1,721,109 research outputs found
Organochalcogen peroxidase mimetics as potential drugs: a long story of a promise still unfulfilled
No full textOrganochalcogen compounds have attracted the interest of a multitude of studies to design potential therapeutic agents mimicking the peroxidase activity of selenium-based glutathione peroxidases (GPx's). Starting from the pioneering ebselen, various compounds have been synthesized over the years, which may be traced in three major classes of molecules: cyclic selenenyl amides, diaryl diselenides, and aromatic or aliphatic monoselenides. These compounds share common features and determinants needed to exert an efficient GPx-like activity, such as polarizing groups in close proximity to selenium and steric effects. Nonetheless, the reactivity of selenium, and tellurium as well, poses serious problems for the predictability of the biological effects of these compounds in vivo when used as potential drugs. These molecules, indeed, interfere with thiols of redox-regulated proteins and enzymes, leading to unexpected biological effects. The various chemical aspects of the reaction mechanism of peroxidase mimetics are surveyed here, focusing on experimental evidence and quantum mechanics calculations of organochalcogen representatives of the various classes
Large-scale prediction of protein structure and function from sequence
No full textThe identification of novel drug targets from genomic data involves the large-scale analysis of many protein sequences. Methods for automated structure and function prediction are an essential tool for this purpose. In this review we concentrate on the recent developments in the field of protein structure prediction and how these can be used to gain hints about the function of proteins. The current state-of-the-art is highlighted through recent community-wide experiments aimed at comparing different approaches. For structure prediction this allows the identification of key improvements to increase the crucial sequence to structure alignment needed for accurate models. Function prediction is a rapidly maturing field that is still being benchmarked. Definitions for protein function are presented and available methods, mostly concentrating on functional site descriptors and structural motifs, presented
Mass spectrometry data analysis in the proteomics era
No full textWith the advent of whole genome sequencing, large-scale proteomics has rapidly come to dominate the post-genomic age. As such, tandem mass spectrometry has emerged as the most promising and powerful technique in this area but analysis of raw spectra remains one of the principle bottlenecks to making effective use of the technology. Analytical approaches for identifying proteins from MS/MS data fall into two categories: comparing measured fragment spectra to theoretical spectra from sequence databases and de novo peptide sequencing. Available methods still have weaknesses, highlighting the need for new powerful algorithms that are able to exploit the enormous volume of data generated by proteomic experiments. Recent efforts have also been directed towards the identification of post-translational modifications, biomarker discovery and quantitative proteomics. Overall, the intended goal of this review is to give as thorough as possible an overview of state-of-the-art approaches and tools developed to analyze tandem mass spectra in different fields and discuss future directions aimed at overcoming the limits of present methods
Matching up Phosphosites to Kinases: A Survey of Available Predictive Programs
No full textOver the past few years, research in phosphoproteomic has assisted a tremendous revolution thanks to instrumental technologies advances in mass spectrometry combined with innovative experimental strategies. This has allowed the identification of thousands of high confidence phosphosites. Presently, almost 60000 non-redundant phosphosites have been identified from similar to 10000 non-redundant proteins and about 80% of these phosphosites have been identified from high throughput experiments in the last six years. The vast majority of phosphosites are still functionally uncharacterized and the kinases responsible of their generation are almost unknown.
Several computational approaches have been developed to link kinase families with putative substrates and although these are powerful tools, they are not commonly used.
Here we discuss about the present approaches and tools developed for predicting the functional link between the kinases and their substrates
Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices
No full textMOTIVATION: Protein and DNA are generally represented by sequences of letters. In a number of circumstances simplified alphabets (where one or more letters would be represented by the same symbol) have proved their potential utility in several fields of bioinformatics including searching for patterns occurring at an unexpected rate, studying protein folding and finding consensus sequences in multiple alignments. The main issue addressed in this paper is the possibility of finding a general approach that would allow an exhaustive analysis of all the possible simplified alphabets, using substitution matrices like PAM and BLOSUM as a measure for scoring.
RESULTS: The computational approach presented in this paper has led to a computer program called AlphaSimp (Alphabet Simplifier) that can perform an exhaustive analysis of the possible simplified amino acid alphabets, using a branch and bound algorithm together with standard or user-defined substitution matrices. The program returns a ranked list of the highest-scoring simplified alphabets. When the extent of the simplification is limited and the simplified alphabets are maintained above ten symbols the program is able to complete the analysis in minutes or even seconds on a personal computer. However, the performance becomes worse, taking up to several hours, for highly simplified alphabets.
AVAILABILITY: AlphaSimp and other accessory programs are available at http://bioinformatics.cribi.unipd.it/alphasim
Comparative analysis of Fe-Fe hydrogenase from Thermotogales indicates the molecular basis of resistance to oxygen inactivation
No full textSeveral Thermotogales, previously reported as being strict anaerobes, have demonstrated the ability to grow and produce hydrogen in the presence of moderate amounts of molecular oxygen. Thermotoga neapolitana seems to be less sensitive to O2 than other members of this order, including Thermotoga maritima, whose hydrogenase has been purified and characterized. Instead, the enzyme responsible for the hydrogen production by T. neapolitana has not yet been identified. After the recent sequencing of the T. neapolitana genome, it has been possible to search for the orthologous gene responsible for this unusal hydrogenase activity. By means of in silico analysis, we built a molecular model for both T. maritima and T. neapolitana proteins and analyzed conservation, focusing on the subtle structural differences responsible for the increased oxygen resistance in the latter and underscoring
two mutations (E475S and T539L) which represent a specific adaption for more effective release of hydrogen in aerobic conditions
Novel insights on the mechanistic aspects of GPx-catalyzed H2O2 reduction: a DFT computational study
No full textA state-of-the-art accurate quantum chemistry computational approach is proposed to investigate the mechanism of H2O2 reduction at the active site of GPx. In the model we consider explicitly six amino acids surrounding the catalytic SEC or CYS residue. The geometries of the plausible intermediate species and transition states as well as the energetics are carefully predicted. The computational protocol, rooted in advanced Density Functional Theory methodologies, is employed to explore possible mechanistic paths involving different initial active species (Se-; SeH; S- ; SH) and stability of protonated surrounding amino acids, in particular Gln (O), Gly (N) and Trp (N).
The data so far acquired have demonstrated the following: i) the chosen amino acids forming the catalytic “cage” are fully optimized and their minimum energy conformation is perfectly superimposed to the initial crystal structure (see Fig. 1) and no difference has been observed when the active site contains either Se or S; ii) the proton of selenol or thiol has been dislocated in all of the available surrounding amino acids and it has been optimized in most of the tested locations leading to the conclusion that it is displaced in the positively charged catalytic pocket rather than exclusively bound to selenium or sulphur, iii) hydrogen peroxide is extremely instable in the active site and selenenic/sulphenic acid and water are formed instantaneously. This transition is the minimum energy path of the system and account for the non saturation kinetics of GPx where there is no evidence for the formation of a stable enzyme substrate complex.
This set of data strongly suggests that for the catalysis of H2O2 reduction the active site of GPx is crucial, while the redox residue can be either SEC or CYS
Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis
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