May the Best Molecule Win: Competition ESI Mass Spectrometry

Electrospray ionization mass spectrometry has become invaluable in the characterization of macromolecular biological systems such as nucleic acids and proteins. Recent advances in the field of mass spectrometry and the soft conditions characteristic of electrospray ionization allow for the investigation of non-covalent interactions among large biomolecules and ligands. Modulation of genetic processes through the use of small molecule inhibitors with the DNA minor groove is gaining attention as a potential therapeutic approach. In this review, we discuss the development of a competition method using electrospray ionization mass spectrometry to probe the interactions of multiple DNA sequences with libraries of minor groove binding molecules. Such an approach acts as a high-throughput screening method to determine important information including the stoichiometry, binding mode, cooperativity, and relative binding affinity. In addition to small molecule-DNA complexes, we highlight other applications in which competition mass spectrometry has been used. A competitive approach to simultaneously investigate complex interactions promises to be a powerful tool in the discovery of small molecule inhibitors with high specificity and for specific, important DNA sequences.     

Exploring Bacterial Heparinase II Activities with Defined Substrates

Bacterial heparinases that cleave heparan sulfate (HS) and heparin are widely used to generate low‐molecular‐weight heparins (LMWHs) and to structurally and functionally characterise heparin and HS biomolecules. We provide novel insights into the substrate specificity of heparinase II from two different bacteria: Pedobacter heparinus (formerly Flavobacterium heparinum) and Bacteroides eggerthii. The activity towards various well‐defined HS oligosaccharides was investigated by ¹H NMR spectroscopy; this revealed distinct specificities for the two heparinases. Heparinase II from P. heparinus appears to be more active and displays a broader substrate specificity than B. eggerthii heparinase II. Furthermore, HS di‐ and tetrasaccharides inhibited B. eggerthii heparinase II activity. A better understanding of heparinase substrate specificity will contribute to the production of homogenous LMWHs, provide better characterisation of heparin and HS and assist therapeutic applications.     

Ion specificity in NaCl solution confined in silicon nanochannels

Ion specificity of Na+and Cl ions for NaCl solution confined in silicon nanochannels is investigated with molecular dynamics(MD)simulations.The MD simulation results demonstrate that ion specificity for Na+and Cl ions exhibits clearly in nanochannels with high surface charge density.The two types of ions show different density distributions perpendicular to the channel surface due to the ion specificity when they act as counterions near negatively and positively charged surfaces,respectively.Both the two counterion distributions cannot be predicted by Poisson-Boltzmann equation within 0.75 nm near the surface.In addition,the ion specificity is also demonstrated through affecting the water density distributions.In the nanochannel with negatively charged surfaces,the presence of the Na+ions reduces the number of water peaks in water density distribution profile.In comparison,when the Cl ions act as counterions near positively charged surfaces,they do not affect the number of the water peaks.Besides the influence on the water density distribution,ion specificity also exhibits through affecting the water molecule orientation in the adsorbed layer.It is found that Cl ions make the water molecules in the adsorbed layer align more orderly than Na+ions do when the two types of ions act as the counterions near the positively and negatively charged surfaces with the same surface charge density.     

Assessment of Substance Cue Reactivity: Advances in Reliability, Specificity, and Validity.

An arousal-control and cross-over design was used to evaluate the reliability, specificity, and validity of the Normative Appetitive Picture System (NAPS), a cue exposure protocol with sets of visual alcohol, cigarette, and control cues. The authors also examined the utility of conceptualizing cue reactivity as a multidimensional phenomenon involving independent approach and avoidance dimensions. University student participants (n=369) rated multiple cue images in terms of arousing properties and capacity to elicit separate approach and avoidance inclinations. They also completed a battery of substance-related individual-difference measures. Results indicated that NAPS protocol reactivity profiles had good reliability and high specificity across cue types and individuals with different substance use histories. Avoidance reactivity independently predicted self-reports of substance-related behaviors, after controlling for approach reactivity. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A mathematical model of immunohistochemical preparations, which provides quantitative predictions

A mathematical model of the reaction between primary antibody and epitope is described using the Law of Mass Action to define the reaction quantitatively. The model explains some of the peculiar properties of immunohistochemical preparations. It also predicts that antibody excess over epitope will not increase staining intensity for very avid primary antibodies. This property can be exploited to measure the amount of epitope in histological sections. The assumptions of the model are not specific to immunohistochemistry, and such reasoning should be widely applicable to tests based on highly avid detection systems with high amplification of the initial signal.     

Comparative study of commercially available lipases in hydrolysis reaction of phosphatidylcholine

Nineteen commercial lipase preparations were compared with respect to their ability to hydrolyze phosphatidylcholine (PC) in a reverse micellar system. In terms of the source organism, lipases from Mucor or Rhizopus species showed comparatively high reactivity, while those from Aspergillus and Humicola sp. exhibited little PC hydrolysis activity. Almost no hydrolysis reaction was observed by positionally nonspecific lipases derived from Candida sp. The results suggest that particular attention should be paid to the source organism in selecting lipases for use in the enzymatic conversion of phospholipids.     

Additive effects of acyl-binding site mutations on the fatty acid selectivity of Rhizopus delemar lipase

The fatty acid specificity and pH dependence of triacylglycerol hydrolysis by the Rhizopus delemar lipase acylbinding site mutant Val206Thr+Phe95Asp (Val, valine; Thr, threonine; Phe, phenylalanine; Asp, aspartic acid) were characterized. The activity of the double mutant prolipase was reduced by as much as 10-fold, compared to the wild-type prolipase. However, the fatty acid specificity profile of the enzyme was markedly sharpened and was dependent on the pH of the substrate emulsion. At neutral pH, strong preference (10-fold or greater) for hydrolysis of triacylglycerols of medium-chainlength fatty acids (C_8:0 to C_14:0) was displayed by the variant prolipase, with no hydrolysis of triacylglycerols of short-chain fatty acids (C_4:0 to C_6:0) and little activity manifested toward fatty acids with 16 or more carbons. At acidic pH values, the fatty acid selectivity profile of the double mutant prolipase expanded to include short-chain triacylglycerols (C_4:0, C_6:0). When assayed against a triacylglycerol mixture of tributyrin, tricaprylin and triolein, the Val206Thr+Phe95Asp prolipase displayed a high selectivity for caprylic acid and released this fatty acid at least 25-fold more efficiently than the others present in the substrate mixture. When presented a mixture of nine fatty acid methyl esters, the wild-type prolipase showed a broad substrate specificity profile, hydrolyzing the various methyl esters to a similar extent. Contrastingly, the double mutant prolipase displayed a narrowed substrate specificity profile, hydrolyzing caprylic methyl ester at nearly wild-type levels, while its activity against the other methyl esters examined was 2.5- to 5-fold lower then that observed for the wild-type enzyme.     

Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization

Engineering the specificity of DNA-modifying enzymes has proven extremely challenging, as sequence recognition by these enzymes is poorly understood. Here we used directed evolution to generate a variant of HaeIII methyltransferase that efficiently methylates a novel target site. M.HaeIII methylates the internal cytosine of the canonical sequence GGCC, but there is promiscuous methylation of a variety of non-canonical sites, notably AGCC, at a reduced rate. Using in vitro compartmentalization (IVC), libraries of M.HaeIII genes were selected for the ability to efficiently methylate AGCC. A two-step mutagenesis strategy, involving initial randomization of DNA-contacting residues followed by randomization of the loop that lies behind these residues, yielded a mutant with a 670-fold improvement in catalytic efficiency (k(cat)/K(m)(DNA)) using AGCC and a preference for AGCC over GGCC. The mutant methylates three sites efficiently (AGCC, CGCC and GGCC). Indeed, it methylates CGCC slightly more efficiently than AGCC. However, the mutant discriminates against other non-canonical sites, including TGCC, as effectively as the wild-type enzyme. This study provides a rare example of a laboratory-evolved enzyme whose catalytic efficiency surpasses that of the wild-type enzyme with the principal substrate.     

Acceptor specificity and inhibition of the bacterial cell-wall glycosyltransferase MurG

A continuous fluorescence coupled enzyme assay was developed to study the acceptor specificity of the glycosyltransferase MurG toward different lipid I analogues with various substituents replacing the undecaprenyl moiety. It was found that most lipid I analogues are accepted as substrates and, amongst these, the saturated C14 analogue exhibits the best activity. This substrate was used to evaluate the inhibition activity of such antibiotics as moenomycin, vancomycin, and two chlorobiphenyl vancomycin derivatives. A vancomycin derivative with a chlorobiphenyl moiety on the aglycon section was identified as a potent inhibitor of MurG.     

Task-related chemical analysis of labial gland volatile secretion in worker honeybees (Apis mellifera ligustica)

Chemical analyses revealed that the labial gland complex of worker honeybees possesses a series of hydrocarbons dominated by odd-numbered carbon chain alkanes along with minor amounts of alkenes and branched alkanes. Foragers contained significantly more secretion than nurse bees. Experiments with bees from colonies induced to have a division of labor independent of age revealed that the differences in the amount of secretion were task, but not age dependent.