NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins

NMR spectroscopy and X-ray crystallography, the two primary experimental methods for protein structure determination at high resolution, have different advantages and disadvantages in terms of sample preparation and data collection and analysis. It is therefore of interest to assess their complementarity when applied to small proteins. Structural genomics/proteomics projects provide an ideal opportunity to make such comparisons as they generate data in a systematic manner for large enough numbers of proteins to allow firm conclusions to be drawn. Here we report a comparison for 263 unique proteins screened by both NMR spectroscopy and X-ray crystallography in our structural proteomics pipeline. Only 21 targets (8%) were deemed amenable to both methods based on an initial 2D 15N-HSQC NMR spectrum and optimized crystallization trials. However, the use of both methods in the pipeline increased the total number of targets amenable to structure determination to 107, with 43 amenable to NMR only and 43 amenable to X-ray crystallographic methods only. We did not observe a correlation between 15N-HSQC spectral quality and the success of the same protein in crystallization screens. Similar results were found for an independent set of 159 proteins as reported in the accompanying paper by Snyder et al. Thus, we conclude that both methods are highly complementary, and in order to increase the number of proteins suited for structure determination, we suggest that both methods be used in parallel in screening of all small proteins for structure determination.     

Potassium-selective optrode based on an immobilized fluorogenic crown ether

A new optical sensor phase for potassium ions has been developed based on the immobilization of the pH-dependent fluorogenic crown ether 4-acryloylamidobenzo-18-crown-6 on the non-ionic polymeric resin Amberlite XAD-2.Two different optical designs, a flow-through sensor and a fibre optic probetype sensor (optrode), have been constructed and their analytical performance characteristics have been evaluated. The resulting fluorimetric sensors for K⁺ ions exhibited detection limits of 0.4 or 0.8 M of K⁺ (16 g/l or 31 g/l), depending on the design, while the linear response occurred from 1 to 25 M of the metal concentrations. The precision, evaluated as the relative standard deviation of measurements of K⁺ levels at around ten times the detection limit (e.g. 5 M), turned out to be around ±2%.Advantageous features of this fluorimetric sensing phase and optrode include ease of construction, simplicity of use, reversibility, short response times (ca. 1 min full scale deflection) selectivity and operational stability, suitable for sensing potassium at low levels in complex matrices such as biological fluids.The fluorimetric optical sensor has been successfully applied to the direct determination of potassium in clinically important samples (serum and urine) and in natural waters. Very good accuracy has been obtained just using adequate synthetic aqueous potassium standards for calibration.     

Electrospray ionization quadrupole time-of-flight and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometric analyses to solve micro-heterogeneity in post-translationally modified peptides from Phoneutria nigriventer (Aranea, Ctenidae) venom

Previous studies of the fractionated venom of the Brazilian armed spider Phoneutria nigriventer, obtained by gel filtration, have demonstrated the presence of a fraction PhM, a pool of small peptides (up to 2000 Da) that provoke contractions in smooth muscle of guinea pig ileum. Initial attempts to sequence these peptides were largely unsuccessful because of the low purification yield and the fact that the majority seemed to be blocked at their N-termini. In the present work, analysis of this venom fraction by mass spectrometry has revealed the existence of a highly complex mixture of peptides with molecular weights corresponding to those observed for the muscle-active peptides previously described (800-1800 Da). These peptides appear to be a family of isoforms with some particular features. The amino acid sequences of 15 isoforms have been determined by tandem mass spectrometry (MS/MS) using both electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q/ToFMS) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-ToF/ToFMS). These molecules contain post-translational modifications such as proteolysis and C-terminal amidation, which combine to generate additional isoforms. All the isoforms sequenced in this study possess an N-terminal pyroglutamic acid residue. A search for sequence similarities with other peptides in databanks revealed that these peptides are structurally related to the tachykinins, a family of neuro-hormone peptides. The data obtained in this study will be essential for the subsequent steps of this research, the synthesis of these peptides and pharmacological characterization of their biological activity.     

Optimization of the Conditions for the Cr (III) Adsorption on Activated Carbon

In order to understand the patterns of the adsorption equilibrium of Cr (III) on activated carbon, the adsorption process was studied by two different ways: classical batch experiments on commercial Norit and Merck activated carbons and their oxidized forms in a wide range of pHs; and extended time-based tests at the same pH values on the same adsorbents. This approach allowed us to understand the role of texture, chemical carbon surface functionality and experimental conditions (initial pH of the solution, contact time and adsorbate/adsorbent ratio) on the effectiveness of Cr (III) removal. The adsorption process of Cr (III) at (24 ± 1^∘C) on Merck and Norit activated carbons and their oxidized forms were studied at pH values between 1.5 and 5 (either adjusted or buffered). Chromium concentration was fixed at 200 ppm. The carbon loading ranged from 1.2 to 20 g/l. The carbon/Cr (III) solution contact time was varied from 0.5–1 month to 5 months, to ensure that the saturation of the carbon level was reached. According to the data obtained, the presence of carboxylic groups on carbon surface seems to enhance Cr (III) uptake at initial pH of the solution in the range between 2 and 4. Depending on the nature of the adsorbent surface chemistry, the contact time to reach equilibrium may range from 3 to 5 months. There is an optimum carbon loading which limits the Cr (III) uptake/removal at given pH value. In order to understand the adsorption process, an ion exchange, surface complex and surface precipitation were considered. This paper was presented in the 5th Brazilian Meeting on Adsorption, held at Natal, Brazil, 18-21 July, 2004.     

A facile tandem carbene-ylide route to 2-fluoropyrrole derivatives

2-Fluoropyrroles were synthesised via 1,3-dipolar cycloaddition of iminiodifluoromethanides derived from corresponding imines and difluorocarbene to dimethyl acetylenedicarboxylate.     

Stereoselective Rh-catalyzed hydrogenation of cyclobutyl chiral enamides: double stereodifferentiation vs catalyst-controlled diastereoselection

The hydrogenation reactions of several cyclobutyl enamides derived from (-)-alpha-pinene or (-)-verbenone have been investigated by using different catalysts. The chiralities of both the substrate and the catalyst as well as the Z/E stereochemistry of the double bond have been considered, and the observed diastereoselectivity has been rationalized. For enamides with the double bond separated from the cyclobutane by a methylene, the Wilkinson catalyst did not induce any diastereoselection, but excellent diastereoselectivity was observed when using Et-DuPHOS-Rh and ChiraPHOS-Rh. The configuration of the new stereogenic center was catalyst-dependent and can be rationalized according to the Halpern mechanism. For (Z)-enamides with the double bond directly linked to the cyclobutane ring, the chirality of the substrate governed the diastereoselection and the Halpern mechanism seemed not to be operative in the hydrogenation with ChiraPHOS, with the configuration of the new stereogenic center being determined by steric effects. On the contrary, the chirality of the catalyst was the factor determining the stereochemistry of the major products with alkyl-DuPHOS-Rh. Z/E stereochemistry influenced the stereodifferentiation, and a different behavior for each Z or E stereoisomer was found. For both (Z)- and (E)-enamides, some instances of match/mismatch between the chirality of the substrate and that of the catalyst were observed. As a result of all of these studies, a series of new cyclobutyl alpha-amino acids has been synthesized. These products are interesting to incorporate into conformationally constrained peptides.     

Trace and major elements in serum of patients with chronic myelogenous leukemia

Summary Major and trace elements were determined in serum of patients with chronic myelogenous leukemia (CML) using total reflection X-ray fluorescence induced by synchrotron radiation (SRTXRF). CML affects 1 to 2 people per 100,000 and accounts for 7-20% cases of leukemia. It was possible to determine the concentrations of the following elements: P, S, Cl, K, Ca, Cr, Mn, Fe, Ni, Cu, Zn, Br and Rb. Using analysis of variance (ANOVA) it was observed that the contents of the P, S, Ca, Cr, Mn, Fe, Cu and Rb elements differed significantly at a = 0.05 between groups of healthy subjects and CML patients and also genders (males and females).     

A family of alkynylgold(III) complexes [AuI(mu-{CH2}2PPh2)2Au(III)(C triple bond CR)2] (R = Ph, tBu, Me3Si): facile and reversible comproportionation of gold(I)/gold(III) to digold(II)

The symmetric digold(II)dichloride bis(ylide) complex [Au2Cl2(mu-{CH2}2PPh2)2] reacts with acetylides to form the asymmetric heterovalent gold(I)/gold(III) complexes [AuI(mu-{CH2}2PPh2)2AuIII(CCR)2] [R = Ph, tBu, and SiMe3], the phenyl analogue of which was characterized by X-ray crystallography. These compounds represent the first examples of gold(III) complexes containing two acetylide ligands. [AuI(mu-{CH2}2PPh2)2AuIII(CCPh)2] undergoes a reversible comproportionation reaction upon treatment with [Ag(ClO4)tht] to give the symmetric digold(II) cationic complex [Au2(tht)2(mu-{CH2}2PPh2)2](ClO4)2. If this complex is treated with phenylacetylene in the presence of base, the heterovalent gold(I)/gold(III) complex is re-formed. This reversible interconversion between binuclear gold(I)/gold(III) and digold(II) bis(ylide) complexes is unprecedented.     

Interactions of D-Maltose and Sucrose with Some Amino Acids in Aqueous Solutions

Calorimetric titrations have been performed at 298.15 K in aqueous solutions to derive the stability constants and thermodynamic parameters of the interactions of D-maltose and sucrose with some amino acids (glycine, DL-alanine, DL-leucine, and L-serine). The apparent molal volumes of the disaccharides in dilute aqueous solutions of the amino acids have been determined from density measurements at 298.15 K. In contrast to D-maltose, sucrose was found to associate with the amino acids and these associated species are preferentially entropy stabilized. These results are interpreted in terms of the influence of the nature of the solutes, their specific conformations, and hydration, on the ability of the disaccharides to form associated complexes with the amino acids.     

Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives

The structural, dynamical, and recognition properties of antiparallel DNA triplexes formed by the antiparallel d(G#G.C), d(A#A.T), and d(T#A.T) motifs (the pound sign and dot mean reverse-Hoogsteen and Watson-Crick hydrogen bonds, respectively) are studied by means of "state of the art" molecular dynamics simulations. Once the characteristics of the helix are defined, molecular dynamics and thermodynamic integration calculations are used to determine the expected stabilization of the antiparallel triplex caused by the introduction of 8-aminopurines. Finally, oligonucleotides containing 8-aminopurine derivatives are synthesized and tested experimentally using several approaches in a variety of systems. A very large stabilization of the triplex is found experimentally, as predicted by simulations. These results open the possibility for the use of oligonucleotides carrying 8-aminopurines to bind single-stranded nucleic acids by formation of antiparallel triplexes.