A protein in solution is a thermodynamic entity, consisting of ensemble of conformers ranging from the lowest-energy folded conformer to the highest-energy unfolded conformer. Under physiological conditions, however, populations of higher energy conformers are small and they are not normally detected by NMR spectroscopy nor by X-ray crystallography. A new type of NMR experiment, utilizing the volume property of a protein in conjunction with pressure, enables structural analysis of semi-stable higher energy conformers, thereby extending the structural analysis essentially to the entire conformational space. The result will provide strong basis for understanding protein function, folding and conformational disease.
Clp is a family of ATP-dependent protease complexes, each composed of an ATPase and a peptidase. Using cryo-electron microscopy and image analysis, we demonstrated that ClpY ATPase binds to ClpQ peptidase via its AAA ATPase domains, not via its intermediate domains which protrude distally and may be involved in substrate binding. The recognition and translocation of substrates by ClpAP was also visualized. The mechanism of proteolysis by Clp is discussed
Dorsal horn, especially substantia gelatinosa(SG; lamina II), neurons in the spinal cord are known to play an important role in regulating pain transmission to the central nervous system from the periphery. The SG neurons receive excitatory(glutamatergic)and inhibitory transmission in a mono- or polysynaptic manner through myelinated Aδ and unmyelinated C primary-afferent fibers. The excitatory transmission is negatively modulated by extrinsic or intrinsic substances through a pre- and/or postsynaptic mechanism, resulting in a relief of pain sensation. It is concluded that pain transmission is regulated at the synapse by a cellular mechanism similar to that in learning and memory.
Having a huge amount of genome sequence data, we have aimed to analyze the data and provide reliable information extracted for biological scientists. Focusing on the protein structure prediction, we have so far analyzed 70 organisms whose complete genomes were sequenced. The main tool employed was PSI-BLAST, a homology search method much more powerful than the conventional ones such as FASTA/BLAST. The fraction of all ORFs in a genome, predictable of their 3D structure, turned out to be as high as 40-50%. All the data analyzed were compiled in a database called GTOP(http://spock.genes.nig.ac.jp/~genome/gtop.html). As an application study of GTOP, a way to identify a significant number of pseudogenes in E. coli is also described.
Heme-based sensor proteins have become known to be a new member of hemeproteins in which the heme acts as the active center for sensing gas molecules such as O2, CO, and NO. HemAT and CooA are the O2 and CO sensor proteins, respectively. HemAT is a signal transducer protein in the aerotaxis control system in Bacillus subtilis. CooA is a transcriptional activator that regulates the expression of some proteins responsible for CO metabolism in Rhodospirillum rubrum. Here, the structure and function of HemAT and CooA are reviewed.
I have established a novel approach for disrupting chemical neurotransmission rapidly and reversibly in a temporally and spatially restricted manner in the intact Drosophila nervous system. The Gal4/UAS system is used to direct expression of temperature-sensitive dynamin in restricted neuronal subsets and neurotransmission from the targeted neurons is then blocked by a mild temperature shift. This approach, together with the advanced Drosophila behavioral genetics, has provided new insight into the neuronal mechanisms underlying higher-order brain functions including associative learning and sexual orientation.