Specificity of protein - Nucleic acid interaction and the biochemical evolution

The water soluble carbodiimide mediated condensation of dipeptides of the general form Gly-X was carried out in the presence of mono- and poly-nucleotides. The observed yield of the tetrapeptide was found to be higher for peptide-nucleotide system of higher interaction specificity following mainly the anticodon-amino acid relationship (Basu, H.S. & Podder, S.K., 1981, Ind. J. Biochem. Biophys.,19, 251-253). The yield of the condensation product of L-peptide was more because of its higher interaction specificity. The extent of the racemization during the condensation of Gly-L-Phe, Gly-L-Tyr and Gly-D-Phe was found to be dependent on the specificity of the interaction -the higher the specificity, the lesser the racemization. The product formed was shown to have a catalytic effect on the condensation reaction. These data thus provide a mechanism showing how the specific interaction between amino acids/dipeptides and nucleic acids could lead to the formation of the lsquoprimitiversquo translation machinery.

Solvent effects on the structure of N-methylpyrrole as studied by nmr in nematic solvents

The proton NMR spectra of N-methylpyrrole oriented in the nematic phases of liquid crystals with positive and negative diamagnetic anisotropies and their mixtures are reported. Geometrical parameters derived from the spectra at the critical point in the mixture of liquid crystals with positive and negative diamagnetic anisotropies, where macroscopic diamagnetic anisotropy vanishes, are similar to those obtained in the solvent with negative diamagnetic anisotropy. However, significant distortions in the molecular structure attributed to solvent effects have been observed in liquid crystals with positive diamagnetic anisotropy. The minimum energy conformation has one C---H of the methyl perpendicular to the ring.

Induction of riboflavin-carrier protein in the immature male rat by estrogen: kinetic and hormonal specificity

The kinetics of estrogen-induced accumulation of riboflavin-carrier protein in the plasma was investigated in immature male rats using a specific and sensitive homologous radio-immunoassay procedure developed for this purpose. Following a single injection of the steroid hormone, plasma riboflavin-carrier protein levels increased markedly after an initial lag period of approximately 24 h, reaching peak levels around 96 h and declining thereafter. A 1.5 fold amplification of the inductive response was evident on secondary stimulation with the hormone. The magnitude of the response was dependent on hormonal dose, whereas the initial lag phase and the time of peak riboflavin-carrier protein induction were unaltered within the range of the steroid doses (0.1–10 mg/ kg body wt.) tested. Simultaneous administration of progesterone did not affect either the kinetics or the maximum level of the protein induced. The hormonal specificity of this induction was further adduced by the effect of administration of antiestrogens viz., En and Zu chlomiphene citrates, which effectively curtailed hormonal induction of the protein. That the induction involvedde novo-protein synthesis was evident from the complete inhibition obtained upon administration of cycloheximide. Passive immunoneutralization of endogenous riboflavin-carrier protein with antiserum to the homologous protein terminated pregnancy in rats confirming the earlier results with antiserum to chicken riboflavin-carrier protein.

Multiple liquid-crystals and NMR

The use of more than one liquid crystal solvents to determine molecular structure and conformation is discussed. Liquid crystals of similar and opposite signs of diamagnetic anisotropies are considered separately since they lead to different novel applications. Advantages of such experiments over those employing single solvents are pointed out with illustrative examples.

Fluorescent probe and NMR studies of the aggregation of bile salts in aqueous solution

The binding of the fluorescent probes 1-anilino-8-naphthalene sulfonate and dansyl cadaverine to the sodium salts of cholic, deoxycholic and dehydrocholic acids has been investigated. Enhanced probe solubilisation accompanies aggregation. Monitoring of fluorescence intensities as a function of bile salt concentration permits the detection of primary micelle formation, as well as secondary association. The transition concentrations obtained by fluorescence are in good agreement with values determined for the critical micelle concentrations, by other methods. Differences in the behaviour of cholate and deoxycholate have been noted. Fluorescence polarisation studies of 1,6-diphenyl-1,3,5-hexatriene solubilised in bile salt micelles suggest a higher microviscosity for the interior of the deoxycholate micelle as compared to cholate. 1H NMR studies of deoxycholate over the range 1–100 mg/ml suggest that micelle formation leads to a greater immobilisation of the C18 and C19 methyl groups as compared to the C21 methyl group. Well resolved 13C resonances are observed for all three steroids even at high concentration. Both fluorescence and NMR studies confirm that dehydrocholate does not aggregate.

Protein Synthesis in Mycobacterium tuberculosis H37Rv and the Effect of Streptomycin in Streptomycin-Susceptible and -Resistant Strains

An efficient in vitro amino acid-incorporating system from Mycobacterium tuberculosis H37Rv was standardized. Ribonucleic acid (RNA) isolated from phage-infected M. smegmatis cells served as natural messenger RNA and directed the incorporation of 14C-amino acids into protein. The effects of various antitubercular drugs and “known inhibitors” of protein synthesis on amino acid incorporation were studied. Antibiotics like chloramphenicol and tetracycline inhibited mycobacterial protein synthesis, though they failed to prevent the growth of the organism. This failure was shown to be due to the impermeability of mycobacteria to these drugs by use of “membrane-active” agents along with the antibiotics in growth inhibition studies. Several independent streptomycin-resistant mutants of M. tuberculosis H37Rv were isolated. Streptomycin inhibited the incorporation of 14C-amino acids into proteins by whole cells of a streptomycin-susceptible strain by more than 90%, whereas very little or no inhibition was observed in either high-level or low-level streptomycin-resistant strains.

Purification, crystallization and partial characterization of the antitumour and insecticidal protein subunit from the delta-endotoxin of Bacillus thuringiensis var. thuringiensis

The antitumour protein from the α-endotoxin of Bacillus thuringiensis var. thuringiensis has been purified, crystallized and partially characterized. The same protein also shows the insecticidal activity. According to amino acid analysis it is an acidic protein with a molecular weight of approx. 13 000.

Two-dimensional NMR spectra of oriented molecules

Abstract is not available.

Natural Abundant Solid State NMR Studies in Designed Tripeptides for Differentiation of Multiple Conformers

Solid state NMR (SSNMR) experiments on heteronuclei in natural abundance are described for three synthetically designed tripeptides Piv-(L)Pro_(L)Pro-(L)Phe-OMe (1), Piv-(D)Pro_(L)Pro_(L)Phe-OMe (2), and Piv-(D)Pro_(L)Pro_(L)Phe-NHMe (3). These peptides exist in different conformation as shown by solution state NMR and single crystal X-ray analysis (Chatterjee et al., Chem Eur J 2008, 14, 6192). In this study, SSNMR has been used to probe the conformations of these peptides in their powder form. The C-13 spectrum of peptide (1) showed doubling of resonances corresponding to cis/cis form, unlike in solution where the similar doubling is attributed to cis/trans form. This has been confirmed by the chemical shift differences of C-beta and C-gamma carbon of Proline in peptide (1) both in solution and SSNMR. Peptide (2) and (3) provided single set of resonances which represented all transform across the di-Proline segment. The results are In agreement with the X-ray analysis. Solid state N-15 resonances, especially from Proline residues provided additional information, which is normally not observable in solution state NMR. H-1 chemical shifts are also obtained from a two-dimensional heteronuclear correlation experiment between H-1-C-13. The results confirm the utility of NMR as a useful tool for identifying different conformers in peptides in the solid state. (C) 2009 Wiley Periodicals, Inc. Biopolymers 91: 851-860, 2009.

Purification, crystallization and partial characterization of the antitumour and insecticidal protein subunit from the σ-endotoxin of Bacillus thuringiensis var. thuringiensisstar, open

The antitumour protein from the α-endotoxin of Bacillus thuringiensis var. thuringiensis has been purified, crystallized and partially characterized. The same protein also shows the insecticidal activity. According to amino acid analysis it is an acidic protein with a molecular weight of approx. 13 000.

Conformation And C-N Rotational Barrier Of Dithiocarbamate Esters Nmr And Molecular-Orbital Studies

The variable temperature proton and ambient temperature carbon-13 NMR spectra of S-methyl dithiocarbamate esters have been recorded. The results of the theoretical energy calculations (CNDO/2 and EHT types) together with the experimental data have been interpreted in terms of the molecular conformations. The barrier heights for the rotation about the thioamide C—N bond are calculated using the CNDO/2 method and the results are discussed in terms of the computed charge densities and bond orders.

Conformation of the LL and LD hairpin bends with internal hydrogen bonds in proteins and peptides

The conformation of three linked peptide units having an internal 4 → 1 type of hydrogen bond has been studied in detail, and the low energy conformations are listed. These conformations all lead to the reversal of the chain direction, and may therefore be called as “hairpin bends” or “U-bends”. Since this bend can occur at the end of two chains hydrogen-bonded in the antiparallel β-conformation, it is also known as the “β-bend”. Two types of conformation are possible when the residues at the second and third Cα atoms are both of type L (the LL bend), while only one type is possible for the LD and the DL bend. The LL bend can also accommodate the sequences LG, GL, GG (G = glycine), while the LD bend can accommodate the sequences LG, GD and GG. The conformations for the sequences DD and DL are exact inverses (or mirror images) of those for the sequences LL and LD, respectively, and have dihedral angles (phi2, ψ2), (phi3, ψ3) of the same magnitudes, but of opposite signs as those for the former types, which are listed, along with the characteristics (length, angle and energy) of the hydrogen bonds. A comparison of the theoretical predictions with experimental data (from X-ray diffraction and NMR studies) on proteins and peptides, show reasonably good agreement. However, a systematic trend is observable in the experimental data, slightly deviating from theory, which indicates that some deformations occur in the shapes of the peptide units forming the bend, differing from that of the standard planar peptide unit.

The 310 Helical Conformation of the Amino Terminal Decapeptide of Suzukacillin. 270 MHz 'H NMR Evidence for Eight Intramolecular Hydrogen Bonds

The amino terminal suzukacillin decapeptide fragment, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aitbh-eO Me, two pentapeptides Boc-AibPrc-Val-AibVal-OMe and Boc-Ala-AibAla-AibAibOMe, and the tripeptide Boc-Ala-AibAibOMe have been studied by 270-MHz 'H NMR spectroscopy. By use of solvent dependence of chemical shifts in a CDC13-(CD3),S0 system and temperature dependence of amide NH chemical shifts in (CD3),S0, the intramolecularly hydrogen bonded NH groups in these peptides have been identified. The tripeptide possesses one hydrogen bond, both pentapeptides show evidence for three intramolecular hydrogen bonds, and the decapeptide has eight NH groups participating in hydrogen bonding. An Ala( 1)-Aib(2) @ turn is proposed for the tripeptide. Both pentapeptides favor 310 helical conformations composed of three consecutive B turns. The decapeptide adopts a 310 helical conformation with some flexibility at the Va1(5)-Ala(6) segment. The proposed conformations are consistent with the known stereochemical preferences of Aib residues.