Computational method for prediction of protein functional sites using specificity determinants

The current available data on protein sequences largely exceeds the experimental capabilities to annotate their function. So annotation in silico, i.e. using computational methods becomes increasingly important. This annotation is inevitably a prediction, but it can be an important starting point for further experimental studies. Here we present a method for prediction of protein functional sites, SDPsite, based on the identification of protein specificity determinants. Taking as an input a protein sequence alignment and a phylogenetic tree, the algorithm predicts conserved positions and specificity determinants, maps them onto the protein's 3D structure, and searches for clusters of the predicted positions. Comparison of the obtained predictions with experimental data and data on performance of several other methods for prediction of functional sites reveals that SDPsite agrees well with the experiment and outperforms most of the previously available methods. SDPsite is publicly available under http://bioinf.fbb.msu.ru/SDPsite.     

Interactions between the ABRUPTUS/PINOID and LEAFY Genes during Floral Morphogenesis in Arabidopsis thaliana (L.) Heynh.

Analysis of interaction between mutations abruptus andleafy and previous data on interactions of abruptuswith homeotic mutations apetala1, apetala2, and apetala3 showed that the functions of the ABRUPTUS/PINOID (ABR/PID) gene are as follows: (1) it determines position of lateral organs on the inflorescence without specifying their identity [floral meristem (FM) or cauline leaves]; (2) in concert with theLEAFY (LFY) gene, it participates in the formation of FM; (3) it is involved in the determination and the formation of floral organ primordia in the first, second, and third whorls. Auxin accumulation in the abr mutant cells in callus culture was shown indicating the involvement of the ABR/PID gene in regulation of auxin efflux from cells. It is suggested that the ABR/PID expression in the sites of formation of FM and floral organs leads to local reduction in auxin level and/or activation of the lateral auxin flow, which in turn, enhance expression of the LFYand homeotic genes responsible for FM formation and differentiation.     

Harry Potter and the structural biologist's (Key)stone

A report on the first European Keystone symposium 'Multi-protein complexes involved in cell regulation', Cambridge, UK, 18-23 August 2006.     

RNA polymerase rifampicin resistance mutations in Escherichia coli: sequence changes and dominance

Five recombinant plasmids, pBK2646, pBK611, pRC3, pRC4 and pRC5, carrying rpoB rifampicin-resistant RNA-polymerase genes were obtained. The sequence analysis of these plasmids revealed certain structural changes in the rpoB gene which specify corresponding alterations in the beta-subunit of RNA polymerase. Some functional properties of the corresponding mutant strains and their RNA polymerases have been investigated.     

Response induced in prog motoneurons by glutamate application

It was shown during experiments on isolated frog brain (fromRana ridibunda) that response to microelectrophoretically injected glutamate on to various points on the somatodendritic motoneuronal membrane (GLU response) displayed the same properties as EPSP induced in the same motoneuron by activation of three different synaptic inputs. Techniques of transmembrane polarization and current chop by means of a single microelectrode were used in this research. Mean levels of reversal potentials of GLU response and EPSP occurring as a result of stimulating the reticular formation, dorsal root, and microstimulation of presynaptic elements at the point of glutamate application equaled –16.9 ± 1.7 (n=13), –6.8 ± 1.7 (n=13), –9.8 ± 1.8 (n=6), and –15.1 ± 1.4 mV (n=13), respectively. Summation of GLU response and EPSP were quasilinear. Changes (upwards) in conductance associated with GLU response did not exceed 10%. Findings would indicate that glutamate, acting on the postsynaptic membrane receptors, induces depolarization and may serve as transmitter in all three inputs investigated.I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Academy of Sciences of the USSR, Leningrad. Translated from Neirofiziologiya, Vol. 20, No. 6, pp. 776–785, November–December, 1988.     

Salmonella typhimurium as a test system for detecting the mutagenic activity of environmental pollutants. I. The mutagenic action of heavy metal salts in in vivo and in vitro systems without metabolic activation]

The work presents the data on mutagenic effects of heavy metal salts (Zn and Cd) on Salmonella typhimurium test strains using mutagenicity test in vitro without metabolic activation and host-mediated assay. The techniques used enabled to determine also the types of mutations arising from the exposure to ZnCl2 and CdCl2.     

Synthesis and immunological properties of the peptide fragment of the hepatitis B virus envelope preS-protein]

We have synthesized the 24-41 fragment of the preS region of the hepatitis B (subtype ayw) envelope. The peptide was prepared by the solid phase synthesis on perfluoropoly-ethylene polymer grafted with polystyrene. The peptide chain was elongated from C-terminus using pentafluorophenyl- and p-nitrophenyl esters of Boc-amino acids. The peptide was cleaved off the solid phase by HBr in CF3COOH, purified by gel filtration, and, after conjugation with serum albumin (BSA), inoculated into mice. The resultant antibodies were shown to react with the peptide. The blood sera from patients with acute hepatitis B reacted with the peptide-BSA conjugates in the immunoenzymic solid phase assay.     

Gonadogenesis and color characteristics of ovaries in Japanese mitten crab <Emphasis Type="Italic">Eriocheir japonicus</Emphasis>

The gonadogenesis was studied in adult and juvenile females of Japanese mitten crab Eriocheir japonicus (Crustacea: Decapoda, Grapsida) inhabiting the rivers of the Maritime Territory. The morphometric parameters of oocytes at different stages of maturity were determined using the methods of computer morphometry and color characteristics were evaluated using the Munsell Book of Color. As a result, a color table was compiled for the ovaries from the beginning of development to gonad maturity, which included light yellow (sandy), yellow, beige, light purple, light brown, dark purple, brown (chocolate), and dark brown (brown). The regular changes in the ovary color of E. japonicus proved to closely correlate with the gonadogenesis, namely, with the composition of cells at each stage of gonad maturity.