Discriminatory experiment for the kinetics of yeast glyoxalase I.

<p>A - Time courses of SDLGS concentration in the discriminatory setup experiment. Black: experimental result, average of 4 replicates (the grey shaded area is within one standard error of the mean). Blue: prediction by model 1. Red: prediction by model 2. Initial concentrations are 0.221 mM for glutathione, 2.0×10⁻³ mM for glyoxalase I, 0.441 mM for methylglyoxal and 4.0×10⁻³ mM for glyoxalase II. The initial concentrations correspond to the solution chosen from of the Pareto front highlighted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032749#pone-0032749-g004" target="_blank">figure 4A</a>. B and C - rates predicted by model 1 (B) and model 2 (C). Red: net rate of hemithioacetal formation, blue: rate of glyoxalase I reaction. green: rate of glyoxalase II reaction.</p

Discrimination of kinetic models by maximization of the extended Kullback-Leibler distance (<i>I </i>).

<p>Conditions are sought that maximize <i>I</i> in both directions between any two models. In a two candidate model scenario (A) two functions must be simultaneously optimized. In a three candidate model scenario (B) six functions must be simultaneously optimized. After optimization, the set of solutions approximate a Pareto front and represent a compromise between the various objectives in the sense that, for any solution, the value of any objective could only be increased if the value of another objective was simultaneously decreased.</p

Landscapes of different measures of model divergences in the allowed optimization range of concentrations of pathway substrates.

<p>Measures of model distances are <i>I</i>_1,2 : extended Kullback-Leibler distance of model 2 from model 1 (equation 6). <i>I</i>_2,1 : extended Kullback-Leibler distance of model 1 from model 2 (equation 6). <i>L</i>₂ : simple <i>L</i>₂ norm (equation 4). <i>L</i>_2<i>w</i> : weighted <i>L</i>₂ norm (equation 5).</p

Capsular Complexes of Nonpolar Guests with Octa Amine Host Detected in the Gas Phase

Nanocapsules, made up of the deep cavitand octa amine and several guests, were prepared in aqueous acidic solution and were found to be stable in the gas phase as detected by electrospray ionization mass spectrometry (ESI-MS). The observed gas phase host–guest complexes contained five positive charges and were associated with several acid molecules (HCl or HBr)

Kinetic models of the glyoxalase pathway.

<p>In model 1 (A), glutathione (GSH) and methylglyoxal (MGO) form a hemithioacetal (HTA) which is the substrate of glyoxalase I. In model 2 (B), glutathione and methylglyoxal are sequential substrates of glyoxalase I and the hemithioacetal is formed at the active centre of the enzyme. Glyoxalase II is a one-substrate-one-product irreversible Michaelis Menten enzyme, catalyzing the hydrolysis of <i>S</i>-D-lactoylglutatione (SDLGS) into D-lactate (D-Lac) and glutathione. The rate laws assumed in the models are expressed in equations 15 to 18.</p

Optimization of experimental design for model discrimination.

<p>A - Optimal initial concentrations of methylglyoxal and glutathione (solutions approximating the Pareto front) for the discrimination of the two models presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032749#pone-0032749-g002" target="_blank">figure 2</a>. B – Corresponding values of the extended Kullback-Leibler distances (optimization objectives); Concentration of glyoxalase I is 2.0×10⁻³ mM and concentration of glyoxalase II is 4.0×10⁻⁴ mM. The red dot indicates the initial concentrations used in the discriminatory experiment.</p

Iminoboronates: A New Strategy for Reversible Protein Modification

Protein modification has entered the limelight of chemical and biological sciences, since, by appending small molecules into proteins surfaces, fundamental biological and biophysical processes may be studied and even modulated in a physiological context. Herein we present a new strategy to modify the lysine’s ε-amino group and the protein’s <i>N</i>-terminal, based on the formation of stable iminoboronates in aqueous media. This functionality enables the stable and complete modification of these amine groups, which can be reversible upon the addition of fructose, dopamine, or glutathione. A detailed DFT study is also presented to rationalize the observed stability toward hydrolysis of the iminoboronate constructs

Functional annotation enrichment analysis of the identified proteins using the Database for Annotation, Visualization and Integrated Discovery (DAVID ) v6.7.

<p>Annotation terms are representative of a particular cluster. FDR – False discovery rate.</p

Detailed expression profiles for all the identified differentially expressed proteins, according to its functional categories: (A) cell metabolism; (B) unknown function; (C) Cell redox homeostasis; (D) protein folding and degradation; (E) translation.

<p>Grey bars represent fold change in protein expression in BTTR-wt versus the control while black bars represent fold change in protein expression in BTTR-L55P versus the control. The vertical axis indicates the identified protein while the horizontal axis represents the fold variation in protein expression. Additional information for each protein, including full name, can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050123#pone-0050123-t001" target="_blank">Table 1</a>. For proteins identified in different spots (with slightly different fold variations) the average is represented in the graph.</p

Differentially expressed proteins identified by MALDI-TOF-TOF MSMS.

<p>All the listed proteins showed a statistical difference of spot volume ratio between the control/BTTR-wt and control/BTTR-L55P with an ANOVA p<0.05.</p>a)<p>Gene code as in the yeast genome database (<a href="http://www.yeastgenome.org" target="_blank">www.yeastgenome.org</a>).</p>b)<p>CM – carbohydrate metabolism; AM – amino acid metabolism; NM – nucleotide metabolism; EM – energy metabolism; LM – lipid metabolism; U – unknown; CRH – cell redox homeostasis; T – translation; TP – transport; PFD – protein folding and degradation.</p>c)<p>Accession code of the uniprot database (<a href="http://www.uniprot.org" target="_blank">www.uniprot.org</a>).</p>d)<p>Spot number on the master gel (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050123#pone-0050123-g001" target="_blank">fig. 1A</a>).</p>e)<p>Summary of the protein identification results. The protein and the peptide score as given by the GPS Explorer software (Applied Biosystems). The number of peptides with MSMS data is also given.</p