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At least 19 recordsLinked to original sources
PubMedDate not supplied

[Protein factor from regenerating rat liver destabilizing secondary DNA structure].

In DNA preparations isolated from regenerating rat liver 22 hours after partial hepatectomy, i.e. at the period of the most intensive DNA synthesis a "Denaturating Protein Factor" (DPF) tightly bound to DNA was found. Isolated protein fraction with a molecular weight of 6500 dalton was found to be homogenous upon SDS-polyacrylamide electrophoresis. The degree of destabilisation of DNA was estimated by its reaction with water-soluble [14C]CME-carbodiimide which modifies selectively guanine and thymine residues only in the denatured DNA regions. Pronase treated DPF loses its DNA-denaturing capacity. Pronase treatment of DNA--DPF complex restores native DNA structure. DPF from rat liver was able to denature DNA from calf thymus and bacteriophage T7 DNA. A hypothesis is proposed that the DPF is responsible for the destabilization of DNA secondary structure in the process of replication.

Animals↗
PubMed1992

Carbodiimide modification reduces the conductance and increases the tetrodotoxin sensitivity in batrachotoxin-modified sodium channels.

The relationship between the channel entrance and the tetrodotoxin (TTX) binding site was investigated by chemical modification at the extracellular surface of bilayer-incorporated batrachotoxin-(BTX) modified sodium channels using an impermeant carbodiimide in the presence or absence of exogenous nucleophiles. Two (classes of) groups could be modified such that the open-channel conductance was decreased while TTX binding was unaffected, and TTX did not protect against this modification. Because the final conductance level depends on the exogenous nucleophile, each covalent modification appears to involve a carboxyl group. In addition, a third (carboxyl) group could be modified such that TTX binding affinity was increased. These results suggest that the channel entrance and the TTX binding site are spatially separate, which supports previous suggestions that the mechanism by which guanidinium toxins close sodium channels involves a conformational change subsequent to toxin binding.

Animals↗
PubMed1986

Voltage dependent modification of sodium channel gating with water-soluble carbodiimide.

Currents through sodium channels in frog myelinated fibre were measured before and after the treatment of the membrane with water-soluble carbodiimide (WSC). The WSC treatment produces dramatic changes both in activation and inactivation when membrane potential during the treatment is held at levels from -80 to -100 mV. Both gating processes are slowed and their voltage dependence is reduced. The effective charge of activation as measured by limiting logarithmic potential sensitivity is reduced after 10 min of the WSC treatment by the factor of 1.66. The same WSC treatment applied at zero potential induced no change in the effective charge of activation. Other parameters of gating are changed after such treatment but to a lesser degree and in a somewhat different fashion than after the treatment at high negative potential. The results are consistent with the hypothesis that part of a mobile gating charge is presented by carboxyl groups migrating from the external surface to the interior of the channel molecule when the channel opens or inactivates.

Animals↗
PubMed1992

Evidence of an essential carboxyl residue in membrane-bound pyrophosphatase of Rhodospirillum rubrum.

Chemical modifications with water-soluble carbodiimides (EDC and CMC) were performed to elucidate whether some carboxyl residues are involved in the catalytic activity of membrane-bound pyrophosphatase of Rhodospirillum rubrum. EDC and CMC cause a loss of hydrolytic activity following pseudo-first-order kinetics up to 10 min of reaction. The enzyme was completely protected against EDC inhibition by PPi or Mg2+, whereas PPi or Mg2+ gave partial protection against CMC inactivation. Mg-PPi protected completely against the inhibition caused by both carbodiimides. These data suggest that the carboxyl moiety modified by EDC is at the active site. At longer times of inactivation with both carbodiimides, we could not observe a linear relationship in semilogarithmic plots of residual activity versus time, indicating that at least two carboxyls are involved in the inactivation, which correlates with the partial protection against CMC inactivation by PPi. We found that the activator site for Mg2+ is apparently at or near the active site of the enzyme. This is supported by the fact that PPi protects completely the activator effect of this divalent cation.

Binding Sites↗
PubMed1975

Changes in DNA secondary structure after gamma-irradiation.

Native calf thymus DNA was gamma-irradiated at 500 mug/ml in 0.01 M NaCl in the presence or absence of oxygen. By irradiation, an increasing amount of DNA becomes reactive with a water-soluble carbodiimide-derivative (CMEC). In the DNA sections reactive with CMEC the nucleotide strands are separated, a phenomenon previously described as radiation-induced denaturation. The dose-effect curve for the formation of denatured DNA shows an upward-bent form; a distinct oxygen effect of about 2 is observed. By a comparative study with DNA samples, degraded partially with DNAse I, it was shown that a minor part of the radiation-induced denaturation results from the formation of the radiation-induced single strand breaks, whereas the major part is a local denaturation independent of the strand breaks. In these locally denatured regions 20 to 50 nucleotide pairs are separated.

Animals↗
PubMed1985

Cross-linked collagen surface for cell culture that is stable, uniform, and optically superior to conventional surfaces.

A new type of collagen surface for use with cultures of peripheral nervous system cells is described. Collagen is derivatized to plastic culture dishes by a cross-linking reagent, l-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide-metho-p-toluene sulfonate (carbodiimide), to form a uniform and durable surface for cell attachment and growth that allows dry storage, long-term culture, and improved microscopy. Surfaces of collagen derivatized to plastic were compared to surfaces of adsorbed or ammonia-polymerized collagen in terms of collagen binding and detachment, growth by dorsal root ganglion cells, and electron microscopy appearances. Derivatized collagen surfaces retained more collagen and showed much less evidence of degradation and cellular damage over periods of many weeks than did conventional adsorbed surfaces. Long-term survival of cells on derivatized collagen was far superior to that on the other surfaces, with almost 90% of cultures still viable after 10 wk. Transmission electron microscopy showed an organized layer of single fibrils that supported cell growth well, and scanning electron microscopy demonstrated an increased uniformity of derivatized collagen surfaces compared to ammoniated collagen surfaces. Applications for this improved substrate surface are discussed.

Adsorption↗
PubMed1985

Chemical modification of S-adenosylhomocysteinase by a water-soluble carbodiimide.

S-Adenosylhomocysteinase (EC 3.3.1.1) from rat liver is inactivated by 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMC) in a pseudo-first-order fashion. The rate of inactivation is linearly related to the concentration of the reagent, and a second-order rate constant of 4.94 +/- 0.27 M-1 min-1 is obtained at pH 5.5 and 25 degrees C. The inactivation does not involve change in the quaternary structure of the enzyme nor modification or release of the enzyme-bound NAD. Lack of modification at tyrosine, serine, cysteine, histidine, and lysine residues and the fact that the inactivation is favored at low pH suggest that the inactivation is caused by the modification of a carboxyl group. Statistical analysis of the relationship between the residual enzyme activity and the extent of modification, and comparison of the number of residues modified in the presence and absence of the substrate adenosine show that, among four reactive residues per enzyme subunit, only one residue which reacts more rapidly with the reagent than the rest is critical for activity. The CMC-modified enzyme binds adenosine and S-adenosylhomocysteine and is able to oxidize the 3' hydroxyl of these substrates, but apparently fails to catalyze the abstraction of the 4' proton of adenosine.

Adenosylhomocysteinase↗
PubMed1992

Direct involvement of the C-terminal extremity of pancreatic lipase (403-449) in colipase binding.

After a selective cleavage of a lipase/colipase cross-linked complex, the colipase has been shown to be bound to a 5 kDa lipase fragment identified as the C-terminal extremity of the chain extending from residue 403 to the C-terminus (Cys 449). The colipase binding site on lipase is therefore localized in a restricted contact area. Moreover, from sequence comparison of lipase from various species, an acidic residue, Glu 440, is likely to be involved in ion pairing with colipase.

Amino Acid Sequence↗
PubMed1985

Direct cross-linking of heptauridilate to E. coli ribosomes by water-soluble carbodiimide in the complex stabilized by codon-anticodon interaction at both A- and P-sites.

Affinity labelling of E. coli ribosomes is performed by treatment with water-soluble carbodiimide of the complex of ribosomes with (pU)7, tRNAPhe at the P-site and with Phe-tRNAPhe (complex I) and without Phe-tRNAPhe (complex II) at the A-site. The extent of modification is, respectively, 0.06 and 0.026 mol (pU)7 per mol ribosomes. Protein S3 is found as a single labelled protein in complex I, whereas S7, S8, L25 are modified in complex II. Thus, in the absence of a large spacer group within the complex stabilized by codon-anticodon interactions at both A- and P-sites, a highly selective modification occurs.

Affinity Labels↗
PubMed1991

Effect of carbodiimides on the activity of Mg(2+)-ATPase of slow-twitch muscle microsomal membranes.

1. The hydrophobic N,N'-dicyclohexylcarbodiimide (DCCD) inhibits the activity of Mg(2+)-ATPase of slow-twitch muscle microsomal fraction. 2. The inhibition is dependent on time and concentration, with half-maximal inhibition occurring at 0.4 mM concentration of carbodiimide after a 0.5 hr incubation at room temperature. 3. ATP does not protect against the inhibition. 4. Two water-soluble carbodiimides, 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide (CMCD) and 1-ethyl-3(3-dimethylaminopropyl)-carbodiimide (EDCD), are not inhibitory. 5. Inhibition of Mg(2+)-ATPase activity by DCCD is accompanied by covalent incorporation of the radioactive agent into the partially purified enzyme preparation.

Animals↗
PubMed1986

Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension.

We have investigated in detail the higher-order structure of 16 S ribosomal RNA, both in its naked form and in 30 S ribosomal subunits. Each base in the 16 S rRNA chain has been probed using kethoxal (which reacts with guanine at N1 and N2), dimethylsulfate (which reacts with adenine at N1 and cytosine at N3) and 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluenesulfonate (which reacts with uracil at N3 and guanine at N1). The sites of reaction were identified by primer extension with reverse transcriptase using synthetic oligodeoxynucleotide primers. These results provide a detailed and rigorous experimental test of a model for 16 S rRNA secondary structure, which was derived mainly from comparative sequence analysis. Our data also provide information relevant to tertiary and quaternary structure of 16 S rRNA. Data obtained with naked 16 S rRNA show reasonably close agreement with the proposed model, and data obtained with 30 S subunits show nearly complete agreement. Apart from an apparent overall "tightening" of the structure (in which many weakly reactive bases become unreactive), assembly of the proteins with 16 S rRNA to form 30 S subunits brings about numerous local structural rearrangements, resulting in specific enhancements as well as protections. In many instances, the ribosomal proteins appear to "tune" the 16 S rRNA structure to bring it into accordance with the phylogenetically predicted model, even though the RNA on its own often seems to prefer a different structure in certain regions of the molecule. Extensive protection of conserved, unpaired adenines upon formation of 30 S subunits suggests that they play a special role in the assembly process, possibly providing signals for protein recognition.

Aldehydes↗
PubMed1990

Structural and functional properties of the segments of lambda cro mRNA that interact with transcription termination factor Rho.

Termination of transcription at tR1, the Rho-dependent terminator between genes cro and cII of bacteriophage lambda, is dependent upon the structure of segments near the 3' end of the nascent cro gene transcript and on contacts between Rho protein and a 3' proximal segment called rut. The characteristics of the structure of cro RNA in the region from residue 220 to residue 355 in free, isolated RNA and in the presence of Rho or NusA proteins were analyzed by measuring relative rates of reactivity of individual nucleotides with chemicals and enzymes of defined specificities. The results indicate that the rut segments are single-stranded and become blocked to the action of the various probes in the presence of Rho factor. They also show that this region contains two stem-loop structures; one involves the boxB sequence of nutR, the other precedes the tR1 subsite II end points. The results provide direct evidence for a primary binding contact between Rho protein and the rut segment of cro RNA and demonstrate that this binding contact remains stable when the cro RNA is serving as a cofactor for ATP hydrolysis, an observation that is consistent with a mechanism in which Rho maintains contact with the rut region while it makes additional interactions with RNA that are coupled to ATP hydrolysis.

Adenosine Triphosphate↗
PubMed1991

Structural analysis of the peptidyl transferase region in ribosomal RNA of the eukaryote Xenopus laevis.

Accessible single-strand bases in Xenopus laevis 28 S ribosomal RNA (rRNA) Domain V, the peptidyl transferase region, were determined by chemical modification with dimethylsulfate, 1-cyclohexyl-3-(2-morpholinoethyl-carbodiimide metho-p-toluene sulfonate and kethoxal, followed by primer extension. The relative accessibilities of three rRNA substrates were compared: deproteinized 28 S rRNA under non-denaturing conditions (free 28 S rRNA), 60 S subunits and 80 S ribosomes. Overall, our experimental results support the theoretical secondary structure model of Domain V derived by comparative sequence analysis and compensatory base-pair changes, and support some theoretical tertiary interactions previously suggested by covariation. The 60 S subunits and 80 S ribosomes generally show increasing resistance to chemical modification. Bases which are sensitive in free 28 S rRNA but protected in 60 S subunits may be sites for ribosomal protein binding or induced structural rearrangements. Another class of nucleotides is distinguished by its sensitivity in 60 S subunits but protection in 80 S ribosomes; these nucleotides may be involved in subunit-subunit interactions or located at the interface of the ribosome. We found a third class of bases, which is protected in free 28 S rRNA but sensitive in 60 S subunits and/or 80 S ribosomes, suggesting that structural changes occur in Domain V as a result of subunit assembly and ribosome formation. One such region is uniquely hypersensitive in eukaryotic ribosomes but is absent in Escherichia coli ribosomes. Sites that we determined to be accessible on empty 80 S ribosomes could serve as recognition sites for translation components.

Aldehydes↗
PubMed1992

Structure analysis of the 5' external transcribed spacer of the precursor ribosomal RNA from Saccharomyces cerevisiae.

Full-length precursor ribosomal RNA molecules were produced in vitro using as a template, a plasmid containing the yeast 35 S pre-rRNA gene under the control of the phage T3 promoter. The higher-order structure of the 5'-external transcribed spacer (5' ETS) sequence in the 35S pre-rRNA molecule was studied using dimethylsulfate, 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluenesulfonate, RNase T1 and RNase V1 as structure-sensitive probes. Modified residues were detected by primer extension. Data produced were used to evaluate several theoretical structure models predicted by minimum free-energy calculations. A model for the entire 5'ETS region is proposed that accommodates 82% of the residues experimentally shown to be in either base-paired or single-stranded structure in the correct configuration. The model contains a high degree of secondary structure with ten stable hairpins of varying lengths and stabilities. The hairpins are composed of the Watson-Crick A.T and G.C pairs plus the non-canonical G.U pairs. Based on a comparative analysis of the 5' ETS sequence from Saccharomyces cerevisiae and Schizosaccharomyces pombe, most of the base-paired regions in the proposed model appear to be phylogenetically supported. The two sites previously shown to be crosslinked to U3 snRNA as well as the previously proposed recognition site for processing and one of the early processing site (based on sequence homology to the vertebrate ETS cleavage site) are located in single-stranded regions in the model. The present folding model for the 5' ETS in the 35 S pre-rRNA molecule should be useful in the investigations of the structure, function and processing of pre-rRNA.

Base Sequence↗