SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

Selenoproteins are a diverse group of proteins usually misidentified and misannotated in sequence databases. The presence of an in-frame UGA (stop) codon in the coding sequence of selenoprotein genes precludes their identification and correct annotation. The in-frame UGA codons are recoded to cotranslationally incorporate selenocysteine, a rare selenium-containing amino acid. The development of ad hoc experimental and, more recently, computational approaches have allowed the efficient identification and characterization of the selenoproteomes of a growing number of species. Today, dozens of selenoprotein families have been described and more are being discovered in recently sequenced species, but the correct genomic annotation is not available for the majority of these genes. SelenoDB is a long-term project that aims to provide, through the collaborative effort of experimental and computational researchers, automatic and manually curated annotations of selenoprotein genes, proteins and SECIS elements. Version 1.0 of the database includes an initial set of eukaryotic genomic annotations, with special emphasis on the human selenoproteome, for immediate inspection by selenium researchers or incorporation into more general databases. SelenoDB is freely available at http://www.selenodb.org

Carbon Dioxide Utilisation -The Formate Route

UIDB/50006/2020 CEEC-Individual 2017 Program Contract.The relentless rise of atmospheric CO2 is causing large and unpredictable impacts on the Earth climate, due to the CO2 significant greenhouse effect, besides being responsible for the ocean acidification, with consequent huge impacts in our daily lives and in all forms of life. To stop spiral of destruction, we must actively reduce the CO2 emissions and develop new and more efficient “CO2 sinks”. We should be focused on the opportunities provided by exploiting this novel and huge carbon feedstock to produce de novo fuels and added-value compounds. The conversion of CO2 into formate offers key advantages for carbon recycling, and formate dehydrogenase (FDH) enzymes are at the centre of intense research, due to the “green” advantages the bioconversion can offer, namely substrate and product selectivity and specificity, in reactions run at ambient temperature and pressure and neutral pH. In this chapter, we describe the remarkable recent progress towards efficient and selective FDH-catalysed CO2 reduction to formate. We focus on the enzymes, discussing their structure and mechanism of action. Selected promising studies and successful proof of concepts of FDH-dependent CO2 reduction to formate and beyond are discussed, to highlight the power of FDHs and the challenges this CO2 bioconversion still faces.publishersversionpublishe

Coordination of selenium to molybdenum in formate dehydrogenase H from \u3ci\u3eEscherichia coli\u3c/i\u3e

Formate dehydrogenase H from Escherichia col contains multiple redox centers, which include a molybdopterin cofactor, an iron-sulfur center, and a selenocysteine residue (SeCys-140 in the polypeptide chain) that is essential for catalytic activity. Here we show that addition of formate to the native enzyme induces a signal typical of Mo(V) species. This signal is detected by electron pm etc resonance (EPR) spectroscopy. Substitution of 77Se for natural isotope abundance Se leads to transformation of this signal, indicating a direct coordination of Se with Mo. Mutant enzyme with cysteine substituted at position 140 for the selenocysteine residue has decreased catalytic activity and exhibits a different EPR signal. Since deternation of the Se content of wild-type enzyme indicates 1 gram atom per mol, we conclude that it is the Se atom of the SeCys-140 residue in the protein that is coordinated directly with Mo. The amino acd sequence flanking the selenocysteine residue in formate dehydrogenase H is s r to a conserved sequence found in several other prokaryotic molybdopterin-dependent enzymes. In most of these other enzymes a cysteine residue, or in a few cases a serine or a selenocysteine residue, occurs in the position corresonding to SeCys-140 of formate dehydrogeme H. By analogy with formate dehydrogenase H in these other enzymes, at least one of the ilgands to Mo should be provided by an amino acid residue of the protein. This igand could be the Se of a selenocysteine residue, sulfur of a cysteine residue, or, in the case of a serine residue, oxygen

Calculation of wind-driven cross ventilation in buildings with large openings

A simplified macroscopic method is commonly used for wind-driven ventilation analysis of buildings with small openings. Consequently, it is reasonable to question if and under what conditions will this method provide accurate results in predicting ventilation flow rates in buildings with large openings. We investigate a single-zone cubic building with two equal large openings using a computational fluid dynamics approach. We analyzed the driving forces and the ventilation flow rates due to wind as a function of the geometry, size and relative location of the two openings. The ventilation flow rates are found to be affected by both wind flows around and through the building when the two openings are relatively large. The simplified macroscopic method can provide reasonable engineering accuracy (i.e., less than 10% error) when the porosity of the building envelope does not exceed a critical value. This critical value is not a constant; instead it depends significantly on the degree of alignment between the wind direction and the character of the dominant stream tube associated with the flow through the room. We found that the simplified macroscopic method fails to provide acceptable accuracy when this stream tube is truly dominant and parallel to the wind direction. The effects of wall thickness and aspect ratio of openings are also investigated. © 2006 Elsevier Ltd. All rights reserved.link_to_subscribed_fulltex