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C L Fisher

Publications and source records attributed to C L Fisher.

32 records · Page 2Linked to original sources
PubMed1992

The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures.

To characterize water binding to proteins, which is fundamental to protein folding, stability and activity, the relationships of 10,837 bound water positions to protein surface shape and residue type were analyzed in 56 high-resolution crystallographic structures. Fractal atomic density and accessibility algorithms provided an objective characterization of deep grooves in solvent-accessible protein surfaces. These deep grooves consistently had approximately the diameter of one water molecule, suggesting that deep grooves are formed by the interactions between protein atoms and bound water molecules. Protein surface topography dominates the chemistry and extent of water binding. Protein surface area within grooves bound three times as many water molecules as non-groove surface; grooves accounted for one-quarter of the total surface area yet bound half the water molecules. Moreover, only within grooves did bound water molecules discriminate between different side-chains. In grooves, main-chain surface was as hydrated as that of the most hydrophilic side-chains, Asp and Glu, whereas outside grooves all main and side-chains bound water to a similar, and much decreased, extent. This identification of the interdependence of protein surface shape and hydration has general implications for modelling and prediction of protein surface shape, recognition, local folding and solvent binding.

Algorithms↗
PubMed1992

Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.

The crystal structure of the DNA repair enzyme endonuclease III, which recognizes and cleaves DNA at damaged bases, has been solved to 2.0 angstrom resolution with an R factor of 0.185. This iron-sulfur [4Fe-4S] enzyme is elongated and bilobal with a deep cleft separating two similarly sized domains: a novel, sequence-continuous, six-helix domain (residues 22 to 132) and a Greek-key, four-helix domain formed by the amino-terminal and three carboxyl-terminal helices (residues 1 to 21 and 133 to 211) together with the [4Fe-4S] cluster. The cluster is bound entirely within the carboxyl-terminal loop with a ligation pattern (Cys-X6-Cys-X2-Cys-X5-Cys) distinct from all other known [4Fe-4S] proteins. Sequence conservation and the positive electrostatic potential of conserved regions identify a surface suitable for binding duplex B-DNA across the long axis of the enzyme, matching a 46 angstrom length of protected DNA. The primary role of the [4Fe-4S] cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone. The crystallographically identified inhibitor binding region, which recognizes the damaged base thymine glycol, is a seven-residue beta-hairpin (residues 113 to 119). Location and side chain orientation at the base of the inhibitor binding site implicate Glu112 in the N-glycosylase mechanism and Lys120 in the beta-elimination mechanism. Overall, the structure reveals an unusual fold and a new biological function for [4Fe-4S] clusters and provides a structural basis for studying recognition of damaged DNA and the N-glycosylase and apurinic/apyrimidinic-lyase mechanisms.

Bacterial Proteins↗
PubMed1992

Faster superoxide dismutase mutants designed by enhancing electrostatic guidance.

The enzyme Cu, Zn superoxide dismutase (SOD) protects against oxidative damage by dismuting the superoxide radical O2-. to molecular oxygen and hydrogen peroxide at the active-site Cu ion in a reaction that is rate-limited by diffusion and enhanced by electrostatic guidance. SOD has evolved to be one of the fastest enzymes known (V(max) approximately 2 x 10(9) M-1 s-1). The new crystal structures of human SOD show that amino-acid site chains that are implicated in electrostatic guidance (Glu 132, Glu 133 and Lys 136) form a hydrogen-bonding network. Here we show that site-specific mutants that increase local positive charge while maintaining this orienting network (Glu----Gln) have faster reaction rates and increased ionic-strength dependence, matching brownian dynamics simulations incorporating electrostatic terms. Increased positive charge alone is insufficient: one charge reversal (Glu----Lys) mutant is slower than the equivalent charge neutralization (Glu----Gln) mutant, showing that the newly introduced positive charge disrupts the orienting network. Thus, electrostatically facilitated diffusion rates can be increased by design, provided the detailed structural integrity of the active-site electrostatic network is maintained.

Amino Acid Sequence↗
PubMed1991

Influence of environment on the antifolate drug trimethoprim: energy minimization studies.

Environmental effects on trimethoprim (TMP), an inhibitor of bacterial dihydrofolate reductase (DHFR), were investigated with energy minimizations in vacuo, in the crystal, and in aqueous solution. The conformations, harmonic dynamics, and energetics of the antibacterial drug calculated in these environments were compared with each other and with those of two enzyme-bound drugs. Valence and torsion angles and their energies and overall intra- and intermolecular energies compensated one another in the minimized TMP structures. The conformations of the isolated and aqueous molecules were similar to that of TMP bound to chicken liver DHFR, while the structures from the TMP crystal and from the Escherichia coli DHFR complex were unique. Since neither the small-molecule crystal nor a local minimum of the isolated molecule gave the conformation of TMP bound to the bacterial enzyme, a combination of several experimental and theoretical techniques may be necessary to probe accessible conformations of a molecule.

Animals↗
PubMed1991

Ligation of membrane Ig leads to calcium-mediated phosphorylation of the proto-oncogene product, Ets-1.

Recent studies have demonstrated that the nuclear protein, Ets-1, which is preferentially expressed in lymphocytes, binds to the long terminal repeat of Moloney murine sarcoma virus and HTLV-1 and regulates gene expression. The association of Ets-1 with DNA has been shown to be lost when the protein is phosphorylated. Thus, Ets-1 may regulate gene expression in lymphocytes and this activity may be determined by its phosphorylation state. To address the possibility that Ets-1 activity may be altered by membrane (m) Ig-mediated signal transduction, we analyzed the effect of mIgM and mIgD ligation on the phosphorylation state of Ets-1. Monoclonal anti-IgM or anti-IgD antibody stimulation of normal mouse B cells led to increased phosphorylation of Ets-1 within 2 min. This response was absolutely dependent on calcium mobilization and could be induced by elevation of intracellular free calcium using the calcium ionophore, ionomycin. Calcium release from intracellular stores was sufficient to mediate the phosphorylation of Ets-1. Treatment of resting B cells with IL-4, TGF beta-1, IFN-gamma, anti-class I, or anti-class II antibodies did not induce Ets-1 phosphorylation. In summary, calcium mobilization from intracellular stores after mIgM or mIgD ligation provides a necessary and sufficient signal for activation of Ets-1 phosphorylation. This phosphorylation event may act in the alteration of gene expression during B cell activation.

Animals↗
PubMed1991

Mechanism and atomic structure of superoxide dismutase.

The active site Cu ion in Cu,Zn superoxide dismutase is alternately oxidized and reduced during the enzymatic dismutation of superoxide to hydrogen peroxide and molecular oxygen. For oxidized Cu,Zn superoxide dismutase, an atomic structure has been determined for the human enzyme at 2.5 A resolution. The resolution of the bovine enzyme structure has been extended to 1.8 A. Atomic resolution data has been collected for reduced and inhibitor-bound Cu,Zn superoxide dismutases, and the interpretation of the electron density difference maps is in progress. The geometry and molecular surfaces of the active sites in these structures, together with biochemical data, suggest a specific model for the enzyme mechanism. Similarities in the active site geometry of the Mn and Fe superoxide dismutases with the Cu,Zn enzyme suggest that dismutation in these enzymes may follow a similar mechanism.

Animals↗
PubMed1991

Probing the structural basis for enzyme-substrate recognition in Cu,Zn superoxide dismutase.

A full understanding of enzyme-substrate interactions requires a detailed knowledge of their structural basis at atomic resolution. Crystallographic and biochemical data have been analyzed with coupled computational and computer graphic approaches to characterize the molecular basis for recognition of the superoxide anion substrate by Cu,Zn superoxide dismutase (SOD). Detailed analysis of the bovine SOD structure aligned with SOD sequences from 15 species provides new results concerning the significance and molecular basis for sequence conservation. Specific roles have been assigned for all 23 invariant residues and additional residues exhibiting functional equivalence. Sequence invariance is dominated by 15 residues that form the active site stereochemistry, supporting a primary biological function of superoxide dismutation. Using data from crystallographic structures and site-directed mutants, we are testing the role of individual residues in the active site channel, including (in human SOD) Glu 132, Glu 133, Lys 136, Thr 137, and Arg 143. Electrostatic calculations incorporating molecular flexibility suggest that the region of positive electrostatic potential in and over the active site channel above the Cu ion sweeps through space during molecular motion to enhance the facilitated diffusion responsible for the enzyme's rapid catalytic rate.

Amino Acid Sequence↗
PubMed1990

Dual molecular mechanisms mediate ligand-induced membrane Ig desensitization.

We have previously shown that ligation of murine B cell membrane IgM or IgD can lead to inactivation of the signal transducing ability of unligated Ag receptors. We describe further studies of the molecular basis of this desensitization. Consistent with the possibility that ligand induced desensitization is mediated by protein kinase C (PKC) are findings that demonstrate that both Ig binding ligands and PKC activators (DIC8 or PMA) induce desensitization in virtually all resting B cells. However, ligand-induced desensitization is longer lived than PMA- or DIC8-induced desensitization and insensitive to the PKC inhibitor staurosporine. Further, biochemical studies indicate that insufficient PKC activation is induced by ligation of membrane Ig to mediate the observed desensitization. Thus data indicate that PKC must play only a minor role in ligand-induced membrane Ig desensitization. Further studies explored the molecular source and target of effectors that mediate ligand-induced desensitization. Data indicate that phosphoinositide hydrolysis is neither necessary nor sufficient for ligand induction of desensitization. Finally, ligand-induced desensitization appears to be mediated by uncoupling of membrane Ig from G proteins that regulate phospholipase C because ligand desensitized cells are hyperresponsive to agents including ALF4- and mastoparan which activate G proteins leading to mobilization of Ca2+. Thus, the function of G proteins and further downstream elements that mediate Ca2+ mobilization is intact. Taken together, these data are most consistent with ligand-induced membrane Ig desensitization being mediated by a non-PKC, non phosphatidylinositol 4,5-bisphosphate hydrolysis involving mechanism that has as its target a structure that is very proximal to the receptor, such as the receptor itself or a transducer complex analogous to CD3.

Amino Acid Sequence↗
PubMed1990

Visualization of molecular flexibility and its effects on electrostatic recognition.

To study the effect of protein flexibility on electrostatic recognition, we have devised two novel computer graphic representations of the changes in the electrostatic field of a protein resulting from its internal motions. The atomic structure of Cu, Zn superoxide dismutase was minimized, and the 200 lowest frequency normal modes of the enzyme were determined. Individual and combined normal-mode vibrations were visualized interactively with the program Flex. Normal-mode motions are fast enough (approximately 10(-11) s cycle-1) to evade solvent damping, thus allowing long-range electrostatic interactions to dominate. The changing electrostatic environment of the protein was examined by animating precalculated frames of electrostatic field vectors with GRAMPS. With Vu, changes in electrostatic potential were displayed as variations in the color-coding of dots lying on a consensus surface that maintains the protein's shape. The consensus surface was calculated with the program Sphinx, and was derived from spherical harmonic approximations of expanded molecular surfaces. The ability to view the effects of molecular motions interactively should be useful in understanding the relationships of protein structure to function.

Computer Graphics↗
PubMed1990

Elucidating the structural chemistry of glycosaminoglycan recognition by protein C inhibitor.

Glycosaminoglycans (GAGs) including heparin accelerate the inhibition of serine proteases by serine protease inhibitors (serpins), an essential process in regulating blood coagulation. to analyze the molecular basis for GAG recognition by the plasma serpin protein C inhibitor (PCI; also known as plasminogen activator inhibitor 3), we have constructed a complete, energy-minimized, three-dimensional model of PCI by using the structure of homologous alpha 1-antitrypsin as a template. Sequence analysis, hydrogen-bonding environment, and shape complementarity suggested that the N-terminal residues of PCI, which are not homologous to those of alpha 1-antitrypsin, form an amphipathic alpha-helix, here designated A+ since it precedes the alpha 1-antitrypsin A helix. Electrostatic calculations revealed a single, highly positive surface region arising from both the A+ and H helices, suggesting that this two-helix motif is required for GAG binding by PCI. The dominant role of electrostatic interactions in PCI-heparin binding was confirmed by the strong ionic strength dependence of heparin stimulation. The involvement of the A+ helix in heparin binding was verified by demonstrating that an anti-PCI antibody that specifically binds the A+ peptide blocks heparin binding.

Amino Acid Sequence↗
PubMed1989

Cellular interactions for the in vitro production of anti-chromatin autoantibodies in MRL/Mp-lpr/lpr mice.

Anti-chromatin autoantibodies are spontaneously produced by autoimmune but not by normal mice. An in vitro system was developed to study the cellular mechanisms of anti-chromatin production in MRL/Mp-lpr/lpr (MRL/lpr) mice. In such cultures, spleen cells from MRL/lpr mice with active autoimmune disease generated substantial amounts of anti-chromatin, as measured by ELISA of culture supernatants and by ELISA spot assay of anti-chromatin-producing cells. In vitro production of anti-chromatin autoantibodies was independent of T cells, even when spleen cells from animals as young as 1 month were examined. In contrast, anti-Sm production under the same conditions was highly T cell dependent. Macrophages and/or macrophage-derived factors were necessary for the in vitro production of anti-chromatin autoantibodies. The lack of anti-chromatin production by cells from nonautoimmune mice could not be ascribed to the presence of suppressor cells. These studies indicate that individual autoantibodies may arise through distinct cellular mechanisms in systemic lupus erythematosus mice. MRL/lpr mice develop global T lymphocyte deficiency along with their autoimmunity. The progressive increase in relatively thymus independent antibodies such as anti-chromatin is consistent with the lack of functional T lymphocytes in aging MRL/lpr mice.

Aging↗
PubMed1988

Quantitation and IgG subclass distribution of antichromatin autoantibodies in SLE mice.

Antibodies to a native chromatin preparation were found in most mice suffering from spontaneous SLE. All MRL/Mp-lpr/lpr (MRL/lpr) sera tested (more than 500) contained antibodies to chromatin and antichromatin levels increased with age. Approximately 50% of the IgG antichromatin antibody in the MRL/lpr sera was of the IgG2a subclass, 30% IgG2b, 10% IgG1, and 10% IgG3. Interestingly, the relative restriction of antichromatin autoantibodies to the IgG2a subclass was apparent in MRL/lpr mice as young as 1 month, well before the onset of lymphadenopathy. Antichromatin autoantibodies were also detectable in sera from MRL/Mp- +/+ (MRL/+), NZB, (NZB x NZW)F1 (B x W), and BXSB mice, but were not found in sera from normal mice. A similar subclass distribution skewed toward IgG2a was seen for MRL/+, B x W, and NZB mice. These results indicate that the spontaneous autoantibody directed against chromatin is a good marker for murine SLE, and is predominantly of the IgG2a subclass.

Age Factors↗
PubMedDate not supplied

The genetics of autoantibody production in MRL/lpr lupus mice.

We have investigated the influence of background genes in the MRL strain, as compared to C57BL/6, on the induction of autoimmunity in homozygous lpr/lpr mice. We have concentrated on two autoantibodies, anti-Sm and anti-chromatin. The propensity to make anti-Sm is controlled by dominant genes from the MRL background. However, the prevalence of this response is under the control of additional recessive genes. The anti-chromatin response is found in both MRL/Mp-lpr/lpr and in C57BL/6-lpr/lpr mice, but it appears earlier and in higher titers in the former strain. This high responder effect is controlled by dominant genes. In F1 mice between these two strains, both anti-Sm and anti-chromatin antibodies preferentially use the b Igh allotype from the low responder B6/lpr parent. In addition, in the progeny of backcross of the F1 to the MRL/lpr strain, the production of both anti-Sm and anti-chromatin is linked to the b allotype. These results demonstrate the contribution of dominant genes from the MRL background on the induction of severe autoimmunity. They also suggest that the B6 background expresses an Igh allotype particularly amenable to autoantibody production, in spite of the relatively mild SLE-like syndrome in this strain.

Animals↗