Nuclear magnetic resonance distance determination

TF Flavel. An evaluation of computational strategies for use m the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog Biophys Mol Biol 56 43, 1991. 

Finally, Burkhard Luy, Andreas Frank and Horst Kessler discuss Conformational Analysis of Drugs by Nuclear Magnetic Resonance Spectroscopy . The determination and refinement of molecular conformations comprehends three main methods distance geometry (DG), molecular dynamics (MD) and simulated anneahng (SA). In principle, it is possible to exclusively make use of DG, MD or... 

The most important advance in determining the structures of proteins in recent years has been the development of high-field nuclear magnetic resonance methods.9,10 These methods enable us to determine the structures of moderately sized (< 30 kDa) proteins in solution.11,12 The principle of the method is quite different from x-ray crystallography in that the overall structure is calculated principally from restraints on the distances between 1H atoms. 

The dependence of the principal components of the nuclear magnetic resonance (NMR) chemical shift tensor of non-hydrogen nuclei in model dipeptides is investigated. It is observed that the principal axis system of the chemical shift tensors of the carbonyl carbon and the amide nitrogen are intimately linked to the amide plane. On the other hand, there is no clear relationship between the alpha carbon chemical shift tensor and the molecular framework. However, the projection of this tensor on the C-H vector reveals interesting trends that one may use in peptide secondary structure determination. Effects of hydrogen bonding on the chemical shift tensor will also be discussed. The dependence of the chemical shift on ionic distance has also been studied in Rb halides and mixed halides. Lastly, the presence of motion can have dramatic effects on the observed NMR chemical shift tensor as illustrated by a nitrosyl meso-tetraphenyl porphinato cobalt (III) complex. 

Several spectroscopic techniques, namely, Ultraviolet-Visible Spectroscopy (UV-Vis), Infrared (IR), Nuclear Magnetic Resonance (NMR), etc., have been used for understanding the mechanism of solvent-extraction processes and identification of extracted species. Berthon et al. reviewed the use of NMR techniques in solvent-extraction studies for monoamides, malonamides, picolinamides, and TBP (116, 117). NMR spectroscopy was used as a tool to identify the structural parameters that control selectivity and efficiency of extraction of metal ions. 13C NMR relaxation-time data were used to determine the distances between the carbon atoms of the monoamide ligands and the actinides centers. The II, 2H, and 13C NMR spectra analysis of the solvent organic phases indicated malonamide dimer formation at low concentrations. However, at higher ligand concentrations, micelle formation was observed. NMR studies were also used to understand nitric acid extraction mechanisms. Before obtaining conformational information from 13C relaxation times, the stoichiometries of the... 

Pease JHB, Wemmer DE. Solution structure of apamin determined by nuclear magnetic resonance and distance geometry. Biochemistry 1988 27 8491-8498. 

T. F. Havel, Prog. Biophys. Mol. Biol., 56, 43 (1991). An Evaluation of Computational Strategies for Use in the Computational Determination of Protein Structure from Distance Constraints Obtained by Nuclear Magnetic Resonance. 

T. F. Havel and K. Wiithrich, Bull. Math. Biol., 182, 673 (1985). A Distance Geometry Program for Determining the Structures of Small Proteins and Other Macromolecules from Nuclear Magnetic Resonance Measurements of Intramolecular >H- H Proximities in Solution. 

R. Morrison and D. Hare, /. Mol. Biol., 204, 483 (1988). Determining Stereospecific H Nuclear Magnetic Resonance Assignments from Distance Geometry Calculations. 

G. Wagner, W. Braun, T. F. Havel, T. Schaumann, N. Go, and K. Wiithrich, /. Mol. Biol., 196, 611 (1987). Protein Structures in Solution by Nuclear Magnetic Resonance and Distance Geometry The Polypeptide Fold of the Basic Pancreatic Trypsin Inhibitor Determined Using Two Different Algorithms. DISGEO and DISMAN. 

J. de Vlieg, R. M. Scheek, W. F. van Gunsteren, H. J. C. Berendsen, R. Kaptein, and J. Thomason, Proteins, 3, 209 (1988). Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination from Nuclear Magnetic Resonance Data Application to the DNA Binding Domain of lac Repressor from Escherichia coli. 

J. de Vlief and W. F. van Gunsteren. Combined procedures of distance geometry and molecular dynamics for determining protein structure from nuclear magnetic resonance data. Methods Enzymol. 202 268-300 (1991). 

Strategies for Use in the Determination of Protein Structure from Distance Constraints Obtained by Nuclear Magnetic Resonance. 

Solid state nuclear magnetic resonance spectroscopy (NMR), e.g. [107-109]. This technique is sensitive to the local environment of certain nuclei, their mobility and orientation [108]. It provides information about the heterogeneity of polymer blends to c. 5 nm or less (spin diffusion experiments) or c. 0.3 nm in cross-polarization experiments, from which the direct (averaged) distance between two types of nuclei in a sample can be determined [107,108]. Motions of moleuclar groups in a polymer chain can be analyzed and correlations with dispersion areas in the mechanical spectra may be possible [109]. Solid state NMR is not a standard technique at the present time but it is becoming increasingly important. 

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