Interpretation of the function of biomolecules at the molecular level requires knowledge of the three-dimensional structure. Electron paramagnetic resonance methods can be used to determine the distance between paramagnetic sites that are intrinsic to a biomolecule or are added by attachment of stable nitroxyl radicals or paramagnetic metals. Techniques have been developed to measure distances ranging from about 5 to 70 Å (0.5 to 7.0 nm). This article provides an overview of techniques and examples of systems to which they have been applied.
Multiple sequence alignment is an important tool for computational analysis of nucleotide or amino acid sequences. It is also a challenging combinatorial optimization problem in computer science. As a large amount of sequence data is becoming available from genome and other large-scale sequencing projects, efficiency, as well as accuracy, is currently required for a multiple sequence alignment program. Several new programs are being developed aiming at improving both efficiency and accuracy. We overview the algorithms and performances of new programs including that by ourselves.
Neuropeptides are perhaps the most diverse intercellular signaling molecules in the animal kingdom. Owing to the high-throughput methodologies using the high-performance liquid chromatography as well as the mass spectrometry, the number of peptides identified from both vertebrates and invertebrates are increasing. In many cases, the multiple structurally related peptides which are unequivocally considered to be members of the same peptide family are found in the nervous system. We call such peptides the multiple family peptides. Here, we show the structure, distribution, and action of two kinds of multiple family peptides recently identified in a marine mollusc, Aplysia.
Plants photoreceptors are divided into two groups, well-known phytochromes and blue-light receptors, such as cryptochromes and phototropins. Regarding one of the later, we proved the role of the LOV domains in the kinase photoactivation. In addition to the plant phytochromes, many bacteriophytochromes have been found in both photosynthetic and nonphotosynthetic prokaryotic microorganisms. One of them has been found to undergo not red/far-red but blue/green photoreversible transformaion. Furthermore, new members of blue-light receptors, FKF1 families and BULF photoreceptors, have been found. Their structures and functions are reviewed.
Light is one of the most important signals providing critical information to biological systems. Four rhodopsins, bacteriorhodopsin (BR), halorhodopsin (hR), sensory rhodopsin (sR) and phoborhodopsin (pR) exist in archaeal membranes. bR and hR work as a light-driven ion pump. sR and pR work as a photo-sensor of phototaxis, and form signaling complexes in membranes with their respective cognate transducer proteins HtrI (with sR) and HtrII (with pR), through which light signals are transmitted to cytoplasm. In this review, we describe our results on the protein-protein interaction of archaeal rhodopsins/HtrII and the signal transfer reaction by the complexes.