Search PubMed⌕ Search

Biomedical subjects

P A Rice

Publications and source records attributed to P A Rice.

At least 19 recordsLinked to original sources
PubMed1996

Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.

Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by >160 degrees, thus reversing the direction of the helix axis within a very short distance. Much of the bending occurs at two large kinks where the base stacking is interrupted by intercalation of a proline residue. IHF contacts the DNA exclusively via the phosphodiester backbone and the minor groove and relies heavily on indirect readout to recognize its binding sequence. One such readout involves a six-base A tract, providing evidence for the importance of a narrow minor groove.

Amino Acid Sequence↗
PubMed1996

Conservation of the lipooligosaccharide synthesis locus lgt among strains of Neisseria gonorrhoeae: requirement for lgtE in synthesis of the 2C7 epitope and of the beta chain of strain 15253.

The present study was undertaken to examine the extent to which the lgt locus varies among strains of gonococci. This locus encodes five glycosyl transferases involved in the synthesis of the lipooligosaccharide (LOS) of Neisseria gonorrhoeae. We examined seven gonococcal strains and found that the structure of the lgt locus is conserved among six of these strains. The locus is strikingly altered in strain 15253. This is one of the few strains where extensive structural analysis of its LOS is available, and therefore, we defined the altered lgt locus and focused on the reactivity of mAB 2C7. We found that strain 15253 contains only two lgt genes, lgtA and lgtE. As in F62, lgtA encodes a GlcNAc transferase and is subject to phase variation. In addition, by analysis of deletion mutants, we found that lgtE, which encodes a galactosyl transferase that is required for elongating the alpha-chain, is also necessary for completing the beta chain.

Blotting, Southern↗
PubMed1996

The pathogenesis of gonococcal urethritis in men: confocal and immunoelectron microscopic analysis of urethral exudates from men infected with Neisseria gonorrhoeae.

Confocal and immunoelectron microscopic analysis of urethral exudates from 12 men with gonococcal urethritis showed that Neisseria gonorrhoeae can invade urethral epithelial cells. Studies with acridine orange stain demonstrated that the majority of organisms within urethral epithelial cells were viable at the time of fixation. Three-dimensional modeling of an infected epithelial cell using image analysis of 21 digitized confocal sections stained with YOYO-1 and DiIC 18(3) revealed that gonococcal invasion of these cells occurred in a polar fashion, most likely at the epithelial luminal surface. Serial immunoelectron micrographs showed evidence of membrane fusion with pedestal formation between the gonococcus and the epithelial cell, gonococci within vacuoles, and occasional gonococci free in the cytoplasm. Immunoelectron microscopy studies showed ruptured vacuoles at the cell surface releasing organisms. These studies demonstrate that urethral epithelial cells are invaded by gonococci during the course of infection in males.

Epithelium↗
PubMed1996

Immunogenicity of Neisseria gonorrhoeae lipooligosaccharide epitope 2C7, widely expressed in vivo with no immunochemical similarity to human glycosphingolipids.

Natural infection with Neisseria gonorrhoeae may elicit a substantial antibody response directed against gonococcal lipooligosaccharide. Monoclonal antibody (MAb) 2C7 recognized a gonococcal lipooligosaccharide epitope, identified the epitope directly in 94% of 68 consecutive culture-positive genital secretions, and recognized 95% of 101 randomly chosen fresh (second-passage) gonococcal isolates. The epitope was stably maintained after multiple in vitro passages and did not compete with any of the known cross-reactive human glycosphingolipid structures. MAb 2C7 mediated in vitro killing and phagocytosis by human polymorphonuclear leukocytes of 1 serum-sensitive (sialylated or not) and 1 stably serum-resistant gonococcal isolate that expressed the epitope. Gonococcal endometritis and disseminated infection elicited increases (6.5-fold IgM, 4.4-fold IgG; 18-fold IgM, 17-fold IgG, respectively) in anti-2C7 epitope antibody. Immunization with a gonococcal outer membrane vaccine elicited a mean 44.5-fold increase in IgG anti-2C7 epitope antibody in 20 of 28 subjects. The epitope identified by MAb 2C7 may represent an excellent target for a potentially protective gonococcal vaccine candidate.

Adult↗
PubMed1996

Experimental immunization with a monoclonal anti-idiotope antibody that mimics the Neisseria gonorrhoeae lipooligosaccharide epitope 2C7.

An anti-idiotope monoclonal antibody (MAb), called CA1 (Ab2), was produced in mice against MAb 2C7, which recognizes a widely in vivo-expressed gonococcal lipooligosaccharide (LOS) epitope. Mice immunized with MAb CA1 initially had a 2.5-fold increase in IgG (12-fold after a booster) but no increase in IgM anti-LOS (Ab1') antibody. Control mice immunized with LOS had a 4.5-fold rise in IgG and 4-fold rise in IgM anti-LOS antibody. In rabbits, MAb CA1 elicited a 9-fold rise in IgG and a 3.3-fold rise in IgM anti-LOS (Ab1') antibody. Ab1' antibody bactericidal activity was 1-2 logs greater than that produced by immunization with LOS. Ab1' mediated complete human polymorphonuclear leukocyte phagocytosis of 2C7 epitope-positive (but not 2C7 epitope-negative) gonococci. MAb CA1 acts as a molecular surrogate (Ab2beta) for the nominal LOS antigen and may form the basis for vaccine candidates for human immunization against Neisseria gonorrhoeae.

Animals↗
PubMed1995

The phage Mu transpososome core: DNA requirements for assembly and function.

The two chemical steps of phage Mu transpositional recombination, donor DNA cleavage and strand transfer, take place within higher order protein-DNA complexes called transpososomes. At the core of these complexes is a tetramer of MuA (the transposase), bound to the two ends of the Mu genome. While transpososome assembly normally requires a number of cofactors, under certain conditions only MuA and a short DNA fragment are required. DNA requirements for this process, as well as the stability and activity of the ensuing complexes, were established. The divalent cation normally required for assembly of the stable complex could be omitted if the substrate was prenicked, if the flanking DNA was very short or if the two flanking strands were non-complementary. The presence of a single nucleotide beyond the Mu genome end on the non-cut strand was critical for transpososome stability. Donor cleavage additionally required at least two flanking nucleotides on the strand to be cleaved. The flanking DNA double helix was destabilized, implying distortion of the DNA near the active site. Although donor cleavage required Mg2+, strand transfer took place in the presence of Ca2+ as well, suggesting a conformational difference in the active site for the two chemical steps.

Bacteriophage mu↗
PubMed1995

The inflammatory cytokine response to Chlamydia trachomatis infection is endotoxin mediated.

Chlamydia trachomatis is a major etiologic agent of sexually transmitted diseases. Although C. trachomatis is a gram-negative pathogen, chlamydial infections are not generally thought of as endotoxin-mediated diseases. A molecular characterization of the acute immune response to chlamydia, especially with regard to the role of its lipopolysaccharide (LPS), remains to be undertaken. We extracted 15 mg of LPS from 5 x 10(12) C. trachomatis elementary bodies (EB) for analysis of structure and biological activity. When methylated lipid A was subjected to high-pressure liquid chromatography followed by mass spectrometry, the majority of the lipid A was found to be pentaacyl. The endotoxin activities of whole C. trachomatis EB and purified LPS were characterized in comparison with whole Salmonella minnesota R595 and with S. minnesota R595 LPS and lipooligosaccharide from Neisseria gonorrhoeae. Both C. trachomatis LPS and whole EB induced the release of tumor necrosis factor alpha from whole blood ex vivo, and C. trachomatis LPS was capable of inducing the translocation of nuclear factor kappa B in a Chinese hamster ovary fibroblast cell line transfected with the LPS receptor CD14. In both assays, however, C. trachomatis was approximately 100-fold less potent than S. minnesota and N. gonorrhoeae. The observation that C. trachomatis is a weak inducer of the inflammatory cytokine response correlates with the clinical observation that, unlike N. gonorrhoeae infection, genital tract infection with C. trachomatis is often asymptomatic. The ability of specific LPS antagonists to completely inhibit the tumor necrosis factor alpha-inducing activity of whole C. trachomatis EB suggests that the inflammatory cytokine response to chlamydia infection may be mediated primarily through LPS. This implies that the role of other surface protein antigens, at least in terms of eliciting the proinflammatory cytokine response, is likely to be minor.

Antigens, CD↗
PubMed1994

Serum resistance of Neisseria gonorrhoeae. Does it thwart the inflammatory response and facilitate the transmission of infection?

N. gonorrhoeae differentially subvert the effectiveness of complement (C) and alter the inflammatory responses elicited in human infection. Disseminated (DGI) isolates typically resist killing by normal serum (are serum-resistant), inactivate more C3b (to iC3b preferentially bound via amide linkages), generate less C5a, and result in less inflammation at local sites. Pelvic inflammatory disease isolates are serum-sensitive, inactivate less C3b (while maintaining active C3b via stable amide linkages), generate more C5a, and result in more inflammation at local sites. Sialylation of SS gonococci, presumed to occur in vivo, converts them to serum-resistant, but it does not change the patterns of C3b inactivation and therefore may not affect local inflammation. IgG antibody directed against gonococcal reduction modifiable protein (Rmp) blocks C-mediated killing of N. gonorrhoeae. Anti-Rmp blocking antibodies may harbor specificity for OmpA sequences shared with other neisserial species or Enterobacteriaceae or may be directed against unique Rmp upstream cysteine loop specific sequences, or both. Preexisting antibodies directed against Rmp facilitate transmission of gonococcal infection to exposed women; exclusion of highly immunogenic Rmp antigens from vaccine candidates may be important.

Antibodies, Bacterial↗
PubMed1994

Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer.

The reverse transcriptase from human immunodeficiency virus type 1 is a heterodimer consisting of one 66-kDa and one 51-kDa subunit. The p66 subunit contains both a polymerase and an RNase H domain; proteolytic cleavage of p66 removes the RNase H domain to yield the p51 subunit. Although the polymerase domain of p66 folds into an open, extended structure containing a large active-site cleft, that of p51 is closed and compact. The connection subdomain, which lies between the polymerase and RNase H active sites in p66, plays a central role in the formation of the reverse transcriptase heterodimer. Extensive and very different intra- and intersubunit contacts are made by the connection subdomains of each of the subunits. Together, contacts between the two connection domains constitute approximately one-third of the total contacts between subunits of the heterodimer. Conversion of an open p66 polymerase domain structure to a closed p51-like structure results in a reduction in solvent-accessible surface area by 1600 A2 and the burying of an extensive hydrophobic surface. Thus, the monomeric forms of both p66 and p51 are proposed to have the same closed structure as seen in the p51 subunit of the heterodimer. The free energy required to convert p66 from a closed p51-like structure to the observed open p66 polymerase domain structure is generated by the burying of a large, predominantly hydrophobic surface area upon formation of the heterodimer. It is likely that the only kind of dimer that can form is an asymmetric one like that seen in the heterodimer structure, since one dimer interaction surface exists only in p51 and the other only in p66. We suggest that both p51 and p66 form asymmetric homodimers that are assembled from one subunit that has assumed the open conformation and one that has the closed structure.

Antibodies, Viral↗
PubMed1994

Refinement of gamma delta resolvase reveals a strikingly flexible molecule.

BACKGROUND: gamma delta resolvase is a 20.5 kDa enzyme that catalyzes a site-specific recombination in the second step of the transposition of the gamma delta transposon and requires no cofactors other than Mg2+ for activity. Dimers of resolvase bind cooperatively to DNA at three inverted repeat sequences of differing geometry but catalyze recombination at only one site. RESULTS: The structure of the catalytic domain of gamma delta resolvase, which provides the protein-protein interactions in the synaptic complex, has been refined to an R-factor of 20% at 2.3 A resolution. The structures of the three independent monomers in the asymmetric unit are similar but not identical. Differences occur in the positions of surface loops and in the overall twist of the central beta-sheet of the molecule. The crystal also gives two independent structures for the dimeric form of the molecule, which also show significant differences in the relative orientations of their subunits. CONCLUSION: Resolvase is an unusually flexible protein. This conformational adaptability may be necessary to allow each of the 12 resolvase subunits in the synaptic complex to play a different but specific role in wrapping DNA, binding sites of differing geometry and catalyzing recombination.

Binding Sites↗
PubMed1994

Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1.

The dipyridodiazepinone Nevirapine is a potent and highly specific inhibitor of the reverse transcriptase (RT) from human immunodeficiency virus type 1 (HIV-1). It is a member of an important class of nonnucleoside drugs that appear to share part or all of the same binding site on the enzyme but are susceptible to a variety of spontaneous drug-resistance mutations. The co-crystal-structure of HIV-1 RT and Nevirapine has been solved previously at 3.5-A resolution and now is partially refined against data extending to 2.9-A spacing. The drug is bound in a hydrophobic pocket and in contact with some 38 protein atoms from the p66 palm and thumb subdomains. Most, but not all, nonnucleoside drug-resistance mutations map to residues in close contact with Nevirapine. The major effects of these mutations are to introduce steric clashes with the drug molecule or to remove favorable protein-drug contacts. Additionally, four residues (Phe-227, Trp-229, Leu-234, and Tyr-319) in contact with Nevirapine have not been selected as sites of drug-resistance mutations, implying that there may be limitations on the number and types of resistance mutations that yield viable virus. Strategies of inhibitor design that target interactions with these conserved residues may yield drugs that are less vulnerable to escape mutations.

Amino Acid Sequence↗
PubMed1994

Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits.

The packing arrangement of the 12 subunits of intact gamma delta resolvase in the unit cell of a hexagonal crystal form suggests a model for site-specific recombination that involves a DNA-mediated synaptic intermediate. The crystal structure has been determined by molecular replacement and partially refined at 2.8/3.5 A resolution. Although the small DNA-binding domain is disordered in these crystals, packing considerations show that only a small region of space in the crystal could accommodate a domain of its size. A family of related models for a synaptic complex between two DNA duplexes and 12 monomers that are arranged as situated in the crystal is consistent with the known topology of the complex and the distances between the three resolvase dimer-binding sites per DNA; further, these models place the two DNA recombination sites in contact with each other between two resolvase dimers, implying that strand exchange is accomplished through direct DNA-DNA interaction. A major role postulated, then, for the resolvase protein assembly is to stabilize a res DNA structure that is close to the topological transition state of the reaction.

Crystallography, X-Ray↗
PubMed1993

Protein-protein interactions directing resolvase site-specific recombination: a structure-function analysis.

Recombination catalyzed by the gamma delta resolvase requires assembly of a nucleo-protein complex, the synaptosome, whose structure is determined by resolvase-res and resolvase-resolvase interactions. In crystals of the resolvase catalytic domain, monomers of resolvase were closely associated with one another across three different dyad axes; one of these subunit contacts was shown to be an essential inter-dimer interaction. To investigate the relevance of the remaining two interfaces, we have made site-directed mutations at positions suggested by the structure. Cysteine substitutions were designed to link the interfaces covalently, mutations to arginine were used to disrupt intersubunit contacts, and mutations to tryptophan were used to study the hydrophobicity and solvent accessibility of potential interfaces by fluorescence quenching. Characterization of the mutant proteins has allowed us to identify the dimer interface of resolvase and to assign a structural role to a second intersubunit contact. The data presented here, together with our previous results, suggest that all three of the dyad-related intersubunit interactions observed in the crystal play specific roles in synapsis and recombination.

Arginine↗
PubMed1992

Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor.

A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of AIDS, reveals an asymmetric dimer. The polymerase (pol) domain of the 66-kilodalton subunit has a large cleft analogous to that of the Klenow fragment of Escherichia coli DNA polymerase I. However, the 51-kilodalton subunit of identical sequence has no such cleft because the four subdomains of the pol domain occupy completely different relative positions. Two of the four pol subdomains appear to be structurally related to subdomains of the Klenow fragment, including one containing the catalytic site. The subdomain that appears likely to bind the template strand at the pol active site has a different structure in the two polymerases. Duplex A-form RNA-DNA hybrid can be model-built into the cleft that runs between the ribonuclease H and pol active sites. Nevirapine is almost completely buried in a pocket near but not overlapping with the pol active site. Residues whose mutation results in drug resistance have been approximately located.

Azepines↗