Biomedical subjects

A M Friedman

Publications and source records attributed to A M Friedman.

At least 19 recordsLinked to original sources

PubMed2004

Geometric analysis of cross-linkability for protein fold discrimination.

Protein structure provides insight into the evolutionary origins, functions, and mechanisms of proteins. We are pursuing a minimalist approach to protein fold identification that characterizes possible folds in terms of consistency of their geometric features with restraints derived from relatively cheap, high-throughput experiments. One such experiment is residue-specific cross-linking analyzed by mass spectrometry. This paper presents a suite of novel lower- and upper-bounding algorithms for analyzing the distance between surface cross-link sites and thereby validating predicted models against experimental cross-linking results. Through analysis and computational experiments, using simulated and published experimental data, we demonstrate that our algorithms enable effective model discrimination.

Algorithms↗

PubMed2001

Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.

BACKGROUND: Restriction endonucleases form a diverse family of proteins with substantial variation in sequence, structure, and interaction with recognition site DNA. BsoBI is a thermophilic restriction endonuclease that exhibits both base-specific and degenerate recognition within the sequence CPyCGPuG. RESULTS: The structure of BsoBI complexed to cognate DNA has been determined to 1.7 A resolution, revealing several unprecedented features. Each BsoBI monomer is formed by inserting a helical domain into an expanded EcoRI-type catalytic domain. DNA is completely encircled by a BsoBI dimer. Recognition sequence DNA lies within a 20 A long tunnel of protein that excludes bulk solvent. Interactions with the specific bases are made in both grooves through direct and water-mediated hydrogen bonding. Interaction with the degenerate position is mediated by a purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the purine N6/O6 and pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active site residues of the DX(n)(E/D)ZK restriction enzyme motif, His253 is positioned to act as a general base. CONCLUSIONS: A catalytic mechanism employing His253 and two metal ions is proposed. If confirmed, this would be the first example of histidine-mediated catalysis in a restriction endonuclease. The structure also provides two novel examples of the role of water in protein-DNA interaction. Degenerate recognition may be mediated by employing water as a hydrogen bond donor or acceptor. The structure of DNA in the tunnel may also be influenced by the absence of bulk solvent.

Catalysis↗

PubMed2000

Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.

BACKGROUND: Formation of isoaspartyl residues is one of several processes that damage proteins as they age. Protein L-isoaspartate (D-aspartate) O-methyltransferase (PIMT) is a conserved and nearly ubiquitous enzyme that catalyzes the repair of proteins damaged by isoaspartyl formation. RESULTS: We have determined the first structure of a PIMT from crystals of the T. maritima enzyme complexed to S-adenosyl-L-homocysteine (AdoHcy) and refined it to 1.8 A resolution. Although PIMT forms one structural unit, the protein can be divided functionally into three subdomains. The central subdomain closely resembles other S-adenosyl-L-methionine-dependent methyltransferases but bears a striking alteration of topological connectivity, which is not shared by any other member of this family. Rather than arranged as a mixed beta sheet with topology 6 upward arrow7 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow, the central sheet of PIMT is reorganized to 7 upward arrow6 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow. AdoHcy is largely buried between the N-terminal and central subdomains by a conserved and largely hydrophobic loop on one rim of the binding cleft, and a conserved Ser/Thr-rich beta strand on the other. The Ser/Thr-rich strand may provide hydrogen bonds for specific interactions with isoaspartyl substrates. The side chain of Ile-206, a conserved residue, crosses the cleft, restricting access to the donor methyl group to a deep well, the putative isoaspartyl methyl acceptor site. CONCLUSIONS: The structure of PIMT reveals a unique modification of the methyltransferase fold along with a site for specific recognition of isoaspartyl substrates. The sequence conservation among PIMTs suggests that the current structure should prove a reliable model for understanding the repair of isoaspartyl damage in all organisms.

Amino Acid Sequence↗

PubMed1996

Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability.

The X-ray crystal structure of the oxidized form of the extremely stable and highly oxidizing cupredoxin rusticyanin from Thiobacillus ferrooxidans has been determined by the method of multiwavelength anomalous diffraction (MAD) and refined to 1.9 A resolution. Like other cupredoxins, rusticyanin is a copper-containing metalloprotein, which is composed of a core beta-sandwich fold. In rusticyanin the beta-sandwich is composed of a six- and a seven-stranded beta-sheet. Also like other cupredoxins, the copper ion is coordinated by a cluster of four conserved residues (His85, Cys138, His143, Met148) arranged in a distorted tetrahedron. Rusticyanin has a redox potential of 680 mV, roughly twice that of any other cupredoxin, and it is optimally active at pH values < or = 2. By comparison with other cupredoxins, the three-dimensional structure of rusticyanin reveals several possible sources of the chemical differences, including more ordered secondary structure and more intersheet connectivity than other cupredoxins. The acid stability and redox potential of rusticyanin may also be enhanced over other cupredoxins by a more extensive internal hydrogen bonding network and by more extensive hydrophobic interactions surrounding the copper binding site. Finally, reduction in the number of charged residues surrounding the active site may also make a major contribution to acid stability. We propose that the resulting rigid copper binding site, which is constrained by the surrounding hydrophobic environment, structurally and electronically favours Cu(I). We propose that the two extreme chemical properties of rusticyanin are interrelated; the same unique structural features that enhance acid stability also lead to elevated redox potential.

Azurin↗

PubMed1995

Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA.

The single-stranded DNA (ssDNA) binding protein gp32 from bacteriophage T4 is essential for T4 DNA replication, recombination and repair. In vivo gp32 binds ssDNA as the replication fork advances and stimulates replisome processivity and accuracy by a factor of several hundred. Gp32 binding affects nearly every major aspect of DNA metabolism. Among its important functions are: (1) configuring ssDNA templates for efficient use by the replisome including DNA polymerase; (2) melting out adventitious secondary structures; (3) protecting exposed ssDNA from nucleases; and (4) facilitating homologous recombination by binding ssDNA during strand displacement. We have determined the crystal structure of the gp32 DNA binding domain complexed to ssDNA at 2.2 A resolution. The ssDNA binding cleft comprises regions from three structural subdomains and includes a positively charged surface that runs parallel to a series of hydrophobic pockets formed by clusters of aromatic side chains. Although only weak electron density is seen for the ssDNA, it indicates that the phosphate backbone contacts an electropositive cleft of the protein, placing the bases in contact with the hydrophobic pockets. The DNA mobility implied by the weak electron density may reflect the role of gp32 as a sequence-independent ssDNA chaperone allowing the largely unstructured ssDNA to slide freely through the cleft.

Amino Acid Sequence↗

PubMed1995

Crystal structure of lac repressor core tetramer and its implications for DNA looping.

The crystal structure of the tryptic core fragment of the lac repressor of Escherichia coli (LacR) complexed with the inducer isopropyl-beta-D-thiogalactoside was determined at 2.6 A resolution. The quaternary structure consists of two dyad-symmetric dimers that are nearly parallel to each other. This structure places all four DNA binding domains of intact LacR on the same side of the tetramer, and results in a deep, V-shaped cleft between the two dimers. Each monomer contributes a carboxyl-terminal helix to an antiparallel four-helix bundle that functions as a tetramerization domain. Some of the side chains whose mutation reduce DNA binding form clusters on a surface near the amino terminus. Placing the structure of the DNA binding domain complexed with operator previously determined by nuclear magnetic resonance onto this surface results in two operators being adjacent and nearly parallel to each other. Structural considerations suggest that the two dimers of LacR may flexibly alter their relative orientation in order to bind to the known varied spacings between two operators.

Crystallography, X-Ray↗

PubMed1994

Monoclonal, antigen-specific, T cell contrasuppressor factor expresses determinants of TCR alpha-chain (not necessarily TCR beta-chain), having a molecular mass of about 40 kDa.

Contrasuppression is a regulatory T cell activity that acts on helper and contact sensitivity effector T cells to protect them from the action of suppressor T cells. In this study, we examined a monoclonal Ag-specific T cell-secreted contrasuppressor factor (TcsF) with Ag specificity for the hapten TNP (trinitrophenyl). This factor positively influences the adoptive cell transfer of contact sensitivity in the presence of active suppression. Results presented in this report demonstrate a relationship between TcsF and the alpha,beta-T cell receptor (TCR). We found that TcsF bound to mAb anti-TCR-alpha (H28) and to mAb anti-TCR-beta (H57) immunoaffinity columns, but not to a mAb anti-TCR-gamma,delta (UC7) column. The bound contrasuppressor activity could be recovered from these affinity columns by base elution. Reduction of TcsF with DTT followed by alkylation with methylmethanethiosulfonate (MMTS), demonstrated that the active subunit of TcsF bound to and eluted from anti-TCR-alpha, but not to anti-TCR-beta columns. The active TcsF that bound to anti-TCR-alpha but not to the anti-TCR-beta column was shown subsequently to have the ability to bind to specific Ag columns TNP-BSA and TNP-BGG Sepharose 4B. The TcsF could be successfully recovered later from Ag columns; thus suggesting that the Ag-binding domain for mAb, and the biologic activity, resides on the TCR-alpha chain of TcsF. Separation of TcsF on SDS-PAGE under reducing conditions, followed by elution and renaturation of proteins from the gel slices, showed that a 35 to 40 kDa protein had the T cell contrasuppressive activity. Western blot analysis of nonreduced TNP-binding TcsF revealed TCR-alpha,beta determinants on an 80-kDa native molecule similar to TCR-alpha,beta from a helper T cell clone. In summary, Ag-specific, Ag-binding T cell-derived contrasuppressor factor has serologic determinants of TCR-alpha and TCR-beta chains, but the TCR-alpha chain and not the TCR-beta chain is required for biologic function. This TCR-alpha determinant-containing factor is absorbed by specific Ag (TNP) columns. SDS-PAGE analysis under reducing conditions suggested a molecular weight of about 35 to 40 kDa for the TNP-specific TcsF. The mechanism of action of the TCR-alpha-containing contrasuppressor factor in the regulation contact sensitivity is discussed.

Animals↗

PubMed1994

Thyrotropin-releasing hormone receptor activation does not elevate intracellular cyclic adenosine 3',5'-monophosphate in cells expressing high levels of receptors.

Activation of TRH receptors (TRH-R) stimulates a signal transduction pathway that leads to the formation of two second messenger molecules, inositol 1,4,5-trisphosphate and 1,2-diacylglycerol. It has been suggested that TRH may also cause an elevation of another second messenger, cAMP. As adenovirus-mediated gene transfer allows expression of TRH-R to high levels in a number of cell types, we tested again whether TRH-R activation might elevate intracellular cAMP in these more sensitive cell systems. In five cell lines, including three human lines, infection with a replication defective adenovirus that encodes the mouse TRH-R complementary DNA (AdCMVmTRHR) induced the expression of 0.2-2 million TRH-R/cell. AdCMVmTRHR-infected cells were activated by a maximally effective dose of TRH, and the levels of inositol phosphates and cAMP were measured. TRH stimulated the production of inositol phosphates from 5- to 9-fold in all cell types, but did not elevate cAMP in any cell type. These data confirm that TRH-R activation does not lead to an elevation of intracellular cAMP.

Adenoviridae↗

PubMed1994

Generation of anti-hapten T cell cytotoxicity in vivo. Relationship to contact sensitivity and the role of contrasuppression.

Immunization procedures that induce contact sensitivity to the trinitrophenyl (TNP) hapten in vivo were investigated for their ability to induce TNP-specific cytotoxic T lymphocytes in vivo. Spleen cells from C3H/HeN mice primed for CS responses either by the topical application of picryl chloride or by the adoptive transfer of PCL immune cells show little or no cytolytic activity in vitro against TNP-coupled target cells. Intravenous immunization with TNP-substituted syngeneic spleen cells, a procedure known to make animals unresponsive to agents normally inducing CS, also failed to induce cytolytic activity in spleen cells. However, both PCL sensitization and adoptive transfer, when combined with the injection of TNP-substituted syngeneic spleen cells, induce significant cytolytic activity against TNP-haptenated BW5147 target cells in vitro. Furthermore, i.v. injection of TNP-spleen cells with surface-bound immune complexes of the IgM or IgG1 isotypes, or with a monoclonal TNP-specific contrasuppressor T cell factor also induces strong antigen-specific cytolytic activity against TNP modified targets. TcsF bears serological determinants of T cell receptor alpha and beta chains and adheres to specific antigen columns. All these immunization regimens were shown to induce CS to TNP as well as the generation of contrasuppressor T cells. The CTL generated in the spleens of immunized mice are Thy1+ CD8+ T cells an are antigen-specific and genetically restricted. The implications of these results with respect to the mechanisms by which cytolytic responses are controlled in vivo is discussed.

Animals↗

PubMed1991

Production of no carrier added 80mBr for investigation of Auger electron toxicity.

80mBr (half-life = 4.43 h) is an Auger electron emitting nuclide with convenient properties for investigating Auger electron cytotoxicity and with potential for labeling in vivo radiotherapeutic agents. We have investigated three cyclotron target systems capable of generating 80mBr of sufficiently high specific radioactivity (no carrier added) for biomedical experiments. A 83Kr gas target irradiated with 21.5 MeV deuterons made 80mBr at a production yield of 1.6 +/- 0.2 mCi/muAh at saturation. A five-fold increase in 80mBr yield was obtained from 15 MeV proton irradiation of thin elemental Se enriched in 80Se targets although technical improvements are expected to further raise this production yield. This route is therefore superior for current medical cyclotrons. Irradiation of a reusable 80Se copper selenide target also yielded multi-millicurie amounts of 80mBr, and recovery of radiobromine by dry distillation is faster and more convenient than in the elemental Se target, but an optimum copper selenide target for 80mBr production has not yet been built.

Bromine Radioisotopes↗

PubMed1990

Generation of a T-cell hybridoma producing a contrasuppressor factor for contact sensitivity.

C3H/HeN mice were immunized to induce contrasuppressor T-cell (Tcs) activity, splenic T cells from these mice were fused with the BW5147 thymoma, and the resulting hybridomas were tested for their ability to produce a contrasuppressor T-cell factor (TcsF). Nine TcsF-producing hybridomas were preliminarily identified by their ability to inhibit the effect of antigen-specific suppressor T-cell factor (TsF) on the adoptive transfer of contact sensitivity. One of these hybrids, AF5.C6, was cloned, the production of a contrasuppressor factor confirmed, and the high-titred TcsF produced by this cloned hybrid characterized. Hybridoma-derived TcsF is antigen-specific and specifically binds its antigen, but does not bear immunoglobulin (Ig) determinants. Thus, hybridoma-derived TcsF is serologically and functionally identical to an antigen-specific contrasuppressor factor for contact sensitivity, whose production from splenocyte cell cultures has previously been described. The generation of a hybridoma secreting a contrasuppressor factor identical to that produced by spleen cells significantly strengthens the hypothesis that the phenomenon of T-cell contrasuppression is mediated by a specific subset of cells whose activity is contrasuppressive. The further advantages of employing T-cell hybridomas for functional, biochemical and molecular genetic analyses of contrasuppression are also discussed.

Animals↗

PubMed1990

[Psychotherapy of depression].

The combination of psychopharmacology and psychotherapy produced the best results in the treatment of depression. These two modalities can be used simultaneously or alternatively. Three forms of psychotherapy are most widely used and effective in depressed patients: interpersonal therapy, cognitive therapy and behavioural therapy.

Cognitive Behavioral Therapy↗

PubMed1989

Evaluation of positron-emitting SCH 23390 analogs as tracers for CNS dopamine D1 receptors.

Two positron-emitting analogs of SCH 23390, one labelled with 75Br (or 76Br) and another with 11C, were evaluated as potential PET tracers for central dopamine D1 receptors. In vivo studies were performed to assess the time course of the biodistribution of these tracers in mice and to determine whether dopamine receptors mediated their uptake in the brains of these animals. Results show that indeed cerebral uptake was consistent with dopamine receptor innervation, i.e. uptake and clearance was regionally consistent with the target receptors and that specific uptake was saturable. Because of the relatively rapid pharmacokinetics of this drug, 11C-labelled SCH 23390 would be best suited for PET imaging although the metabolism of this compound needs to be further examined.

Animals↗

PubMed1989

Prevention of tumor growth and enhancement of cell-mediated immunity by an antigen-specific contrasuppressor factor from a T cell hybridoma.

We have produced a contrasuppressor T cell hybridoma which has positive effects on multiple forms of cell-mediated immunity. First of all, it protects the adoptive transfer of contact sensitivity from suppressor cells and factors. In addition, TcsF modifies the response to normally tolerogenic administrations of hapten, leading mice to develop contact sensitivity and CTL activity instead of tolerance. Most relevant to this conference, mice which have been both treated with AF5.C6 TcsF and painted with TNCB resist challenge with highly malignant TNP-modified tumors. These experiments suggest a decisive role for contrasuppression in tumor rejection.

Animals↗

PubMed1988

212Bismuth linked to an antipancreatic carcinoma antibody: model for alpha-particle-emitter radioimmunotherapy.

For comparison of cytotoxicity from alpha-particle irradiation with that from conventional x-irradiation, 212Bi, an alpha-emitting radionuclide, was attached to a monoclonal antibody that recognizes a cell surface antigen on human pancreatic carcinoma cells. For a given level of survival, the 212Bi-antibody complex was found to be approximately 20 times more efficient in cell killing than x-irradiation and 5 times more cytotoxic when compared with the cytotoxicity of an antigen-negative cell line or an isotype-matched control antibody. High linear energy transfer radioimmunotherapy using alpha emitters linked to monoclonal antibodies may be useful in vivo and in vitro for selectively killing target cell populations, especially those resistant to other forms of treatment.

Antibodies, Monoclonal↗

PubMed1988

Bromine-80m-labeled estrogens: Auger electron-emitting, estrogen receptor-directed ligands with potential for therapy of estrogen receptor-positive cancers.

To assess their possible use for estrogen receptor (ER)-directed radiotherapy of estrogen receptor-containing cancers, two estrogens were synthesized with the Auger electron-emitting nuclide bromine-80m and administered to immature female rats. Both the triphenylethylene-based estrogen, [80mBr]-2-bromo-1,1-bis(4-hydroxyphenyl)phenylethylene (Br-BHPE) and the steroidal estrogen [80mBr]17 alpha-bromovinylestradiol, showed substantial diethylstilbestrol-inhibitable localization only in the estrogen target tissues, the uterus, pituitary, ovaries, and vagina and, except for the liver and intestines, generally lower concentrations in all other tissues at both 0.5 and 2 h. The [80mBr]Br-BHPE (specific activity, 8700 Ci/mmol), was shown to bind specifically to the low salt extractable ER of the rat uterus. Comparing i.p., i.v., and s.c. administration of [80mBr]BHPE the i.p. route was found to be particularly advantageous to effect maximum, DES-inhibitable concentrations of radiobromine in the ER-rich target organs in the peritoneal cavity. When the tissue distribution of the [80mBr]Br-BHPE was compared with that of sodium bromide-80m, it was apparent that no substantial amounts of radiobromine were released from the bromoestrogen prior to its target tissue localization. The substantial concentration of these bromine-80m-labeled estrogens in ER-rich tissues, combined with previously reported evidence for the effective radiotoxicity of Auger electron-emitting nuclides within cell nuclei suggest a good potential for such ligands for therapy of ER positive cancers.

Animals↗

PubMed1988

An improved generator for the production of 212Pb and 212Bi from 224Ra.

We have developed an improved generator for the production of the alpha emitting radionuclide 212Bi and its parent, 212Pb. These radionuclides are well suited to use as radiotherapeutic agents due to their relatively short half lives and appropriate particle particle emissions. The parent, 224Ra, is available from a long-lived parent and can be isolated on a generator which produces the daughters in good yield and low breakthrough. The 212Bi can be eluted by itself or in equilibrium with its parent.

Bismuth↗

PubMed1988

Production of 75Br via the 78Kr (d,n alpha)75Br reaction.

The production of 75Br by the 78Kr (d,n alpha)75Br reaction using a 21.5 MeV deuteron beam was investigated. With our 78Kr gas target, the production yield was found to be 5.9 +/- 0.9 mCi/microA at saturation. The major impurities in the 75Br product were 76Br and 77Br which amounted to about 6 and 2.5% respectively, at EOB. Sufficient amounts of 75Br could easily be prepared by this method for use in chemistry and animal experiments but deuteron energies greater than 20 MeV are required.

Bromine Radioisotopes↗