Soluble proteins consist of one to several globular functional domains. A globular domain is decomposed into several modules. Module is a sub-structure within a globular domain and it has a compact conformation consisting of a contiguous sequence of 10 to 40 amino acid residues. Close correlation of module boundaries with intron positions implies that a gene encoding a globular functional domain was created by joining exons in early evolution. Some introns seem to be deleted on different lineages in evolutionary time scale.
The pump/probe time-resolved resonance Raman (TR3) spectroscopy can detect a protein structural change in nsec resolution. The technique with 532nm pump and 416nm probe pulses was applied to observe a temporal change of the Fe-CO stretching vibration of MbCO which might take place during relaxation from 'open' to 'closed' forms upon CO binding. The UV TR3 experiment with 419nm pump and 217.8nm probe pulses revealed that β 37-Trp of HbCO was altered at 10-20 μs following photolysis, suggesting a likely mechanism of the quaternary structure transition upon CO dissociation.
Dynamic structures of proteins derived from X-ray crystallography are described. A new method of dynamic structure refinement is proposed. In the method, Debye-Waller factor is expanded in terms of the low-frequency normal modes whose amplitudes and eigenvectors are experimentally optimized in the process of the crystallographic refinement. Application of the method to human lysozyme showed; (1) Debye-Waller factor consists of two parts, highly anisotropic internal fluctuations and almost isotropic external terms. The former is smaller than the latter. (2) Correlation of fluctuations corresponding to the hinge-bending motion was detected.
The crystal structure of a copper-containing enzyme, galactose oxidase, is reported. The protein entirely consists of almost entirely β-structure. with one domain showing pseudo sevenfold symmetry. The copper coordination is square pyramidal with one exogenous ligand. The discovery of an unexpected intramnolecular thioether bond between Tyr272 and Cys228 at the copper site strongly supports a model where a tyrosine free radical is involved in the catalytic mechanism as a secondary redox cofactor. Comparison with other related enzymes are also made.
Marine Vibrio swims in sea water by rotating a single, sheathed polar flagellum and swarms over viscous surfaces by numerous unsheathed lateral flagella, which are produced when cells are in viscous environment. Surprisingly, the motors of these flagella use different coupling ions for energy transduction: the energy source for the polar flagellar motor is the sodium-motive force, whereas the lateral flagellar motors are driven by the proton-motive force. Furthermore, the polar flagellum idiosyncratically functions as a tactile sensor controlling transcription of the genes for lateral flagella production by sensing viscous drag that restrict its movement.
We have determined the entire coding sequences for two novel cadherin-related molecules, termed protocadherins by molecular cloning. The overall structure is similar to that of typical cadherins, but they have unique features as well. Interestingly, the new molecules share many properties with the fat gene product of Drosophila. The molecules were expressed mainly in the nervous system and their expression was developmentally regulated. Many cDNAs with similar properties were isolated from human, rat, mouse, Xenopus, Drosophila and C. elegans, suggesting that similar moiecules are widely expressed in various organisms. These molecules may play an important role, especially in the central narvous system.