1,721,013 research outputs found
A new program for the conformational analysis by NMR of the sugar ring of nucleosides and nucleotides in solution: HETROT. Application to the sugar ring of AZT in solution
No full textA new program for the conformational analysis by NMR of the sugar ring of nucleosides and nucleotides in solution, based on both 1H- 1H and long range 1H- 13C coupling constants is presented. The experimental conditions for the accurate measurement of long range heteronuclear coupling constants in natural abundance are discussed, together with the implementation of a computational algorithm (HETROT) that calculates the range of values of the five parameters describing the conformation of the furanose ring (pn, τmN, PS, τmS, τmS and xN) that reproduces all the measured couplings within their estimated errors. HETROT was applied to the conformational analysis of the sugar ring of 3′-azido-3′-deoxylhymidine (AZT) in DMSO and D2O. In both solvents the sugar ring exists in fast equilibrium between roughly equally populated N- and S- type conformers. The degree of definition of the precise geometry of such conformers. and their relative population, that can be obtained from the experimental data is analysed and graphically presented
Sensitivity enhancement of a two-dimensional experiment for the measurement of heteronuclear long range coupling constants, by a new scheme of coherence selection by gradients
Full text linkIn this work we present a new pulse sequence for the measurement of long-range heteronuclear coupling constants in which the optimization of coherence selection by pulsed field gradients offers a net increase in sensitivity. This type of experiments is extremely valuable for conformational studies of molecules in natural abundance and in this context the use of gradients is essential for an efficient suppression of (12)C bound proton signals. A comparative analysis of the different gradient schemes available is presented with a conclusive elucidation of the relative sensitivities. Our gradient scheme could be advantageous as a building block for other related experiments
NMR analysis of molecular flexibility in solution (NAMFIS): a new method for the study of complex distributions of rapidly exchanging conformations. Application to a 13 residue peptide with an 8 residue loop
Full text linkA new methodology, called NAMFIS (NMR analysis of molecular flexibility in solution), is described for
the analysis of flexible molecules in solution. Once a complete set of conformations is generated and is able to
encompass all the possible states of the molecule that are not a priori incompatible with the available experimental
NMR evidence, NAMFIS allows for the examination of the Occurrence and relevance of arbitrary elements of secondary
structure, even when extensive conformational averaging defies a detailed experimental characterization. The analysis
is based on the available experimental NMR data
Conformational Analysis by NMR Spectroscopy of 2'-Deoxy-2'-C-Alkyl-nucleosides: Building Blocks of New Antisense Fragments
No full textHACACO revisited: Residual dipolar coupling measurements and resonance assignments in proteins
No full textThe revisited version of the HACACO experiment here presented, is more robust and straightforward to implement and continues to be, to a greater extent, a convenient too] for protein backbone resonance assignment. Additionally, it turns out to be a sensitive and accurate method to measure C-alpha-H-alpha residual dipolar couplings (RDCs). The performance of our new pulse scheme for measurement of RDCs was tested on two proteins with different secondary structures: one characterized by a high beta-sheet content, the second dominated by the presence of alpha-helices. In both examples the new method provided significantly more accurate data, compared to all previously published 3D techniques. (c) 2006 Elsevier Inc. All rights reserved
High resolution solution structure of two members of a conformationally homogneous combinatorial peptide library based on the classical zinc finger motif
No full textWe describe the high-resolution structure by NMR of two peptides that belong to a combinatorial library based on the zinc-finger motif. The library represents, to the best of our knowledge, the first example of a conformationally homogeneous peptide library and was obtained by introducing random residues in five positions of the alpha-helical portion of a 26-residue 'consensus' peptide (CP1) belonging to the Cys(2)-Hys2 zinc-finger family. The result was shown to be a highly homogeneous alpha-helical library (Bianchi et al., 1995). The structures of the parent compound (CPI) and of a representative member (CPlm) that was selected by screening the library with a monoclonal antibody are compared in detail as an example of the very high stability of the zinc-finger scaffold upon sequence variability. The two peptides exhibit an extremely high degree of structural similarity. The use of this type of conformationally constrained combinatorial library might represent a step forward in the design of peptidomimetics, as it considerably accelerates the process of the identification of the spatial relationship among the pharmacophoric groups
Accurate measurement of heteronuclear long-range coupling constants from 1D-subspectra in crowded spectral regions
Full text linkImproved Sensitivity in Indirect Monitoring of Chemical Shifts of Proton-Heteronuclear spin pairs (1H-13C and 1H-15N) in 3D and 4D NMR Spectroscopy
Full text linkIn three-dimensional and four-dimensional experiments on doubly labelled proteins not only heteronuclear (13C or 15N) but also proton (1H) frequencies are often indirectly monitored, rather than being directly observed. In this communication we show how in these experiments by overlaying 1H and heteronuclear evolutions one can obtain decreased apparent relaxation rates of 1H signals, yielding improved sensitivity. The new method applies to spin pairs like 1H-15N, as in amide groups, or 1H-13C, as in methine groups of alpha or aromatic systems
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