EfeO-cupredoxins: major new members of the cupredoxin superfamily with roles in bacterial iron transport

The EfeUOB system of Escherichia coli is a tripartite, low pH, ferrous iron transporter. It resembles the high-affinity iron transporter (Ftr1p-Fet3p) of yeast in that EfeU is homologous to Ftr1p, an integral-membrane iron-permease. However, EfeUOB lacks an equivalent of the Fet3p component—the multicopper oxidase with three cupredoxin-like domains. EfeO and EfeB are periplasmic but their precise roles are unclear. EfeO consists primarily of a C-terminal peptidase-M75 domain with a conserved ‘HxxE’ motif potentially involved in metal binding. The smaller N-terminal domain (EfeO-N) is predicted to be cupredoxin (Cup) like, suggesting a previously unrecognised similarity between EfeO and Fet3p. Our structural modelling of the E. coli EfeO Cup domain identifies two potential metal-binding sites. Site I is predicted to bind Cu²⁺ using three conserved residues (C41 and 103, and E66) and M101. Of these, only one (C103) is conserved in classical cupredoxins where it also acts as a Cu ligand. Site II most probably binds Fe³⁺ and consists of four well conserved surface Glu residues. Phylogenetic analysis indicates that the EfeO-Cup domains form a novel Cup family, designated the ‘EfeO-Cup’ family. Structural modelling of two other representative EfeO-Cup domains indicates that different subfamilies employ distinct ligand sets at their proposed metal-binding sites. The ~100 efeO homologues in the bacterial sequence databases are all associated with various iron-transport related genes indicating a common role for EfeO-Cup proteins in iron transport, supporting a new copper-iron connection in biology.     

Pre-clinical toxicity of IDPH-791: a new centrally acting muscle relaxant in rats.

IDPH-791, a novel centrally acting muscle relaxant, in doses up to 500 mg/kg (po) for 14 days did not result in any appreciable adverse effect on body weight gain, food or water consumption including biochemical and haematologica parameters in rats. Variations observed in the biochemistry and haematology were either comparable to controls or were within normal limits.     

Role of large hydrophobic residues in proteins

Large Hydrophobic Residues (LHR) such as phenylalanine, isoleucine, leucine, methionine and valine play an important role in protein structure and activity. We describe the role of LHR in complete set of protein sequences in 15 different species. That is the distribution of LHR in different proteins of different species is reported. It is observed that the proteins prefer to have 27% of large hydrophobic residues in total and all along the sequence. It is also observed that proteins accumulate more LHR in its active sites. A window analysis on these protein sequences shows that the 27% of LHR is more frequent at window length of 45 amino acids. The influenza virus and P. falciparum show a random distribution of LHR in its proteins compared to other model organisms.     

MimoSA: a system for minimotif annotation

Background  

Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature.     

Carbon distribution to toxic effect in toxin proteins

The role of hydrophobic force in biological function through the formation of several local macro-molecular structures is evident. Carbon is the element that contributes to biological function in living systems. We show that carbon distribution is related to protein activity using an example. The carbon distribution profile is foreseen to help undestand unfolded and misfolded regions of protein structures. The carbon distribution profile in a toxin protein that is found associated with the toxic shock syndrome is described in this study. The carbon profile provides insight to the association of specific residues responsible for toxicity.     

Temperature and Photoperiod Influence Postharvest Needle Abscission of Selected Balsam Fir (Abies balsamea L. (Mill.)) Genotypes by Modulating ABA Levels

Seasonal changes in the concentration of abscisic acid (ABA) in current-year needles of two different genotypes (AB-NSD-004 and AB-NSD-184) were monitored in branches collected from 20-year-old balsam fir (Abies balsamea L. (Mill.)) trees over a period of 11 months. A significant genotype × harvesting time interaction was observed for endogenous ABA levels and postharvest needle retention duration (NRD). A consistent pattern of seasonal variation in ABA concentration was observed in both genotypes, with the highest amount of ABA (7,887 ng g^?1 DW) accumulating in April and May. The highest levels of ABA coincided with the lowest postharvest NRD regardless of genotype. Nevertheless, genotypes differed in their ABA concentrations. Branches of genotype AB-NSD-184 sampled during August exhibited 170 days of NRD whereas those collected in May and June registered the lowest NRD of around 40 days. There was a significant negative correlation (P < 0.05) between endogenous ABA concentrations and postharvest NRD in genotype AB-NSD-184. Also, an inverse relationship was observed between the average daily photoperiod and the postharvest NRD (R ² = 0.35; P = 0.000) in the same genotype. Together with average daily temperature, the R ² value for this correlation reached the highest (0.75; P ≤ 0.00). Genotypes differed in their physiological responses to environmental cues and thus differed in their postharvest qualities. Average daily photoperiod and maximum daily temperature are strongly linked to the postharvest NRD through modulating endogenous ABA concentration.