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.     

Polyaniline and polypyrrole: A comparative study of the preparation

Aniline and pyrrole have been oxidized with ammonium peroxydisulfate in aqueous solutions, in the presence of equimolar quantities of hydrochloric acid. The oxidation of pyrrole was faster; the induction period typical of aniline oxidation was absent in the case of pyrrole. As the proportion of oxidant-to-monomer molar concentration increased up to 1.5, the yield increased in both cases. Similarities between the two oxidations are illustrated and discussed. The oxidant-to-monomer molar ratio 1.25 is proposed to be the optimum stoichiometry, in the accordance with the data published in the literature. The conductivities of the polymers prepared were only slightly dependent on the oxidant-to-monomer ratio in the range 0.3-1.5, and were of the order of 10⁰ S cm⁻¹ for polyaniline and ∼10⁻²-10⁻¹ S cm⁻¹ for polypyrrole. Outside this interval, the conductivity of both polymers was reduced. Polyaniline having conductivity ∼10 S cm⁻¹ was produced in solutions of phosphoric acid of various concentrations. On the contrary, the conductivity of polypyrrole was reduced as the concentration of phosphoric acid became higher. The type of protonation is discussed with the help of FTIR spectra by analyzing the ammonium salts obtained after deprotonation. Sulfate or hydrogen sulfate anions produced from peroxydisulfate always constitute a part of the counter-ions.     

Palladium-catalyzed reactions for the synthesis of chlorins and 5,10-porphodimethenes

The palladium-catalyzed reaction of RLi with various 5,10,15,20-tetrasubstituted porphyrins offers a convenient synthetic route to chlorins and porphodimethenes (calixphyrins). The reactions utilized various Pd catalysts and CuI and yielded either 2,3-substituted chlorins or 5,10-disubstituted porphodimethenes in yields ranging from 20-40%. The reaction of octaethylporphyrin with t-BuLi in the presence of a Pd-catalyst generated the corresponding 5,10-porphodimethene in 72% yield.     

Modeling Formation and Removal of Limescale in Water Treatment Systems

Doklady Mathematics - Modeling the processes of formation and removal of limescale formed in water treatment systems is considered to develop closed-loop technologies. Solid deposits that form over...     

A Heuristic Decomposition Algorithm for Scheduling Problems on Mixed Graphs

We consider a scheduling problem where a set of n jobs has to be processed on a set of m machines and arbitrary precedence constraints between operations are given. Moreover, for any two operations i and j values a _ij >0 and a _ji >0 may be given where a _ij is the minimal difference between the starting times of operations i and j when operation i is processed first. Often, the objective is to minimize the makespan but we consider also arbitrary regular criteria. Even the special cases of the classical job shop problem J//C_max belong to the set of NP-hard problems. Therefore, approximation or heuristic algorithms are necessary to handle large-dimension problems. Based on the mixed graph model we give a heuristic decomposition algorithm for such a problem, i.e. the initial problem is partitioned into subproblems that can be solved exactly or approximately with a small error bound. These subproblems are obtained by a relaxation of a subset of the set of undirected edges of the mixed graph. The subproblems are successively solved and a proportion of the results obtained for one subproblem is kept for further subproblem definitions. Numerical results of the algorithm presented here are given.     

Preparation of lucifer yellow fluorescent liposomes: A method for cells' membrane labeling

This report describes a method to conjugate lucifer yellow to the external surface of liposomes. The heterobifunctional cross-linking reagentN-succinimidyl 3-(2-pyridyldithio)propionate has been used to activate DMPE molecules. The DMPE-dithiopyridine product has been mixed with DMPC to prepare liposome vesicles. These have been reduced by DTT and finally reacted with lucifer yellow-iodoacetamide to produce the fluorescence-labeled vesicles. The quenching of their fluorescence intensity by Kl is consistent with fully exposed fluorophores. The decay of the fluorescence intensity of the lipid-bound lucifer yellow is biexponential (₁=7.9 ns; ₂=1.1 ns), with a relative yield of 0.16. When the fluorescent liposomes are mixed with cells, the lucifer yellow-DMPE derivative is transferred. Boar spermatozoa and peripheral human blood lymphocytes have been used as cellular models. The extent of incorporation is dependent on the incubation time and temperature. At 36°C, lucifer yellow fluorescence appears in the spermatozoa cells after 10 min of incubation and reaches its maximum at about 60 min. The fluorescent phospholipid derivative seems to incorporate specifically into membrane structures. The highest labeling ratio is observed with integer, scarcely motile, spermatozoa. A poorer labeling yield (15%) is found with lymphocytes. Interestingly, photobleaching due to epiillumination of the labeled cells is apparently negligible and cells are clearly visible after irradiation times ranging from several minutes to few hours.A preliminary account of this work was presented at the Quarto Simposio su Biotecnologie Biochimiche, Capri, 28–30 June 1992.     

Nucleophilic substitution of hydrogen in meso-nitroaryl-substituted porphyrins—unprotected at the NH-centers in the core ring

Unprotected 5-(4-nitrophenyl)-10,15,20-triphenylporphyrin and 5,10-bis(4-nitrophenyl)-15,20-diphenylporphyrin react in the presence of a base at low temperature with carbanions (which bear a leaving group X at the carbanionic center) affording vicarious nucleophilic substitution of hydrogen (VNS) products in good yields (50-89%). The reactivity is explained in terms of the predominance of the porphyrin N-anion resonance forms at this temperature.     

Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem

Herein, we present results from MD simulations of the Michaelis complex formed between the dizinc beta-lactamase from B. fragilis and imipenem. We considered two catalytically important configurations, which differ in the presence or absence of a hydroxide bridge connecting the two zinc ions in the active site. The structural and dynamical effects induced by substrate binding, the specific roles of the conserved residues and the zinc-bound water molecules, the near attack conformers of the Michaelis complex, and so forth, are discussed in detail. The relative stability of the two configurations was estimated from QM linear scaling calculations on the enzyme-substrate complex combined with Poisson-Boltzmann electrostatic calculations and normal mode calculations. Importantly, we find that the two configurations have similar energies, indicating that these two structures could readily be interchanged, thereby facilitating catalysis. The configuration with the hydroxide bound to the two zinc ions is predicted to be the resting form of the enzyme, while the configuration without the bridge is the reactive form that was found to place the hydroxide in position to attack the carbonyl of the beta-lactam ring. Thus, we propose that the enzyme initiates catalysis by converting from the hydroxide bridge form into the configuration that lacks the hydroxide bridge. This interconversion increases the nucleophilicity of the hydroxide ion and exposes it to the beta-lactam carbonyl, which ultimately facilitates nucleophilic attack. The implications of the observed modes of binding, the possible influence of mutating the Lys184 and Asn193 residues on substrate binding, and the reaction mechanism are also discussed in detail.     

Spontaneously formed trans-anethol/water/alcohol emulsions: mechanism of formation and stability

We studied the spontaneous emulsification and droplet growth mechanism in trans-anethol/water/ethanol solutions, also known as the beverage ouzo, using dynamic light scattering spectroscopy. This simple ternary mixture is a generic example of a system that forms microemulsions spontaneously when brought into the two-phase region. The volume fraction of the dispersed phase was found to profoundly affect the growth rates of the droplets, which is a new finding that has not been predicted by the Lifshitz-Slyozov-Wagner theory. Time-dependent measurements show that the droplet growth is governed by Ostwald ripening (OR), and no coalescence was observed. Furthermore, the OR rates increase with increasing oil concentration at low alcohol content. We attribute this behavior to enhanced droplet-droplet interactions. At high ethanol concentrations, we found that the measured rates decreased as the oil concentration increased. The OR growth mechanism completely correlates with changes in droplet size. The kinetics of droplet growth shows that the ripening has a saturation limit at a droplet radius of about 1.5 mum. Thus, formed emulsions remain stable for months.     

Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations

To investigate the molecular details of the phosphoryl-transfer mechanism catalyzed by cAMP-dependent protein kinase, we performed quantum mechanical (QM) calculations on a cluster model of the active site and molecular dynamics (MD) simulations of a ternary complex of the protein with Mg(2)ATP and a 20-residue peptide substrate. Overall, our theoretical results confirm the participation of the conserved aspartic acid, Asp(166), as an acid/base catalyst in the reaction mechanism catalyzed by protein kinases. The MD simulation shows that the contact between the nucleophilic serine side chain and the carboxylate group of Asp(166) is short and dynamically stable, whereas the QM study indicates that an Asp(166)-assisted pathway is structurally and energetically feasible and is in agreement with previous experimental results.