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.     

1,8-Naphthyridines. Part III. Synthesis of some 6-substituted-1,8-naphthyridin-2(1H)ones

The syntheses of some 1,8-naphthyridines substituted in the 6-position with heterocyclic groups are described. A synthetic route to 6-amino-5,7-dimethyl-1,8-naphthyridin-2(1H)one is also presented.     

Selection of terms for a CI wavefunction to preserve potential surface features

A cumulative selection procedure for choosing configuration functions for inclusion in CI calculations is described. The objective of the method is to obtain equal energy loss, relative to unselected calculations, for different states and different regions of the potential surface. Results obtained from calculations on the BH molecule indicate an overall advantage in comparison to the threshold selection procedure, particularly with regard to molecular geometry changes.     

Application of solid phase microextraction in the determination of paralytic shellfish poisoning toxins

A SPME-HPLC-post-column fluorescent derivatization method for the direct determination of saxitoxin (STX), the most potent paralytic shellfish poisoning (PSP) toxin, in water has been developed. Commercially available SPME devices with 50 microm Carbowax templated resin (CW/TPR) coating was found to be able to pre-concentrate STX from aqueous media. A special pre-conditioning treatment of soaking the SPME coating in 0.1 M NaOH solution significantly improved the extraction efficiency. The optimal pH for the SPME process is 8.1 and the equilibration time is 40 min. The partition coefficient, K, of the distribution of STX between the SPME coating and the aqueous media was measured to be 2.99 +/- 0.04 x 10(3). Extracted toxin on the SPME stationary phase was difficult to be desorbed by the HPLC mobile phase under dynamic desorption mode. A static ion-pairing desorption technique using a desorption solvent mixture of 20 mM sodium 1-heptanesulfonate in 30% aqueous acetonitrile acidified with 50 mM sulfuric acid was developed to overcome this problem. The method detection limit and repeatability achieved by this SPME-HPLC method were 0.11 ng ml(-1) and 3.7%, respectively, with a sample volume of just 5 ml of water. This analytical method is adequate for the monitoring of the PSP toxin in fresh/drinking waters. However, serious interference was observed when this technique was applied to saline water samples. This is probably due to competition of sodium ions with the cationic STX for absorption into the SPME stationary phase.     

Acrylonitrile polymerization by Cy3PCuMe and (Bipy)2FeEt2

Cy(3)PCuMe (1) undergoes reversible ligand redistribution at low temperature in solution to form the tight ion pair [Cu(PCy(3))(2)][CuMe(2)] (3). The structure of 3 was assigned on the basis of (i) the stoichiometry of the 1 = 3 equilibrium, (ii) the observation of a triplet for the PCy(3) C1 (13)C NMR resonance due to virtual coupling to two (31)P nuclei, and (iii) reverse synthesis of 1 by combining separately generated Cu(PCy(3))(2)(+) and CuMe(2)(-) ions. Complex 1 and [Cu(PCy(3))(2)][PF(6)] (5) coordinate additional PCy(3) to form (Cy(3)P)(2)CuMe and [Cu(PCy(3))(3)][PF(6)], respectively, while 3 does not. Complex 1, free PCy(3), and (bipy)(2)FeEt(2) (2) each initiate the polymerization of acrylonitrile. In each case, the polyacrylonitrile contains branches that are characteristic of an anionic polymerization mechanism. The major initiator in acrylonitrile polymerization by 1 is PCy(3), which is liberated from 1. A transient iron hydride complex is proposed to initiate acrylonitrile polymerization by 2.     

Deactivation of vibrationally excited CD3H using laser-induced fluorescence

Infrared fluorescence observed after exciting to ν₆ (ν=1) of CD₃H with a Q-switched CO₂ laser yields the exponential deactivation rate constant of 0.84 ms^?1 torr^?1. Rate constants for deactivation of CD₃H by rare gases vary from 1.4 (for He) to 0.029 (for Xe) ms^?1 torr^?1.     

Evaluation of enzymatic digestion and liquid chromatography-mass spectrometry peptide mapping of the integral membrane protein bacteriorhodopsin

A method for the complete peptide mapping of the model integral membrane protein bacteri-orhodopsin is demonstrated. Utilizing more effective enzymatic digestion, procedures with capillary liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) and tandem mass spectrometry (MS/MS), all predicted tryptic digestion products were detected, as well as peptides from all previously reported post-translational modifications of bacteriorhodopsin. A significant contribution of chymotryptic-like digestion products was also observed. A characterization of the behavior of hydrophobic integral membrane peptides in a reversed-phase liquid chromatographic separation is also provided. The method reported here offers improved compatibility of the solubilizing reagents with both the chromatography and mass spectrometry, rendering it suitable for high-throughput proteomic applications.     

Enzymatic surface modification of Kevlar fibers

Horseradish peroxidase catalyzed grafting of acrylamide (AM) onto Kevlar fibers has been studied. The modified fiber has been characterized with scanning electron microscopy (SEM), elemental analysis and the grafting yield. From the SEM micrographs, the surface of the grafted Kevlar fiber is rougher than that of the untreated fiber, and the elemental analysis indicated that the nitrogen content of the treated fibers is higher than that of the untreated fiber. All the results suggested that AM must have been grafted onto the Kevlar surface through HRP-mediated radical initiated grafting reaction. The probably mechanism of HRP catalyzed grafting of AM onto Kevlar surface is proposed.     

Total synthesis of (+)-epiquinamide

The stereoselective total synthesis of the novel quinolizidine alkaloid (+)-epiquinamide is presented, starting from the amino acid l-allysine ethylene acetal. Key steps in the synthesis involved a highly diastereoselective N-acyliminium ion allylation and a ring-closing metathesis reaction to provide the bicyclic skeleton. [reaction: see text]