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T K Kumar

Publications and source records attributed to T K Kumar.

48 records · Page 3Linked to original sources

Identification of 'molten globule'-like state in all beta-sheet protein.

The cardiotoxin analogue III (CTX III), isolated from the Taiwan Cobra venom (Naja naja atra), is a sixty amino acid, all beta-sheet protein. The 2,2,2-trifluoro ethanol (TFE) induced unfolding of CTX III is studied under acidic conditions (pH 2.5). Using circular dichroism, 1-anilino-8-napthalene sulphonic acid binding and NMR experiments, it is shown that stable, partially structured state(s) ['molten globule'-like state] is formed between 50 and 80% TFE concentrations. The protein was found to exist in an unfolded state in 80% TFE containing 2M urea. The TFE induced unfolding process is shown to be completely reversible. In the 'molten globule' state of CTX III in 80% TFE, though portion(s) of the backbone of the protein assume helical conformation, most of the original beta-sheet secondary structural elements in the protein are intact. In our opinion, this is the first report of the identification of a 'molten globule'-like state in the unfolding pathway of an all beta-sheet monomeric protein.

Anilino Naphthalenesulfonates↗

Fluorescent staining for proteins on polyacrylamide gels with 5-dimethylamino-1-naphthalenesulfonyl chloride (dansyl chloride).

A simple and sensitive post electrophoresis fluorescent staining technique for proteins on polyacrylamide gels using 5-dimethylamino-1-naphthalene sulfonyl chloride (dansyl chloride) has been developed. Dansyl chloride staining increases the sensitivity, 0.125 micrograms protein per band can be visualised by this technique. The staining method appears to be applicable to all types of proteins including proteoglycans.

Dansyl Compounds↗

Conformational studies of a synthetic cyclic decapeptide fragment of rat transforming growth factor-alpha.

The solution conformation of a synthetic cyclic decapeptide [with sequence mimicking the third disulfide loop of rat transforming growth factor-alpha (rTGF-alpha)] in deuterated dimethyl sulfoxide was studied by 2D NMR. The determination of solution structures was based on NOE interproton distances, using a combination of distance geometry and simulated annealing protocols. The convergence of the selected structures was evident from the small atomic pairwise root-mean-square deviation values among them. Good agreement was noted between the experimental and simulated NOESY spectra, thereby reflecting the accuracy of the calculated solution structures. Analysis of the structures indicates that the residues Tyr5 and Arg9 exhibit similar side chain orientation as that in the corresponding disulfide loop of human transforming growth factor-alpha.

Amino Acid Sequence↗

Trichloroacetic acid-induced unfolding of bovine pancreatic ribonuclease. Existence of molten globule-like state.

The exposure of ribonuclease A to trichloroacetic acid was earlier shown to alter the conformation of the protein resulting in reduced enzymatic activity (Sagar, A. J., Subbiah, V., and Pandit, M. W. (1989) Biochim. Biophys. Acta 995, 144-150). We have studied the structure and enzymatic activity of ribonuclease A treated with trichloroacetic acid over a wide range of acid concentrations (0-40%). The far ultraviolet circular dichroism spectra of ribonuclease A, on exposure to acid concentrations less than 10%, indicated an exceptionally high degree of chiral structure. Exposure of ribonuclease A to acid concentrations between 10 and 30% resulted in the formation of a molecule with significant chiral structure (conventionally assigned to residual secondary structure) but reduced tertiary structure (characteristics very similar to those of molten globule). Increased binding of the hydrophobic probe 1-anilinonaphthalene-8-sulfonate to the enzyme treated with 15-30% acid, as compared with the untreated or completely unfolded protein, supported the existence of a state having characteristics of molten globule. Reversed phase high performance liquid chromatography corroborated the data obtained by circular dichroism as well as 1-anilino-naphthalene-8-sulfonate-binding studies. Beyond acid concentrations of 30%, the ribonuclease is completely denatured. The trichloroacetic acid-induced unfolding is shown to be completely reversible.

Anilino Naphthalenesulfonates↗

Refolding of RNAse A at high concentrations: identification of non-native species.

In this paper, we present an analysis of the soluble species formed on refolding of RNase A at various concentrations, in order to characterize these species with respect to structure and activities. Studies were carried out using reverse-phase high-performance liquid chromatography, circular dichroism, chromatography and ultracentrifugation. At all concentrations of protein used, RNase A refolded to the native form, together with formation of non-native species. These non-native species are either misfolded monomers or aggregates; the percentage of such species increases with increasing concentration of enzyme. Such aggregation appears to be a non-random process governed by intermolecular disulfide crosslinking between monomers. These results reaffirm the principle that the information for folding of the protein is encoded in the amino acid sequence itself.

Chromatography, High Pressure Liquid↗

Origin of multiple bands of proteins on sodium dodecyl sulphate-polyacrylamide gel electrophoresis--intermolecular disulphide cross-linking due to the presence of oxidizing components in the reducing agent.

The presence of oxidized products in the reducing agent used in sodium dodecyl sulphate-polyacrylamide gel electrophoresis is shown to yield multiple bands from otherwise homogeneous RNase A. The role of oxidized products in generating multiple bands is elucidated by using varying proportions of oxidized and reduced glutathione in a mixture as a reducing agent.

Cross-Linking Reagents↗

Effect of cationic drugs on suprahelical organization of DNA.

Interaction of a minor groove-binding drug Hoechst-33258, and an intercalating drug, proflavin, with the PSI(+) form of DNA, was studied using CD spectroscopy. Both drugs are shown to relax the suprahelical organization of DNA, leading to the formation of a B-like structure, above a certain drug to phosphate ratio. However, unlike proflavin, Hoechst-33258 brings about further structural changes after formation of the B-like structure whereas proflavin does not. A reversal of the CD signal in the 300-450-nm spectral region is also observed with Hoechst-33258, indicating a change in the handedness of the suprahelical organization of DNA. To the best of our knowledge, drug-mediated changes as presented in this paper have not been reported so far.

Animals↗

Multiple bands on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of proteins due to intermolecular disulfide cross-linking.

Gel electrophoresis has been used extensively as an analytical technique to check the purity and to determine the molecular weight of proteins. Improved levels of detection of proteins by silver staining of the gels have made the technique more sensitive in detecting heterogeneity. We report here some interesting observations about the anomalous behavior of some proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). This report is concerned with the appearance of multiple bands, after silver staining, on the SDS-PAGE gels of proteins which are shown by HPLC to be homogeneous. We also show the reasons for the appearance of bands that originate from 2-mercaptoethanol itself.

Cross-Linking Reagents↗

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Heart Diseases↗

Effect of modification of tyrosine residues in cytotoxin-1 from Indian cobra venom. (Naja naja naja).

The role of tyrosine residues in the biological activity of cytotoxin-1 was evaluated using N-bromo succinimide. N-bromo succinimide effected the oxidation of tyrosine residues in cytotoxin-1 with an increase in absorption at 260 nm. N-chloro succinimide was ineffective in the oxidation of tyrosine residues in the toxin. Oxidation of a single tyrosine residue (at 3.50 equivalents of N-bromo succinimide/mole of the toxin) resulted in complete loss of lethal activity of the toxin. The lytic activity of the toxin (lysis of erythrocytes) remained uneffected even after three of the four tyrosine residues in the toxin were oxidised.

Animals↗