Memories of the moments spent with Edward Cameron Kirby (1934 – 2019)

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The Mechanism of Peptide Hydrolysis Catalysed by Dipeptidyl Peptidase III from Bacteroides thetaiotaomicron

Dipeptidyl peptidase III (DPP III) is a zinc- dependent peptidase that cleaves dipeptides off of N-termini of its substrates. Previous studies on human DPP III reveal a reaction mechanism similar to that of thermolysin. Since the active site is conserved within the DPP III family, it is not surprising that the mechanism determined for Bacteroides thetaiotaomicron DPP III (BtDPP III) closely resembles that of hDPP III. However, the hydrogen bond network within the model differs slightly from that in the human ortholog, which results in two proposed pathways. The calculated Gibbs activation energy of 90.1 kJ mol–1 is larger than the one calculated from kinetic data for the preferred substrate Arg2-2-naphthylamide at room temperature (69 kJ mol–1), suggesting the importance of treating the whole DPP III enzyme in the calculations

COMBINE analysis of nuclear receptor-DNA binding specificity: Comparison of two sets of data

To identify the major determinants of the DNA binding specificity of nuclear transcription factors, the Comparative Binding Energy (COMBINE) analysis has been performed for two datasets. In Tomic et al.,l COMBINE QSAR models were derived for a set of 320 complexes of DNA and glucocorticoid receptor mutants. Here, we derive COMBINE QSAR models for a set of 32 complexes. This set differs from the larger one in two aspects. The complexes have additional mutation sites in the DNA binding domain and, instead of just activity measurements, both activity and binding affinity measurements are available. Models of better predictive ability were obtained with the smaller, but experimentally better characterized, dataset. The parameters important for determining binding specificity are nevertheless similar for both datasets: the electrostatic interaction energies between the mutated nucleotides and mutated residue(s) as well as some charged amino acid residues (Arg-447, Arg-470, Arg-477), and the solvation free energies of the mutated base(s). However, the relative importance of these parameters is different in the two datasets

Demystifying DPP III Catalyzed Peptide Hydrolysis-Computational Study of the Complete Catalytic Cycle of Human DPP III Catalyzed Tynorphin Hydrolysis

Dipeptidyl peptides III (DPP III) is a dual-domain zinc exopeptidase that hydrolyzes peptides of varying sequence and size. Despite attempts to elucidate and narrow down the broad substrate- specificity of DPP III, there is no explanation as to why some of them, such as tynorphin (VVYPW), the truncated form of the endogenous heptapeptide spinorphin, are the slow-reacting substrates of DPP III compared to others, such as Leu- enkephalin. Using quantum molecular mechanics calculations followed by various molecular dynamics techniques, we describe for the first time the entire catalytic cycle of human DPP III, providing theoretical insight into the inhibitory mechanism of tynorphin. The chemical step of peptide bond hydrolysis and the substrate binding to the active site of the enzyme and release of the product were described for DPP III in complex with tynorphin and Leu-enkephalin and their products. We found that tynorphin is cleaved by the same reaction mechanism determined for Leu- enkephalin. More importantly, we showed that the product stabilization and regeneration of the enzyme, but not the nucleophilic attack of the catalytic water molecule and inversion at the nitrogen atom of the cleavable peptide bond, correspond to the rate-determining steps of the overall catalytic cycle of the enzyme

COMBINE Analysis of Nuclear Receptor-DNA Binding Specificity: Comparison of Two Sets of Data

To identify the major determinants of the DNA binding specificity of nuclear transcription factors, the Comparative Binding Energy (COMBINE) analysis has been performed for two datasets. In Tomić et al.,1 COMBINE QSAR models were derived for a set of 320 complexes of DNA and glucocorticoid receptor mutants. Here, we derive COMBINE QSAR models for a set of 32 complexes. This set differs from the larger one in two aspects. The complexes have additional mutation sites in the DNA binding domain and, instead of just activity measurements, both activity and binding affinity measurements are available. Models of better predictive ability were obtained with the smaller, but experimentally better characterized, dataset. The parameters important for determining binding specificity are nevertheless similar for both datasets: the electrostatic interaction energies between the mutated nucleotides and mutated residue(s) as well as some charged amino acid residues (Arg-447, Arg-470, Arg-477), and the solvation free energies of the mutated base(s). However, the relative importance of these parameters is different in the two datasets

Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests

Identifying interaction sites in proteins provides important clues to the function of a protein, and is becoming increasingly relevant in topics like systems biology and drug discovery. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using i) a combination of sequence and structure-derived parameters ; and ii) sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and the F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with the F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modelling the Ras-Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information

New EU Directive on the prevention of the use of the financial system for the purposes of money laundering and terrorist financing

The new Fifth Directive on the prevention of the use of the financial system for the purposes of money laundering and terrorist financing is the European Union's response to the 2016 terrorist attacks in Europe and the Panama Papers scandal. This directive aims to strengthen the standards that improve, as much as possible, the conditions for preventive action against money laundering and terrorism financing

Investigation of Residual Blaze Functions in Slit-Based Echelle Spectrograph

We have studied the Residual Blaze Functions (RBF) resulting from division of individual echelle orders by extracted flat-field in spectra obtained by slit-fed OES spectrograph of 2m telescope of Ond\v{r}ejov observatory, Czech Republic. We have eliminated the dependence on target and observation conditions by semiautomatic fitting of global response function, thus getting the instrument-only dependent part, which may be easily incorporated into data reduction pipeline. The improvement of reliability of estimation of continuum on spectra of targets with wide and shallow lines is noticeable and the merging of all orders into the one long spectrum gives much more reliable results.Comment: 12 pages, 12 figures, SPIE conferences Astronomical Telescopes and Instrumentation, Marseille, 200

Fizioterapijska procjena funkcionalnog statusa laringektomiranih bolesnika

Efikasnost liječenja onkološkog bolesnika procjenjuje se duljinom preživljavanja i postignutom kvalitetom života. Nakon totalne laringektomije, a pogotovo ako je učinjena i disekcija vrata, postoje odstupanja od normalnog funkcionalnog statusa gornjeg dijela torza i vrata zbog kirurških postupaka na koži i mišićima tog dijela tijela. Svrha ovoga rada je bila kroz fizioterapijsku procjenu, utvrditi funkcionalni status osoba nakon operacije totalne laringektomije /sa ili bez disekcije vrata/. Istraživan je: - status pokretljivosti Cx,Tx,G/H - status respiratornog indexa - mišićna snaga i sinergija G/H - sposobnost izvođenja svakodnevnih aktivnosti - postoje li odstupanja od normale u posturalnom status