwise extensively complementary surfaces to form an interface. The bonding between surfaces on adjacent G5BP units is the primary source of the cooperativity of binding observed for G5BP. The interacting amino acid residues at the interface are described.

Binding Sites↗
PubMed1984

Biochemical and x-ray diffraction analysis of concanavalin B crystals from jack bean.

Parallel biochemical and crystallographic studies have been carried out on the protein concanavalin B from Jack Bean (Canavalis ensiformis). The studies show the protein to be a monomer of 33,000 daltons with unexceptional amino acid composition and no covalently bound carbohydrate. The molecule contains a single, firmly bound zinc ion and we present evidence that the protein specifically binds nucleotide coenzymes including at least NADPH and flavin mononucleotide. An electron density map of the concanavalin B crystals (space group P6(1), a = b = 80.9 A, c = 102.2 A) has been calculated from phases based on six isomorphous heavy atom derivatives. A description of the structure of the protein based on the 5.0 A resolution x-ray diffraction study is provided. The structure appears to contain a substantial amount of alpha-helix as well as an extensive beta-sheet and these are organized into two domains of unequal size. The position of the bound zinc is indicated by anomalous difference Fouriers and the nucleotide binding site by conventional difference Fourier maps.

Journal Article↗