PubMed Health⌕ Search

Biomedical subjects

S L Brenner

Publications and source records attributed to S L Brenner.

At least 19 recordsLinked to original sources
PubMed1993

Multiple oligomeric states regulate the DNA binding of helix-loop-helix peptides.

To study the protein-protein interactions that allow Id, a negative regulator of cell differentiation, to inhibit the DNA-binding activities of MyoD and E47, we have synthesized peptides corresponding to the helix-loop-helix domains of MyoD, E47, and Id. We show that Id preferentially inhibits the sequence-specific DNA-binding activity of MyoD, a muscle-specific protein, as compared to E47, a more ubiquitous protein. The Id helix-loop-helix domain itself forms stable tetramers, and its inhibitory activity arises from the formation of a heterotetrameric structure with MyoD. The formation of this higher order complex provides a general mechanism by which inhibitory proteins can generate sufficient interaction free energy to overcome the large DNA-binding free energy of dimeric DNA-binding proteins.

Amino Acid Sequence↗
PubMed1993

Analysis of two distinct single-stranded DNA binding sites on the recA nucleoprotein filament.

The binding stoichiometry of Escherichia coli recA protein to single-stranded DNA (ssDNA) determined by two separate assays differs by a factor of 2.2-2.4. Using the fluorescence of etheno-DNA (epsilon DNA), a chemically modified ssDNA, the stoichiometry was found to be 7.0 +/- 0.6 bases/recA protein monomer in a nucleo-protein filament. Using a competition assay, a similar stoichiometry, 7.5 bases/recA, is found for unmodified poly(dT). Using the DNA-dependent ATPase of recA, which monitors bound protein rather than bound DNA, we find that each recA monomer needs to bind only 3.1 +/- 0.5 bases to fully activate the ATPase. The difference in site size determined by the two assays indicates that there are two DNA binding sites with differential effects on ATPase activation. When recA protein is mixed with ssDNA at a ratio of 7 bases/recA or greater, the complex that forms contains 7 bases/recA and acts as a kinetic trap for the ssDNA. Upon further addition of recA protein, no additional ATPase activity is observed. If, on the other hand, the ssDNA is initially mixed with excess recA (at a ratio of 3-3.5 bases/recA or less) the ATPase activity is twice as high. Analysis of the binding curves suggests that the first DNA strand binds recA to form a filament with a stoichiometry of 3-3.5 bases/protein monomer. The ATPase activity of recA is completely active in this complex. A second strand of DNA can then be bound to this filament yielding a final stoichiometry of approximately 7 bases/protein monomer. The presence of this second strand neither enhances nor inhibits ATP hydrolysis. This ternary complex may mimic the structures formed by recA in searching for homologous DNA sequences and/or in the strand exchange reaction.

Adenosine Triphosphatases↗
PubMed1992

Molecular characterization of helix-loop-helix peptides.

A class of regulators of eukaryotic gene expression contains a conserved amino acid sequence responsible for protein oligomerization and binding to DNA. This structure consists of an arginine- and lysine-rich basic region followed by a helix-loop-helix motif, which together mediate specific binding to DNA. Peptides were prepared that span this motif in the MyoD protein; in solution, they formed alpha-helical dimers and tetramers. They bound to DNA as dimers and their alpha-helical content increased on binding. Parallel and antiparallel four-helix models of the DNA-bound dimer were constructed. Peptides containing disulfide bonds were engineered to test the correctness of the two models. A disulfide that is compatible with the parallel model promotes specific interaction with DNA, whereas a disulfide compatible with the antiparallel model abolishes specific binding. Electron paramagnetic resonance (EPR) measurements of nitroxide-labeled peptides provided intersubunit distance measurements that also supported the parallel model.

Amino Acid Sequence↗
PubMed1991

Arthroscopic treatment of degenerative joint disease of the knee.

The role of arthroscopy in the management of degenerative conditions of the knee continues to evolve. This study was undertaken to: (1) assess the efficacy of arthroscopic treatment, (2) identify significant prognostic factors, and (3) further define the indications for treatment. A retrospective review of charts and operative videotapes along with follow-up evaluation was obtained for 43 knees in 40 patients. Average age was 54 years. Average follow up was 24 months; 72.1% of patients had good results at follow up, 16.3% had fair results, and 11.6% were treatment failures. Preoperative clinical status, severity of degenerative changes, and number of pathologic entities encountered at the time of surgery correlated with the results of treatment. We believe that arthroscopic debridement is an effective means of treatment for mild to moderate degenerative joint disease after failure of conservative measures. By using this treatment option, more extensive surgical procedures may be delayed or avoided.

Arthritis, Rheumatoid↗
PubMed1990

RecA protein self-assembly. II. Analytical equilibrium ultracentrifugation studies of the entropy-driven self-association of RecA.

We have investigated the self-association of RecA protein from Escherichia coli by equilibrium ultracentrifugation. Monomeric RecA (Mr = 37,842) was observed in reversible equilibrium with trimers, hexamers and dodecamers in the presence of 1.5 M-KCl, 5 mM-Hepes, 1 mM-EDTA, 2 mM-ATP (pH 7.0) at 1 degrees C. The equilibrium was strongly temperature-dependent, with polymerization being favored as the temperature was raised from 1 degrees C 21 degrees C, and was reversible with respect to temperature. The values of both the standard enthalpy and entropy of self-association were positive, indicating that it is an entropy-driven process under these conditions. In the absence of KCl, in 50 mM-citrate, 5 mM-ATP, 5% (v/v) glycerol (pH 6.0) at 4 degrees C, only small amounts of RecA monomer could be detected, while in 10 mM-Tris-acetate, 10% glycerol (pH 7.5) at 4 degrees C, the smallest species present in significant concentration appeared to be the trimer. The majority of the species observed had molecular weights between 228,000 and 456,000, suggesting dominant stoichiometries of six to 12 monomers per oligomer. At pH 6.0, in the absence of ATP, much larger oligomers containing at least 24 monomers also appeared to be present. The data are consistent with an equilibrium mixture of monomers, trimers, hexamers, dodecamers, 24-mers and higher oligomers, with the distribution of oligomers being dependent on solution conditions. Thermodynamic analysis indicates that these oligomeric species are in reversible equilibrium with each other. It is not certain whether trimers assemble directly into hexamers, or whether disassembly into monomers is a prerequisite for the formation of higher oligomers. The possible role of higher-order RecA oligomers in the formation of RecA nucleoprotein filaments is discussed.

Adenosine Triphosphate↗
PubMed1990

recA protein filaments bind two molecules of single-stranded DNA with off rates regulated by nucleotide cofactor.

To probe the role of nucleotide cofactor in the binding of single-stranded DNA to recA protein, we have developed a sedimentation assay using 5'-labeled 32P-poly(dT).recA.poly(dT) complexes sediment quantitatively when centrifuged at 100,000 x g for 45 min, whereas free poly(dT) remains in the supernatant. In the presence of ATP, between 6 and 7 bases cosediment per recA monomer; but when ADP is present or in the absence of added nucleotide cofactor, only 3-3.5 bases/recA monomer cosediment. In competition experiments in which recA.32P-poly(dT) complexes are incubated with unlabeled poly(dT), we again find 3-3.5 bases of labeled poly(dT) cosedimenting per recA monomer when no nucleotide cofactor is present. However, when the same experiment is performed with ATP, only half of the expected 6-7 bases of labeled poly(dT) remain bound to the DNA, demonstrating that half of the poly(dT) in the complex exchanges rapidly with free poly(dT), whereas the other half equilibrates slowly, like poly(dT) in the absence of nucleotide. The rate of exchange of the second more tightly bound poly(dT) is accelerated when ADP is present. Our observations are rationalized by a model in which each recA protein helical filament binds two strands of poly(dT) with a stoichiometry of 3-3.5 bases/recA monomer/strand.

Adenosine Diphosphate↗
PubMed1989

An alpha-helical peptide model for electrostatic interactions of proteins with DNA. The N terminus of RecA.

A series of synthetic peptides have been studied as models for non-specific protein-DNA interactions. In an alpha-helical conformation, the charged amino acid residues of the N-terminal 24 residues of RecA protein are asymmetrically distributed; at neutral pH there is a +4 charge on one face of the helix and a -3 charge on the other face. Modeling suggests that the positive face of the helix can bind five DNA phosphate groups by electrostatic interactions. Circular dichroism (c.d.) spectra indicate that the analogous peptide, Rec24 (AIDENKQKALAAALGQIEKQFGKG-amide), is largely unstructured in water but becomes highly helical in the presence of DNA. Peptide titrations of fluorescent etheno-DNA confirm that the changes in the c.d. spectrum of the peptide are associated with binding, although a dependence of the c.d. signal on the degree of DNA saturation is observed, indicating that peptide can be bound in more than one conformation. At saturation the peptide binds to 5.0(+/- 0.5) DNA phosphate groups as predicted and the electrostatic nature of the binding is confirmed by a strong dependence on salt concentration. A "mutant" peptide where an acidic glutamate residue replaces an alanine on the basic face of the Rec24 helix exhibits weaker binding to single-stranded DNA, also consistent with the electrostatic nature of the proposed peptide-DNA interaction. Extending Rec24 by ten amino acid residues, where the additional residues do not participate in the helical motif, does not noticeably affect binding. Thus, we show experimentally that an asymmetric charge distribution on an alpha-helix can represent an important element for binding nucleic acids.

Alanine↗
PubMed1989

Race and the shaken baby syndrome: experience at one hospital.

At Children's Hospital of Michigan there seemed to be a disproportionate number of white infants with shaken baby syndrome (SBS) relative to the proportion of white infants in our physically abused population. All reports of suspected child abuse on children less than or equal to 18 months from Children's Hospital from 1980-1985 were reviewed. The total number of abused children 18 months or younger was 545 (447 black, 87 white, 1 unknown). There were 20 children in the SBS group. Eight of 87 (9%) of white abused infants had SBS compared with 12 of 447 (2.7%) of black abused infants. The occurrence of SBS in white abused infants was disproportionately higher than in blacks. This finding has not been previously reported. Before generalizations can be made, additional data must be obtained.

Black or African American↗
PubMed1988

RecA protein self-assembly. Multiple discrete aggregation states.

Light scattering, sedimentation and electron microscopy have been used to investigate the aggregation states of highly purified RecA protein in solution. We show that RecA protein will self-assemble into a discrete series of quaternary structures depending upon protein concentration, ionic environment, and nucleotide cofactors. In a stock solution at moderate concentration (10 to 50 microM) RecA protein exists as small particles approximately 4 nm in diameter, larger particles approximately 12 nm in diameter (most probably rings of RecA protein), 10 nm diameter rods varying from 50 to 200 nm in length, and finally as much larger bundles of rods. The addition of monovalent salt shifts the distribution of RecA protein between its various oligomeric states. Increasing protein concentration favors more highly aggregated structures. At a given protein concentration, addition of mM levels of MgCl2 promotes the rapid formation of rods and slow formation of bundles. Under conditions typical of in vitro strand exchange reactions, RecA protein was found to exist as a mixture of rods and 12 nm particles with relatively few monomers.

Adenosine Triphosphate↗
PubMed1987

recA protein-promoted ATP hydrolysis occurs throughout recA nucleoprotein filaments.

When recA protein binds cooperatively to single-stranded DNA to form filamentous nucleoprotein complexes, it becomes competent to hydrolyze ATP. No correlation exists between the ends of such complexes and the rate of ATP hydrolysis. ATP hydrolysis is not, therefore, restricted to the terminal subunits on cooperatively bound recA oligomers, but occurs throughout the complex. Similarly, during recA protein-promoted branch migration (during DNA strand exchange), ATP hydrolysis is not restricted to recA protein monomers at the branch point. DNA cofactors of lengths varying from 16 bases to over 12,000 bases support ATP hydrolysis. The maximum value of kcat at infinite DNA concentration is about 29/min independent of the length of the DNA cofactor. The apparent dissociation constant, however, is a strong function of DNA length, providing evidence for a minimum site size of 30-50 bases for efficient binding of recA protein.

Adenosine Triphosphatases↗
PubMed1987

Inhibition of actin polymerization by latrunculin A.

Latrunculin A, a toxin purified from the red sea sponge Latrunculia magnifica, was found previously to induce striking reversible changes in the morphology of mammalian cells in culture and to disrupt the organization of their microfilaments. We now provide evidence that latrunculin A affects the polymerization of pure actin in vitro in a manner consistent with the formation of a 1:1 molar complex between latrunculin A and G-actin. The equilibrium dissociation constant (Kd) for the reaction in vitro is about 0.2 microM whereas the effects of the drug on cultured cells are detectable at concentrations in the medium of 0.1-1 microM.

Actins↗
PubMed1986

Arrangements of kinetochores in mouse cells during meiosis and spermiogenesis.

Antibodies from the serum of patients with the autoimmune disease scleroderma CREST were used to investigate the association and distribution of kinetochores in mouse cells during meiosis and spermiogenesis. The pattern of indirect immunofluorescent staining in pachytene nuclei indicated that each autosomal bivalent contains one fluorescent spot. Throughout pachytene, the kinetochores were arranged non-randomly into several clusters and distributed around the periphery of the nucleus. In subsequent stages of meiotic prophase I, distribution was random and the number of fluorescent spots increased from 21 to 40 corresponding to the diploid chromosome number and the number of halfbivalents oriented to the spindle poles at the metaphase I. Twenty pairs of kinetochores were observed at metaphase II. During spermiogenesis, the number of kinetochores correlated with the haploid chromosome number in early spermatids but tandem association of centromeres and clustering into a conspicuous chromocenter corresponded to a significant reduction in the number of fluorescent foci in mid-spermatid nuclei. The number of stained sites per nucleus continued to decrease during sperm maturation and total absence of staining was apparent in mature spermatozoa. Immunoblotting of proteins extracted from mature sperm however, indicated that a kinetochore antigen of Mr 80,000 was still present. Therefore, the absence of kinetochore staining in mature spermatozoa is probably due to the blockage of epitopes during chromatin condensation.

Animals↗
PubMed1985

The amino acid sequence of Acanthamoeba profilin.

The complete amino acid sequence of Acanthamoeba profilin was determined by aligning tryptic, chymotryptic, thermolysin, and Staphylococcus aureus V8 protease peptides together with the partial NH2-terminal sequences of the tryptophan-cleavage products. Acanthamoeba profilin contains 125 amino acid residues, is NH2-terminally blocked, and has trimethyllysine at position 103. At five positions in the sequence two amino acids were identified indicating that the amoebae express at least two slightly different profilins. Charged residues are unevenly distributed, the NH2-terminal half being very hydrophobic and the COOH-terminal half being especially rich in basic residues. Comparison of the Acanthamoeba profilin sequence with that of calf spleen profilin (Nystrom, L. E., Lindberg, U., Kendrick-Jones, J., and Jakes, R. (1979) FEBS Lett. 101, 161-165) reveals homology in the NH2-terminal region. We suggest, therefore, that this region participates in the actin-binding activity.

Amino Acid Sequence↗
PubMed1984

Preparation and polymerization of skeletal muscle ADP-actin.

Skeletal muscle ADP-G-actin was prepared from ADP-F-actin, which had been freed of residual ATP by repeated sonication, by depolymerization in 5 mM Tris-HCl, 0.2 mM ADP, 0.2 mM dithiothreitol, 0.1 mM CaCl2, 0.1 mM MgCl2, and 0.01% NaN3, pH 8.0. The ADP had been freed of traces of ATP by DEAE-chromatography, and 5 microM diadenosine pentaphosphate was added to inhibit myokinase activity. The kinetics of the spontaneous polymerization of ADP-actin in 1 mM MgCl2 + 0.1 M KCl were compatible with the simple nucleation-elongation model previously used to explain the polymerization of ATP-actin. The critical concentrations of ADP-actin were 8.0 and 2.0 microM in 1 mM MgCl2 and 1 mM MgCl2 + 0.1 M KCl, respectively. These values are 20-30-fold higher than the corresponding values in ATP. Using cross-linked actin trimers to nucleate polymerization, the association rate constants were found to be 0.8 and 0.9 microM-1 S-1 in MgCl2 and MgCl2 + KCl, respectively, which are 0.4 and 0.2 times the values for ATP-actin. The dissociation rate constants, calculated from the critical concentrations and the association rate constants, were 6.4 and 1.8 S-1, respectively, which are 10 and 5 times the corresponding values for ATP-actin.

Actins↗
PubMed1984

Rate constants for actin polymerization in ATP determined using cross-linked actin trimers as nuclei.

Chemically cross-linked actin trimer, prepared from F-actin covalently cross-linked by N-N'-p-phenylenebismaleimide, was used to nucleate the assembly of actin polymers under a variety of ionic conditions at 25 degrees C. Gel-filtered G-actin (5% labeled with N-pyrenyl iodoacetamide) was prepared in buffers containing 5 mM Tris X HCl, 0.2 mM ATP, 0.05 mM MgCl2 or 0.1 mM CaCl2, 0.2 mM dithiothreitol, and 0.01% sodium azide, pH 7.5. Polymerization was initiated by adding salt to a solution of actin monomer (2-25 microM) mixed with actin trimer (0-24 nM). Pseudo-first-order polymerization kinetics were observed in all cases following a lag phase of 30-75 s. The length of the lag phase was independent of trimer concentration, monomer concentration, or preincubation of monomer or trimer in polymerizing buffer. A simple model is presented which explains all of the observed features of the lag phase. Lower limits for the sums of the elongation rate constants at the two filament ends, calculated assuming each trimer acts as a seed, were in the range 1.4-5.2 microM-1 s-1, and lower limits for the polymer dissociation rate constants (calculated from the elongation rate constants and the critical actin concentration) were 0.4-1.9 s-1, depending on ionic conditions. The observed rate constants were independent of actin concentration or trimer concentration under a given ionic condition. These polymerization rate constants are in good agreement with the values others have obtained by measuring the growth of actin filaments by electron microscopy.

Actins↗
PubMed1984

The critical concentration of actin in the presence of ATP increases with the number concentration of filaments and approaches the critical concentration of actin.ADP.

F-actin at steady state in the presence of ATP partially depolymerized to a new steady state upon mechanical fragmentation. The increase in critical concentration with the number concentration of filaments has been quantitatively studied. The data can be explained by a model in which the preferred pathway for actin association-dissociation reactions at steady state in the presence of ATP involves binding of G-actin . ATP to filaments, ATP hydrolysis, and dissociation of G-actin . ADP which is then slowly converted to G-actin . ATP. As a consequence of the slow exchange of nucleotide on G-actin, the respective amounts of G-actin . ATP and G-actin . ADP coexisting with F-actin at steady state depend on the filament number concentration. G-actin coexisting with F-actin at zero number concentration of filaments would then consist of G-actin . ATP only, while the critical concentration obtained at infinite number of filaments would be that for G-actin . ADP. Values of 0.35 and 8 microM, respectively, were found for these two extreme critical concentrations for skeletal muscle actin at 20 degrees C, pH 7.8, 0.1 mM CaCl2, 1 mM MgCl2, and 0.2 mM ATP. The same value of 8 microM was directly measured for the critical concentration of G-actin . ADP polymerized in the presence of ADP and absence of ATP, and it was unaffected by fragmentation. These results have important implications for experiments in which critical concentrations are compared under conditions that change the filament number concentrations.

Actins↗