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.     

The surface of ordered mesoporous benzene-silica hybrid material: an infrared and ab initio molecular modeling study

Joint IR and computational results allow a detailed characterization of the surface properties of a mesoporous benzene-silica hybrid material with crystal-like wall structure. After outgassing at 450 degrees C, hydroxyl species mainly consist of noninteracting silanols, with both O-H and Si-O stretching modes at lower frequencies than those of SiOH in silica. Interaction with several probe molecules, followed both by experiment and calculus, shows that the aryl group in the coordination sphere of Si imparts a lesser acidity with respect to the isolated silanol in silica. In contrast, adsorption isotherms indicate that the interaction with acetone is stronger with benzene-silica than with silica: this is interpreted in terms of secondary interactions taking place between the slightly acidic CH in acetone and the electronic cloud in benzene-like rings. This suggests that both the inorganic component and the organic one play a role in dictating the surface behavior.     

Chemical reaction studies in CH4/Ar and CH4/N2 gas mixtures of a dielectric barrier discharge

Chemical reactions in a dielectric barrier discharge at medium pressure of 250-300 mbar have been studied in CH(4)/Ar and CH(4)/N(2) gas mixtures by means of mass spectrometry. The main reaction scheme is production of H(2) by fragmentation of CH(4), but also production of higher order hydrocarbon molecules such as C(n)H(m) with n up to 9 including formation of different functional CN groups is observed. Formation of C(2)H(2), C(2)H(4), and C(2)H(6) molecules has been investigated in some detail. Significant differences are noted in comparison to a theoretical estimate.     

MgF(3)(-) as a transition state analog of phosphoryl transfer

The formation of complexes between small G proteins and certain of their effectors can be facilitated by aluminum fluorides. Solution studies suggest that magnesium may be able to replace aluminum in such complexes. We have determined the crystal structure of RhoA.GDP bound to RhoGAP in the presence of Mg(2+) and F(-) but without Al(3+). The metallofluoride adopts a trigonal planar arrangement instead of the square planar structure of AlF(4)(-). We have confirmed that these crystals contain magnesium and not aluminum by proton-induced X-ray emission spectroscopy. The structure adopted by GDP.MgF(-) possesses the stereochemistry and approximate charge expected for the transition state. We suggest that MgF3(-) may be the reagent of choice for studying phosphoryl transfer reactions.     

Antihydrophobic cosolvent effects for alkylation reactions in water solution, particularly oxygen versus carbon alkylations of phenoxide ions

Antihydrophobic cosolvents such as ethanol increase the solubility of hydrophobic molecules in water, and they also affect the rates of reactions involving hydrophobic surfaces. In simple reactions of hydrocarbons, such as the Diels-Alder dimerization of 1,3-cyclopentadiene, the rate and solubility data directly reflect the geometry of the transition state, in which some hydrophobic surface becomes hidden. In reactions involving polar groups, such as alkylations of phenoxide ions or S(N)1 ionizations of alkyl halides, cosolvents in water can have other effects as well. However, solvation of hydrophobic surfaces is still important. By the use of structure-reactivity relationships, and comparing the effects of ethanol and DMSO as solvents, it has been possible to sort out these effects. The conclusions are reinforced by an ab initio computer model for hydrophobic solvation. The result is a sensible transition state for phenoxide ion as a nucleophile, using its oxygen n electrons to avoid loss of conjugation. The geometry of alkylation of aniline is very different, involving packing (stacking) of the aniline ring onto the phenyl ring of a benzyl group in the benzylation reaction. The alkylation of phenoxide ions by benzylic chlorides can occur both at the phenoxide oxygen and on ortho and para positions of the ring. Carbon alkylation occurs in water, but not in nonpolar organic solvents, and it is observed only when the phenoxide has at least one methyl substituent ortho, meta, or para. The effects of phenol substituents and of antihydrophobic cosolvents on the rates of the competing alkylation processes indicate that in water the carbon alkylation involves a transition state with hydrophobic packing of the benzyl group onto the phenol ring. The results also support our conclusion that oxygen alkylation uses the n electrons of the phenoxide oxygen as the nucleophile and does not have hydrophobic overlap in the transition state. The mechanisms and explanations for competing oxygen and carbon alkylations differ from previous proposals by others.     

Elucidation of solid-state complexation in ground mixtures of cholic acid and guest compounds

The solid-state complexation between cholic acid (CA) and either methyl p-hydroxybenzoate (MPB) or ibuprofen (IBP) was investigated. Powder X-ray diffractometry, IR spectroscopy and thermal analysis suggested the complex formation between CA and MPB as well as between CA and IBP by co-grinding method. The stoichiometry of CA-MPB was 1 : 1 while that of CA-IBP was 2 : 1, reflecting the effect of guest size on complex formation. The guest compounds were assumed to be included in the channel of complexes formed by hydrogen bonds among CA molecules.     

Direct observation of the multistep helix formation of poly-L-glutamic acids

The helix formation dynamics of poly-L-glutamic acids (PGAs) were observed by the microsecond-resolved Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopies. The helix formation of 34-residue PGA from random coil at pH (or pD for FTIR) 8.0 was initiated by a pH jump to 4.9 using the rapid solution mixer whose mixing dead time is 50 micros. The amide I' line in the time-resolved FTIR spectra exhibited the fast (<100 micros) increase of the total helical content. The time-resolved CD spectra of the same process also showed the fast (<150 micros) formation of short helical segments (5 +/- 1 residues), which was followed by the slower (<1 ms) elongation of the short helices to longer helices (>10 residues). Similar dynamics were observed for the same pH jump of approximately 190-residue PGA, although there were additional steps that made the helix formation of approximately 190-residue PGA more complex. The observed multistep helix formation is likely caused by the strong hydrogen-bonding interactions between the protonated side chains of PGAs.     

Surface-renewable cobalt(II) hexacyanoferrate-modified graphite organosilicate electrode and its electrocatalytic oxidation of thiosulfate

Cobalt(II) hexacyanoferrate (CoHCF) was deposited on graphite powder by an in situ chemical deposition procedure and then dispersed into methyltrimethoxysilane-derived gels to prepare a surface-renewable CoHCF-modified electrode. The electrochemical behavior of the modified electrode in different supporting electrolyte solutions was characterized by cyclic voltammetry. In addition, square-wave voltammetry was employed to investigate the pNa-dependent electrochemical behavior of the electrode. The CoHCF-modified electrode showed a high electrocatalytic activity toward thiosulfate oxidation and could thus be used as an amperometric thiosulfate sensor.     

Structural characterization and magnetic properties of sandwich-type tungstoarsenate complexes. Study of a mixed-valent VIV2/VV heteropolyanion

Complexes K11Na1[As2W18(Mn(H2O))3O66]x27H2O (1) and Na12[As2W18(Co(H2O))3O66]x34H2O (2) have been characterized. 1 crystallizes in the orthorhombic space group Pnma, with a = 30.6484(4) A, b = 14.9946(2) A, and c = 19.17080(10) A (Z = 4), while 2 crystallizes in the monoclinic space group C2/c, with a = 14.124(2) A, b = 23.294(3) A, c = 32.247(3) A, and beta = 98.935(10) degrees (Z = 4). Structures of the anions of 1 and 2 are similar, the divalent metals adopting a square pyramidal environment. K11[As2W18(VO)3O66]x23H2O (3) crystallizes in the orthorhombic space group Pnma, with a = 30.6240(5) A, b = 14.9861(2) A, and c = 19.2651(3) A (Z = 4). The structure has revealed a disorder on two of the three metals linking the [alpha-AsW9O33]9- parts. For these two vanadium atoms, the V=O bonds are directed alternatively toward the inside or the outside of the [alpha-AsW9O33]9- cavity. The remaining vanadium shows a V=O bond always directed toward the outside of the cavity. Titration of VIV by CeIV revealed that 3 is the mixed-valent VIV2VV species. Magnetic measurements are in agreement with this formulation. The high-temperature molar magnetic susceptibility of a powdered sample of 3 clearly confirms the presence of two d1 centers. The two VIV are antiferromagnetically coupled, with J = -2.9 cm-1 and g = 1.93. Crystallographic data do not permit the location of the two VIV to be distinguished from the location of the VV. As expected, the Mn(II) are very weakly antiferromagnetically coupled in compound 1. The complex Na8[Ni(H2O)6]2[As2W18(Ni(H2O))3O66]x20H2O (4) has been synthesized. The anion crystallized with two octahedral [Ni(H2O)6]2+ as counterions. Magnetic data have been fitted assuming that the only exchange-coupled centers are the nickels of the polyanion. 4 exhibits an antiferromagnetic coupling with J = -1.7 cm-1, g = 2.27, and theta = -1.5 K.     

Structure-activity relationships of a new antifungal imidazole, AFK-108, and related compounds

Fungicidal activity of widely used imidazole antifungal drugs in topical applications is not so strong in spite of their fungistatic activities against dermatophytes and pathogenic yeasts. In order to improve fungicidal activity of imidazole antifungal agents, a series of novel imidazole derivatives having a hydrophobic substituent derived from isoprenoid were synthesized. The efficacy of these compounds was evaluated with respect to direct cell-membrane damaging activity, ergosterol biosynthesis inhibition, minimum growth-inhibitory concentration (MIC) and therapeutic effect for experimental dermatophytosis of guinea pigs. Among the newly synthesized compounds, the geranyl derivative named AFK-108 (2a) showed the highest in vivo fungicidal activity with both cell membrane damaging activity and ergosterol biosynthesis inhibition in vitro.