Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination

X-ray crystallography and NMR spectroscopy provide the only sources of experimental data from which protein structures can be analyzed at high or even atomic resolution. The degree to which these methods complement each other as sources of structural knowledge is a matter of debate; it is often proposed that small proteins yielding high quality, readily analyzed NMR spectra are a subset of those that readily yield strongly diffracting crystals. We have examined the correlation between NMR spectral quality and success in structure determination by X-ray crystallography for 159 prokaryotic and eukaryotic proteins, prescreened to avoid proteins providing polydisperse and/or aggregated samples. This study demonstrates that, across this protein sample set, the quality of a protein's [15N-1H]-heteronuclear correlation (HSQC) spectrum recorded under conditions generally suitable for 3D structure determination by NMR, a key predictor of the ability to determine a structure by NMR, is not correlated with successful crystallization and structure determination by X-ray crystallography. These results, together with similar results of an independent study presented in the accompanying paper (Yee, et al., J. Am. Chem. Soc., accompanying paper), demonstrate that X-ray crystallography and NMR often provide complementary sources of structural data and that both methods are required in order to optimize success for as many targets as possible in large-scale structural proteomics efforts.     

Analysis of gadobenate dimeglumine by capillary zone electrophoresis coupled with electrospray-mass spectrometry

Highly reliable and accurate analytical methods are needed for the determination of magnetic resonance imaging (MRI) contrast agents in complex matrices of clinical interest. We demonstrate the reliability of capillary zone electrophoresis (CZE) coupled with electrospray ionization-mass spectrometry (ESI-MS) for the analysis of MultiHance (gadobenate dimeglumine), a gadolinium-based MRI agent. A sheath liquid interface connected the CE system with an electrospray mass spectrometer equipped with an ion-trap analyzer. CZE with ultraviolet (CZE-UV) and with mass detection (CZE-MS) were compared by analyzing gadobenate dimeglumine and the free ligand diluted in water and in biological fluids (i.e., human serum and urine). The optimization of some relevant CZE-MS parameters was accomplished, like CE buffer composition, sheath liquid composition and flow, and type and length of the separation capillary. CZE-UV was highly influenced by the biological sample components, which hindered a reliable quantification of both gadobenate and free ligand in serum and urine. In CZE-MS, on the other hand, the electrophoretic runs turned out to be independent of the clinical matrices, due to the informative potential and to the selectivity of MS detection.     

Chemical waves and pattern formation in the 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/water lamellar system

The present work deals with the spatially extended oscillatory Belousov Zhabotinsky reaction-diffusion system carried out in an anisotropic environment of phosphatidylcholines/water binary system, which presents layered aqueous domains separated by lipid bilayers. We report the occurrence of stable Turing patterns, spiral waves, and other exotic structures in phospholipids bilayers that are generally used as a models for cell plasma membranes.     

Synthesis of Glycosylrifamycins,a new type of semisynthetic rifamycins

Glycosylrifamycins, a new type of semisynthetic rifamycin derivatives, can be easily obtained by reaction of 3-(2-aminoethylthio)rifamycin SV ( 2 ) with a glycosyl compound carrying a coupling group, such as isothicyanate or carboxy. We prepared O-acetylated and free glucopyranosyl and arabinopyranosyl derivatives of rifamycin S and SV (see 3–10 ). Additionally, derivatives with D -saccharo-1,4-lactone and with shikimic acid were obtained (see 11–15 ). Glycosylrifamycins show an interesting inhibitory power on Gram-positive bacteria (Table).     

Oxidation of propene over various doped tungsten oxides

The oxidation of propene was studied on several tungsten oxides which contained small amounts of Ti, Ta, Nb and Sn. Only the Sn-containing specimen was found to be selective in the conversion of propene to acrolein. The catalytic results are correlated with crystal structures determined by electron microscopy.

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, Ti, Ta, Nb Sn. , , Sn, . , .

     

Discriminating the helical forms of peptides by NMR and molecular dynamics simulation

The HNCO NMR pulse sequence was applied to three selectively labeled (15)N and (13)C isotopic homologues of the peptide Ac-WAAAH(AAARA)(3)A-NH(2) to probe directly for hydrogen bonds between residues 8 and 11 (characteristic of a 3(10)-helix), 8 and 12 (alpha-helix), and 8 and 13 (pi-helix). The experiments demonstrate conclusively, and in agreement with circular dichroism studies, that the center of the peptide is alpha-helical; there is no discernible 3(10)- or pi-helix at these specific positions. Molecular dynamics simulations of the preceding peptide and Ac-(AAAAK)(3)A-NH(2) in water using the potential energy parameter set CHARMM22/CMAP correctly yield an alpha-helix, in contrast to simulations with the set CHARMM22, which result in a pi-helix.     

Substituent control of hydrogen bonding in palladium(II)-pyrazole complexes

Inter- and intramolecular hydrogen bonding of an N-H group in pyrazole complexes was studied using ligands with two different groups at pyrazole C-3 and C-5. At C-5, groups such as methyl, i-propyl, phenyl, or tert-butyl were present. At C-3, side chains L-CH(2)- and L-CH(2)CH(2)- (L = thioether or phosphine) ensured formation of chelates to a cis-dichloropalladium(II) fragment through side-chain atom L and the pyrazole nitrogen closest to the side chain. The significance of the ligands is that by placing a ligating side chain on a ring carbon (C-3), rather than on a ring nitrogen, the ring nitrogen not bound to the metal and its attached proton are available for hydrogen bonding. As desired, seven chelate complexes examined by X-ray diffraction all showed intramolecular hydrogen bonding between the pyrazole N-H and a chloride ligand in the cis position. In addition, however, intermolecular hydrogen bonding could be controlled by the substituent at C-5: complexes with either a methyl at C-5 or no substituent there showed significant intermolecular hydrogen bonding interactions, which were completely avoided by placing a tert-butyl group at C-5. The acidity of two complexes in acetonitrile solutions was estimated to be closer to that of pyridinium ion than those of imidazolium or triethylammonium ions.