SSRD: simple sequence repeats database of the human genome

Simple sequence repeats are predominantly found in most organisms. They play a major role in studies of genetic diversity, and are useful as diagnostic markers for many diseases. The simple sequence repeats database (SSRD) for the human genome was created for easy access to such repeats, for analysis, and to be used to understand their biological significance. The data includes the abundance and distribution of SSRs in the coding and non-coding regions of the genome, as well as their association with the UTRs of genes. The exact locations of repeats with respect to genomic regions (such as UTRs, exons, introns or intergenic regions) and their association with STS markers are also highlighted. The resource will facilitate repeat sequence analysis in the human genome and the understanding of the functional and evolutionary significance of simple sequence repeats. SSRD is available through two websites, http://www.ccmb.res.in/ssr and http://www.ingenovis.com/ssr.     

Deducing hydration sites of a protein from molecular dynamics simulations

Invariant water molecules that are of structural or functional importance to proteins are detected from their presence in the same location in different crystal structures of the same protein or closely related proteins. In this study we have investigated the location of invariant water molecules from MD simulations of ribonuclease A, HIV1-protease and Hen egg white lysozyme. Snapshots of MD trajectories represent the structure of a dynamic protein molecule in a solvated environment as opposed to the static picture provided by crystallography. The MD results are compared to an analysis on crystal structures. A good correlation is observed between the two methods with more than half the hydration sites identified as invariant from crystal structures featuring as invariant in the MD simulations which include most of the functionally or structurally important residues. It is also seen that the propensities of occupying the various hydration sites on a protein for structures obtained from MD and crystallographic studies are different. In general MD simulations can be used to predict invariant hydration sites when there is a paucity of crystallographic data or to complement crystallographic results.     

Isolation and characterization of a small molecular weight protein of linseed meal

A small M_r, protein from linseed meal has been isolated by CM-Sephadex chromatography. The protein was found to be homogeneous by the techniques of gel filtration, polyacrylamide gel electrophoresis and ultracentrifugation. It had S_20,w value of 1.6S. Amino acid composition of the protein revealed a high amount of glutamic acid, cystine, arginine and glycine. The absorption spectrum of the protein consisted of a peak at 280 nm with a shoulder at 290 nm. The fluorescence emission maximum was at 340 nm. The protein contained large amounts of α-helix and β-structure. SDS-PAGE showed the protein to consist of a single polypeptide chain. The M_r estimated by Archibald's method, sedimentation-diffusion method and gel filtration was 17 000,16 000 and 15 000 respectively. Difference spectra studies as a function of pH and temperature showed no variation in the conformation of the protein, probably due to disulphide bridges.     

Protein complex compositions predicted by structural similarity

Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we present structure-based predictions of 3387 binary and 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 and 195 proteins, respectively. To generate candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates. These candidate complexes were then assessed using a statistical potential, derived from binary domain interfaces in PIBASE (http://salilab.org/pibase). The statistical potential discriminated a benchmark set of 100 interface structures from a set of sequence-randomized negative examples with a false positive rate of 3% and a true positive rate of 97%. Moreover, the predicted complexes were also filtered using functional annotation and sub-cellular localization data. The ability of the method to select the correct binding mode among alternates is demonstrated for three camelid VHH domain-porcine alpha-amylase interactions. We also highlight the prediction of co-complexed domain superfamilies that are not present in template complexes. Through integration with MODBASE, the application of the method to proteomes that are less well characterized than that of S.cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE (http://salilab.org/modbase).     

Photosynthesis Parameters in Two Cultivars of Mulberry Differing in Salt Tolerance

Three-month-old mulberry (Morus alba L.) cultivars (salt tolerant cv. S1 and salt sensitive cv. ATP) were subjected to different concentrations of NaCl for 12 d. Leaf area, dry mass accumulation, total chlorophyll (Chl) content, net CO₂ assimilation rate (P _N), stomatal conductance (g _s), and transpiration rate (E) declined, and intercellular CO₂ concentration (C _i) increased. The changes in these parameters were dependent on stress severity and duration, and differed between the two cultivars. The tolerant cultivar showed a lesser reduction in P _N and g _s coupled with a better C _i and water use efficiency (WUE) than the sensitive cultivar. This revised version was published online in June 2006 with corrections to the Cover Date.     

Cation exchange assisted binding-elution strategy for enzymatic synthesis of human milk oligosaccharides (HMOs)

A cation exchange assisted binding-elution (BE) strategy for enzymatic synthesis of human milk oligosaccharides (HMOs) was developed. An amino linker was used to provide the cation ion under acidic condition which can be readily bound to cation exchange resin and then eluted off by saturated ammonium bicarbonate. Ammonium bicarbonate in the collections was easily removed by vacuum evaporation. This strategy circumvented the incompatible issue between glycosyltransferases and solid support or large polymers, and no purification was needed for intermediate products. With current approach, polyLacNAc backbones of HMOs and fucosylated HMOs were synthesized smoothly.