287 resultados para Nuclear Proteins


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A simple algorithm has been developed to detect β-bends and 'loops'-chain reversals containing five amino acid residues, using only coordinates of Cα-atoms from crystal structure data of globular proteins using the above algorithm. Analysis of bends have showed that the total number of bends in each protein (TB) is linearly related to total number of non-hydrophobic residues in that protein which in turn is related linearly to total number of amino acid residues. Secondly, we found that a large number of consecutive bends occur in each protein which give rise to on an average only three independent residues per turn. Positional preference of amino acid residues in chain reversals is stressed. Consideration of pairs of amino acid residues in positions (i + 1) and (i + 2) of bends seems to provide a more reliable basis for predicting chain reversals in proteins.

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Complexation of valinomycin (VM) with the divalent cation Ca2+ in a lipophilic solvent, acetonitrile (CH3-CN), has been studied by using circular dichroism and proton and carbon- 13 nuclear magnetic resonance (‘H NMR and I3C NMR). From analyses of the spectral data, it is concluded that VM forms a 2:l (peptideion-peptide) sandwich complex with Ca2+, at low concentration of VM. At moderate conocentrations of the salt, in addition to the sandwich complex, an equimolar (1:l) complex different from those observed for potassium and sodium is also observed. At very large concentrations of the calcium salt, the data suggested a complex with a conformation similar to that of the free VM in polar solvents. Possible conformations for the sandwich and the equimolar VM-calcium complexes are proposed.

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From the proton nmr studies of 2-thiocoumarin and coumarin, it is concluded that the relative interproton distances in the two oxygen heteroatom bicyclic systems are similar. The values for the phenyl ring protons do not deviate significantly from the regular hexagonal geometry, unlike bicyclic systems with nitrogens as the heteroatoms, such as diazanaphthalenes. Larger values of the indirect spin-spin couplings within the protons of the ring containing the oxygen heteroatom, compared to the values between the ortho protons in the phenyl rings in coumarin and 2-thiocoumarin, correspond to the olefinic nature of these protons. This is in contrast to results for the nitrogen heterocycles where both the rings are aromatic.

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Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites. Results: We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins. Conclusion: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

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The temperature variation of the 3’Cl n.q.r. frequencies in 3,5- and 2,3- dichloroanisoles has been reported here. Both compounds show two lines each, and these have been assigned to the two chlorines in the same molecule with the help of the additive model for the substituent effect. The temperature dependence has been analysed in terms of Bayer-Kushida-Brown model.The torsional frequencies and their temperature dependence have been calculated numerically under a two-mode approximation. 0.n comparing the results in 3,5-dichloroanisole with those in 3,5-dichlorophenol it can be seen that they show similar behaviour owing to the absence of hydrogen bonding in both.

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From the proton NMR spectra of Nfl-dimethyluracil oriented in two different nematic solvents, the internal rotation of the methyl groups about the N-C bonds is studied. It has been observed that the preferred conformation of the methyl group having one carbonyl in the vicinity is the one where a C-H bond is in the ring plane pointing toward the carbonyl group. The results are not sensitive to the mode of rotation of the other methyl group. These data are interpreted in terms of the bond polarizations.

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A method to identify β-sheets in globular proteins from extended strands, using only α-carbon positions, has been developed. The strands that form β-sheets are picked up by means of simple distance criteria. The method has been tested by applying it to three proteins with accurately known secondary structures. It has also been applied to ten other proteins wherein only α-carbon coordinates are available, and the list of β-sheets obtained. The following points are worth noting: (i) The sheets identified by the algorithm are found to agree satisfactorily with the reported ones based on backbone hydrogen bonding, wherever this information is available. (ii) β-Strands that do not form parts of any sheet are a common feature of protein structures. (iii) Such isolated β-strands tend to be short. (iv) The conformation corresponding to the preferred right-handed twist of the sheet is overwhelmingly observed in both the sheet-forming and isolated β-strands.

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The relative concentrations of the major histones, namely, H1, TH1, H2A, H2B, H3 and H4 are not significantly changed in the testes of the vitamin A-deficient rats, as compared to those in the normal controls. But the testis-specific protein, TP, which is synthesized at the mid-spermatid stage, is markedly reduced in the testes of the deficient rats. On supplementation of the deficient rats with retinyl acetate for 28 days, there was a 50% recovery in the relative concentration of the TP with respect to the total amounts of H1 and TH1.

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Studies on the conformational and binding characteristics of the ionophoric antibiotic X-537A (lasalocid-A)�calcium ion complexes have been carried out in deuteriated acetonitrile (CD3 CN) using proton and carbon-13 nuclear magnetic resonance (1 H and 13C n.m.r.) spectroscopy. Detailed analysis of the salt-induced chemical shifts at various X-537A to calcium concentration ratios indicated that X-537A forms charged complexes with calcium with 2 : 1 and 1 : 1 stoicheiometries. The conformational model for the complex based on the n.m.r. data showed that the calcium ion is preferentially bound to one end of the molecule, which is binding to three oxygen atoms, the other end (the salicylic acid part) being relatively free. In the 2 : 1 (sandwich) complex, the calcium ion is sandwiched between two X-537A molecules with three oxygen atoms binding to it from each molecule.

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Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone H-1(alpha) and C-13' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to alpha-helical/beta-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

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Tetrapeptide sequences of the type Z-Pro-Y-X were obtained from the crystal structure data on 34 globular proteins, and used in an analysis of the positional preferences of the individual amino acid residues in the β-turn conformation. The effect of fixing proline as the second position residue in the tetrapeptide sequence was studied by comparing the data obtained on the positional preferences with the corresponding data obtained by Chou and Fasman using the Z-R-Y-X sequence, where no particular residue was fixed in any of the four positions. While, in general, several amino acid residues having relatively very high or very low preferences for specific positions were found to be common to both the Z-Pro-Y-X and Z-R-Y-X sequences, many significant differences were found between the two sets of data, which are to be attributed to specific interactions arising from the presence of the proline residue.

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Empirical potential energy calculations have been carried out to determine the preferred conformations of some oligosaccharides having the trimannosidic core structure (Man3GlcNAc2) and which interact with concanavalin A. In the minimum energy conformations for the trimannosidic core the mannose residue on the Man α(1–6) arm comes close to one of the N-acetylglucosamine residues of the core. The addition of N-acetylglucosamine residues to the terminal mannose residues does not alter the preferred conformation of the trimannosidic core although it alters the relative preference of some of the higher energy conformations. The minimum energy conformation broadly agrees with available X-ray data. The presence of a bisecting N-acetylglucosamine residue on the middle mannose does not push the trimannosidic core to any new conformation but it does alter the relative preference for a particular conformation.

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The circular dichroism bands of (+) gossypol in the spectral region 300–400 nm have been shown to be sensitive to interactions with proteins. Using CD spectroscopy, gossypol has been shown to interact with lactate dehydrogenase, malate dehydrogenase, alkaline phosphatase, lysozyme, protamine and poly-L-lysine. Binding to proteins generally results in a pronounced red shift of the long wavelength CD band (not, vert, similar 380–430 nm) accompanied by a reduction in ellipticity. The changes in spectral parameters of the 1Lb binaphthyl transtion may reflect a distortion from a nearly perpendicular gossypol conformation, on binding to proteins.

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Several molecules like ionophores, vitamins, ion-binding cyclic peptides, acidic phospholipids, surfactants are known to expose the inner side of vesicles, to the externally added cations. Whereas ionophores and certain other systems bring about these changes by a selective transport (influx) of the cation by specialized mechanisms known as the carrier and channel mechanism, other systems cause lysis and vesicle fusion. These systems have been successfully studied using1H,31 P and13C nuclear magnetic resonance spectroscopy after the demonstration, fifteen years ago, of the ability of paramagnetic lanthanide ions to distinguish the inside of the vesicle from the outside. The results of these ’nuclear magnetic resonance kinetics’ experiments are reviewed.