The family of mono-ADP-ribosyltransferase includes not only bacterial toxins but also mammalian enzymes. Recently, crystal structures of arginine-specific ADP-ribosyltransferase have been revealed, giving a better understanding of type IV toxin. They are VIP2 from Bacillus and Ia from Clostridium perfringens. VIP2 and Ia ADP-ribosylate the Arg177 of actin. They consist of topologically similar N- and C-domains, which have not been expected from the amino acid sequence. C-domain is an enzymatic domain. N-domain interacts with VIP1 and Ib, respectively. C-domain structures were basically the same but the surface charge of N-domain was found significantly different between VIP2 and Ia. Rat ART2.2 and rho-targeted C3 toxin(asparagine-specific)consist of only one domain and the structure is similar to the C-domain of Ia. We summarize the crystal structure and the reaction mechanism of Ia.
Two kinds of blue-light receptors, cryptochrome and phototropin, have been found in higher plants. Cryptochrome mediates the inhibition of hypocotyl elongation and anthocyanin accumulation, and controls the timing of flowering and the circadian clock. Phototropin mediates phototropism, light-dependent chloroplast movement, stomata opening and leaf expansion. Here we review the characteristics of these photoreceptors and the signal transduction mechanisms downstream of the blue-light receptors.
The cytoplasm of living cells is filled with cytoskeletal filament networks that dictate the shape and motility of cells. The dynamic and heterogeneous nature of the cytoskeletal network has been visualized, but the limited accessibility of living cytoplasm prevents easy characterization of its physical properties. From the simple observation that the Brownian motion of a particle reveals the mechanics of its microenvironment, a new approach, microrheology, emerged and successfully applied to living cells. Here, we review recent progress in microrheology and the implication for the understanding of subcellular processes in biology.
Combinatorial protein libraries allow us to examine a huge number of sequences. Such methods are being used for de novo design of proteins and to investigate the determinants of protein folding. Since the diversity of possible sequences is beyond what can be explored in experiments, some restrictions have to be imposed during design of the library. Recently, theoretical tools have been developed to bias and characterize the ensembles of sequences that fold into a given structure. Such tools can be applied to the design and interpretation of combinatorial experiments and to the design of particular protein structures.
Powerful new technologies, such as DNA microarrays, provide simple and economical ways to explore gene expression patterns against some kinds of gene perturbations such as disruption or over expression. Based on experimentally observed gene expression data on the steady state and transient state, recent advances of technology in bioinformatics have made it possible to infer the genetic interactions and to develop a biosimulator for analyzing metabolic networks in the cell. In this overview I will briefly explain the contribution of information science technology to the research on systems life sciences especially focused on the up-to-date development of biosimulator for metabolic networks.