Many real systems can be described as networks, composed of a set of nodes and a set of edges connecting the nodes. Interestingly, it has been found that most real networks have a common architecture, termed scale-free or broad-tail topology. Here we review key well-established concepts in network science: small world, scale-free network and network motif, with special emphasis on biological networks. Key mechanisms responsible for the emergence of the scale-free property are discussed along with a simple evolutionary model of protein-protein interaction networks.
Protein-protein and protein-nucleic acid interactions are fundamental in self and non-self recognition in immune system. Leukocyte immunoglobulin-like receptor B1 (LILRB1) and LILRB2 are human inhibitory receptors which recognize major histocompatibility complex (MHC) class I molecules and take part in immune regulation. In this review, we demonstrated detailed thermodynamic and kinetic studies of interactions between LILRs and MHC class I molecules, and structural analyses by X-ray crystallography and NMR. Our data shows the binding mode involving some conformational adjustment without a very large conformational reduction in flexibility at the binding interface.
Homologous recombination promotes faithful segregation of homologous chromosomes during meiosis. Two RecA homologues, Rad51 and Dmc1, work together to catalyze homology search and strand exchange process in the recombination. We recently identified a protein complex containing two meiosis-specific proteins, Mei5 and Sae3, which promotes the assembly of Dmc1 on the Rad51 ensembles. In this review, I will discuss the function of Dmc1-containing protein machinery in meiotic-recombination and possible asymmetric distribution of the two RecA homologues on chromosomes.
Autophagy is a bulk degradation system that is responsible for various cellular processes such as starvation response, cellular clearance and immune response. In this process, a double membrane structure called an autophagosome sequesters a portion of cytoplasm and delivers the contents to vacuoles/lysosomes. In yeast, at least 17 Atg proteins are shown to be essential for autophagosome formation. Here, we describe the comprehensive structural studies on Atg proteins by X-ray crystallography. Based on structural information and mutational analyses, we discuss the molecular roles of Atg proteins on autophagosome formation.
c-type cytochromes are electron transfer proteins that are essential for the life of virtually all organisms. They characteristically carry covalently-bound heme via thioether bonds to two cysteines in the protein. In Gram-negative bacteria, biogenesis of c-type cytochrome is conducted by a multiprotein complex system known as the cytochrome c maturation (Ccm) system. This system is consisted of 8 gene products (CcmA-CcmH). CcmE, which is called as a heme chaperon, binds heme and delivers it to apocytochrome c. In this article, I discuss the structure of CcmE and how it works as a heme chaperone protein.
F1-ATPase is a rotary molecular motor in which unidirectional rotation of the central γ-subunit is powered by ATP hydrolysis in three catalytic sites arranged 120° apart around γ. To see how hydrolysis reactions produce mechanical rotation, we observed rotation of γ under the optical microscope, while watching which of the three sites bound and released a fluorescent ATP analog. The reaction scheme, including both the number of site occupancy and reactions that trigger substeps, is now established.
Wrong:1H NMR spectrum of G-quadruplex DNA formed from TTAGGG at room temperature. Imino proton signals at the indicated DNA concentrations are also shown. Signals labeled by M and D arise from monomer and dimer of G-quadruplex DNA, respectively.
Right:1H NMR spectra of [(TTAGGG)4]. M and D represent monomer and dimer, respectively.