Advances in the postgenomic technology produce huge data regarding molecular interactions. Systems biology requires a model-based analysis to understand the molecular architecture of biological systems. Systems biology consists of four stages: network identification, system analysis, system control, and system design. First, a large-scale biochemical network model is reconstructed in computer by elucidating gene functions or by inferring gene regulation networks from postgenomic data. Second, we analyze the network architectures that generate robust properties to various types of perturbations and explore some design principles underlying molecular architectures. Third, dynamic behaviors are controlled at the molecular level. Finally, we develop new technologies to rationally design a biochemical system at the molecular levels.
The medium of biomolecules in a living cell differs remarkably from a dilute solution, and many properties of biomolecules that are not observed in vitro are emerged as a result of such intracellular environments. Molecular crowding which is one of the important intracellular environments changes equilibria and rates of biomolecular interactions. Studies with solutions containing high concentration of water-soluble inert cosolutes reveal influences of the molecular crowding on the structures and interactions of proteins and nucleic acids, providing significant insights not only into traditional biology but also bionanotechnology.
Many secretory proteins undergo oxidative folding, during which they acquire intra- or intermolecular disulfide bonds. In the periplasm of Escherichia coli, DsbA functions as a primary disulfide bond donor. DsbB, which is responsible for reoxidation of DsbA, acts as a molecular machine that transforms an oxidizing equivalent of ubiquinone into a protein disulfide. A similar oxidative system exists in the ER of eukaryotic cells, where Ero1p and FAD play a pivotal role in the disulfide bond creation. This review describes the reaction mechanism of ubiquinone-dependent dithiol oxidation in Escherichia coli and proposes its similarities to the eukaryotic FAD-dependent one.
DNA that carries vital genetic information constantly suffers from oxidative damage. Oxidative DNA damage is generally repaired by the base excision repair (BER) pathway initiated by damage-specific DNA glycosylases. Although the basic mechanism of BER is conserved from bacteria to mammals, recent studies indicate that mammalian cells use an elaborate and efficient repair network to cope with oxidative DNA damage. It remains elusive how BER enzymes gain access to and repair DNA lesions in the condensed nucleosome organization of the eukaryotic genome.
The radioresistant bacterium Deinococcus radiodurans possesses the efficient repair capacity to DNA double strand breaks. By analyzing the DNA damage repair-deficient mutant, a novel DNA repair promoting protein PprA that plays a critical role in the radiation resistance was identified. Here we review our current understanding of DNA repair and radiation response mechanisms around PprA protein.