Molecular recognition is often mediated by flexible loops that have widely fluctuating structures and are sometimes disordered, but that form particular complex structures following ligand binding. In fact, many loop structures found in the PDB database are too flexible to be determined precisely. A new loop modeling method was therefore developed using force-biased multicanonical molecular dynamics with the implicit solvent model to generate an ensemble of putative loop structures with low free energy values. The method was then used to create ensembles for several flexible loops that were compared with the corresponding NMR and X-ray structures. The induced-fit structural change of dihydrofolate reductase (DHFR) was also predicted from a structural ensemble of ligand-free M20 loop conformations and successive docking simulations.

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Kinesin is a motor protein that processively moves step by step along a microtubule. To investigate the effects of temperature on run length, i.e., processivity of kinesin motility, we performed a single-molecular bead assay at temperature range of 20–40°C. An increase in the walking velocity of kinesin corresponded to the Arrhenius activation enthalpy of 48 kJ/mol, being consistent with the previous reports. Here, we found that the run length increased, that is, the kinesin processivity enhanced with increasing temperature. Then, we estimated the probability of detachment of kinesin from a microtubule per one 8-nm stepping event, and found that it diminishes from 0.014 to 0.006/step with increasing temperature from 20 to 40°C. And we noticed that prolonged incubation at 30, 35 and 40°C significantly slowed down the walking velocity, but further increased the run length and duration. Those results are interpreted according to the effect of temperature on the rate constants of some key kinetic steps in the ATPase cycle.

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To investigate possible roles of S···X (X=O, N, S) interactions in the functions and evolution of a protein, two types of database analyses were carried out for a vertebrate phospholipase A₂ (PLA₂) family. A comprehensive search for close S···X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S···O interactions and one common S···N interaction for the PLA₂ domain group (PLA₂-DG), while an additional three S···O interactions were found for the snake PLA₂ domain group (sPLA₂-DG). On the other hand, a phylogenetic analysis on the conservation of the observed S···O and S···N interactions over various amino acid sequences of sPLA₂-DG demonstrated probable clustering of the interactions on the dendrogram. Most of the interactions characterized for PLA₂ were found to reside in the vicinity of the active site and to be able to tolerate the conformational changes due to the substrate binding. These observations suggested that the S···X interactions play some role in the functions and evolution of the PLA₂ family.

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Presented is an evaluation of phase contrast techniques in transmission electron microscopy. The traditional defocus phase contrast is compared to two recently developed phase plate techniques. One is the Zernike phase contrast transmission electron microscope, the other is the Hilbert differential contrast thransmission electron microscope. The imaging characteristics of each technique are discussed. Phase plate techniques provide improved contrast for ice-embedded biological samples which are a challenge for the conventional defocus phase contrast. The flat spectral response of the Zernike and Hilbert modes extends towards the low frequencies which are severely suppressed in the conventional defocus mode. Target applications for each of the phase contrast techniques are discussed based on the specifics of image formation and spectral transfer.

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Complicated pH-properties of the tetraheme cytochrome c₃ (cyt c₃) from Desulfovibrio vulgaris Miyazaki F (DvMF) were examined by the pH titrations of ¹H-¹⁵N HSQC spectra in the ferric and ferrous states. The redox-linked pK_a shift for the propionate group at C13 of heme 1 was observed as the changes of the NH signals around it. This pK_a shift is consistent with the redox-linked conformational alteration responsible for the cooperative reduction between hemes 1 and 2. On the other hand, large chemical shift changes caused by the protonation/deprotonation of Glu41 and/or Asp42, and His67 were redox-independent. Nevertheless, these charged residues affect the redox properties of the four hemes. Furthermore, one of interesting charged residues, Glu41, was studied by site-directed mutagenesis. E41K mutation increased the microscopic redox potentials of heme 1 by 46 and 34 mV, and heme 2 by 35 and 30 mV at the first and last reduction steps, respectively. Although global folding in the crystal structure of E41K cyt c₃ is similar to that of wild type, local change was observed in ¹H NMR spectrum. Glu41 is important to keep the stable conformation in the region between hemes 1 and 2, controlling the redox properties of DvMF cyt c₃. In contrast, the kinetic parameters for electron transfer from DvMF [NiFe] hydrogenase were not influenced by E41K mutation. This suggests that the region between hemes 1 and 2 is not involved in the interaction with [NiFe] hydrogenase, and it supports the idea that heme 4 is the exclusive entrance gate to accept the electron in the initial reduction stage.

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To develop an artificial photosynthesis model, the anionic water-soluble carotenoid dye crocetin was electrostatically immobilized onto the surface of cationic surfactant cetyltrimethylammonium bromide (CTAB) micellar medium including Mg chlorophyll-a and b (MgChl-a and b) (Cro/MgChl), and its photophysical properties were studied using UV-vis absorption and fluorescence spectroscopy. The fluorescence of MgChl-a and b was observed, with the excitation wavelength attributed to the absorption band of crocetin, indicating that photoinduced energy transfer from the photoexcited state of crocetin to MgChl-a and b occurs. The photostability of MgChl-a and b in Cro/MgChl was investigated under continuous irradiation. After 60 min irradiation, the absorbance decreases at 660 nm Cro/MgChl and MgChl-a/b, without crocetin, were 3.0 and 17%, respectively. These results indicate that the photo-bleaching rate of MgChl-a/b in Cro/MgChl on irradiation is suppressed by the crocetin molecule on the surface of micelles.

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Gene expression patterning is crucial for environmental nutritional responses such as the nitrogen response in Escherichia coli. The nitrogen response is primarily regulated by the expression of glutamine synthetase (GS), which catalyzes the sole reaction of glutamine formation, by cis-logic regulatory circuits. Here, by removing the entire corresponding operator and promoter regions required for the control of GS, we constructed an E. coli strain that enables the detection of the basal GS gene expression, which is expressed from a plain promoter unrelated to the nitrogen response, and measured by co-transcribed GFP expression, an indicator of GS expression. Using strain cultures, we found that the GS expression level was able to shift inversely against the change of the environmental glutamine concentration. As a control experiment, we repeated similar experiments with another strain in which the GS regulatory region remained intact and the GFP gene following the plain promoter was introduced into a different chromosomal site. For this strain, we found that the GFP expression level did not shift in accordance with the environmental glutamine concentration. These results showed that GS expression from the plain promoter exhibited a responsive ability to buffer environmental changes, whereas the GS expression shift did not correlate with the specific characteristics of the plain promoter and GFP expression. This study identifies the inherent characteristics of basal gene expression in response to environmental changes, facilitating a deeper understanding of cellular design principles.

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