Three-dimensional nuclear magnetic resonance

Mishkovsky M, Kupce E, Frydman L (2007) Ultrafast-based projection-reconstruction three-dimensional nuclear magnetic resonance spectroscopy. J Chem Phys 127 034507... 

The structures of vanicosides A (1) and B (2) and hydropiperoside (3) were established primarily by one- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy techniques and fast atom bombardment (FAB) mass spectrometry (MS).22 The presence of two different types of phenylpropanoid esters in 1 and 2 was established first through the proton (4H) NMR spectra which showed resonances for two different aromatic substitution patterns in the spectrum of each compound. Integration of the aromatic region defined these as three symmetrically substituted phenyl rings, due to three p-coumaryl moieties, and one 1,3,4-trisubstituted phenyl ring, due to a feruloyl ester. The presence of a sucrose backbone was established by two series of coupled protons between 3.2 and 5.7 ppm in the HNMR spectra, particularly the characteristic C-l (anomeric) and C-3 proton doublets... 

G. M. Clore, P. T. Wingfield, and A. M. Gronenborn, Biochemistry, 30,2315 (1991). High-Resolution Three-Dimensional Structure of Interleukin IB in Solution by Three- and Four-Dimensional Nuclear Magnetic Resonance Spectroscopy. 

Present day techniques for structure determination in carbohydrate chemistry are sub stantially the same as those for any other type of compound The full range of modern instrumental methods including mass spectrometry and infrared and nuclear magnetic resonance spectroscopy is brought to bear on the problem If the unknown substance is crystalline X ray diffraction can provide precise structural information that m the best cases IS equivalent to taking a three dimensional photograph of the molecule... 

Spectrometric Analysis. Remarkable developments ia mass spectrometry (ms) and nuclear magnetic resonance methods (nmr), eg, secondary ion mass spectrometry (sims), plasma desorption (pd), thermospray (tsp), two or three dimensional nmr, high resolution nmr of soHds, give useful stmcture analysis information (131). Because nmr analysis of or N-labeled amino acids enables determiaation of amino acids without isolation from organic samples, and without destroyiag the sample, amino acid metaboHsm can be dynamically analy2ed (132). Proteia metaboHsm and biosynthesis of many important metaboUtes have been studied by this method. Preparative methods for labeled compounds have been reviewed (133). 

A review is given of the application of Molecular Dynamics (MD) computer simulation to complex molecular systems. Three topics are treated in particular the computation of free energy from simulations, applied to the prediction of the binding constant of an inhibitor to the enzyme dihydrofolate reductase the use of MD simulations in structural refinements based on two-dimensional high-resolution nuclear magnetic resonance data, applied to the lac repressor headpiece the simulation of a hydrated lipid bilayer in atomic detail. The latter shows a rather diffuse structure of the hydrophilic head group layer with considerable local compensation of charge density. 

The problem of characterizing the three-dimensional structure of G-protein-coupled receptors by x-ray crystallography or nuclear magnetic resonance (NMR) has been particularly difficult to solve. The receptors are complicated membrane proteins that are difficult to produce in sufficiently large quantities. When they have been available, it has been difficult to make them form useful... 

Structural investigations into the degree of branching and into the position and nature of glycosidic bonds and of non-carbohydrate residues in polysaccharides may include periodate oxidation and other procedures such as exhaustive methylation. X-ray diffraction and spectroscopic techniques such as nuclear magnetic resonance and optical rotatory dispersion also give valuable information especially relating to the three-dimensional structures of these polymers. 

Aside from the direct techniques of X-ray or electron diffraction, the major possible routes to knowledge of three-dimensional protein structure are prediction from the amino acid sequence and analysis of spectroscopic measurements such as circular dichroism, laser Raman spectroscopy, and nuclear magnetic resonance. With the large data base now available of known three-dimensional protein structures, all of these approaches are making considerable progress, and it seems possible that within a few years some combination of noncrystallo-graphic techniques may be capable of correctly determining new protein structures. Because the problem is inherently quite difficult, it will undoubtedly be essential to make the best possible use of all hints available from the known structures. 

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