Protein conformational changes, which regulate the activity of proteins, are induced by the alternation of intramolecular interactions. Therefore, the detection of the local environmental changes around the key amino acid residues is essential to understand the activation mechanisms of functional proteins. Here we developed the methods to scan the local environmental changes using the vibrational band of cysteine S-H group. We validated the sensitivity of this method using bathorhodopsin, a photoproduct of rhodopsin trapped at liquid nitrogen temperature, which undergoes little conformational changes from the dark state as shown by the X-ray crystallography. The cysteine residues were individually introduced into 15 positions of Helix III, which contains several key amino acid residues for the light-induced conformational changes of rhodopsin. The shifts of S-H stretching modes of these cysteine residues and native cysteine residues upon the formation of bathorhodopsin were measured by Fourier transform infrared spectroscopy. While most of cysteine residues demonstrated no shift of S-H stretching mode, cysteine residues introduced at positions 117, 118, and 122, which are in the vicinity of the chromophore, demonstrated the significant changes. The current results are consistent with the crystal structure of bathorhodopsin, implying that the cysteine scanning is sensitive enough to detect the tiny conformational changes.

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In 1999, Clarke et al. ((1999) Proc. Natl. Acad. Sci. USA 96, 7232-7237) reported that the nucleation rate of α-helix of oligopeptide AK16 is as slow as 60 ms. In the present study, we measured the nucleation rate of oligopeptide, C17 (DLTDDIMCVKKILDKVG, corresponding to α-helical region of 84th to 100th amino acids of bovine α-lactalbumin) using the same method as Clarke et al. We found only initial bursts of the increase of α-helices at temperatures higher than −50°C in the presence of 70% methanol. The result with AK16 was the same as Clarke et al. reported. We also found that the folding rate of polyglutamic acid is too fast to be detected by the stopped-flow apparatus at 4°C. These results demonstrate that the α-helix formation rates in C17, AK16 and polyglutamic acid are shorter than the dead time of the stopped-flow apparatus (6 ms).

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The norovirus RNA replicase (NV3D^pol, 56 kDa, single chain monomeric protein) can amplify double-stranded (ds) RNA isothermally. It will play an alternative role in the in vitro evolution against traditional Qβ RNA replicase, which cannot amplify dsRNA and consists of four subunits, three of which are borrowed from host E.coli. In order to identify the optimal 3′-terminal sequence of the RNA template for NV3D^pol, an in vitro selection using the serial transfer was performed for a random library having the 3′-terminal sequence of ---UUUUUUNNNN-3′. The population landscape on the 4-dimensional sequence space of the 17^th round of transfer gave a main peak around ---CAAC-3′. In the preceding studies on the batch amplification reaction starting from a single-stranded RNA, a template with 3′-terminal C-stretch was amplified effectively. It was confirmed that in the batch amplification the ---CCC-3′ was much more effective than the ---CAAC-3′, but in the serial transfer condition in which the ----CAAC-3′ was sustained stably, the ---CCC-3′ was washed out. Based on these results we proposed the existence of the “shuttle mode” replication of dsRNA. We also proposed the optimal terminal sequences of RNA for in vitro evolution with NV3D^pol.

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Bacteriochlorophylls (BChls) play an important role as light harvesters in photosynthetic bacteria. Interestingly, bacteriochlorophylls (BChls) a, b, and g selectively tune their visible (Q_x) and near IR (Q_y) absorption bands by the substituent changes. In this paper, we theoretically study the mechanism for the selective control of the absorption bands. Density functional theory (DFT) and time-dependent DFT (TD-DFT) and four-orbital model analyses reveal that the selective red-shift of the Q_y band with the substituent change from BChl a to b occurs with the lower-energy shift of the (HOMO, LUMO) excited state directly induced by the molecular-orbital energy changes. In contrast, the Q_x band hardly shifts by the cancellation between the higher- and lower-energy shifts of the (HOMO-1, LUMO) excited state directly induced by the molecular-orbital energy changes and configuration interaction, respectively. On the other hand, with the substituent changes from BChl a to g, the Q_x band selectively blue-shifts by the larger higher-energy shift of the (HOMO-1, LUMO) excited state directly induced by the molecular-orbital energy shifts than the lower-energy shift due to the configuration interaction. In contrast, the Q_y band hardly shifts by the cancellation between the higher- and lower-energy shifts of the (HOMO, LUMO) excited state directly induced by the molecular-orbital energy changes and configuration interaction, respectively. Our work provides the important knowledge for understanding how nature controls the light-absorption properties of the BChl dyes, which might be also useful for design of porphyrinoid chromophores.

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The bacterial flagellar motor generates torque by converting the energy of proton translocation through the transmembrane proton channel of the stator complex formed by MotA and MotB. The MotA/B complex is thought to be anchored to the peptidoglycan (PG) layer through the PG-binding domain of MotB to act as the stator. The stator units dynamically associate with and dissociate from the motor during flagellar motor rotation, and an electrostatic interaction between MotA and a rotor protein FliG is required for efficient stator assembly. However, the association and dissociation mechanism of the stator units still remains unclear. In this study, we analyzed the speed fluctuation of the flagellar motor of Salmonella enterica wild-type cells carrying a plasmid encoding a nonfunctional stator complex, MotA/B(D33N), which lost the proton conductivity. The wild-type motor rotated stably but the motor speed fluctuated considerably when the expression level of MotA/B(D33N) was relatively high compared to MotA/B. Rapid accelerations and decelerations were frequently observed. A quantitative analysis of the speed fluctuation and a model simulation suggested that the MotA/B(D33N) stator retains the ability to associate with the motor at a low affinity but dissociates more rapidly than the MotA/B stator. We propose that the stator dissociation process depends on proton translocation through the proton channel.

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Toward reconstitution of living cells by artificial cells technology, it is critical process to understand the differences between mixtures of biomolecules and living cells. For the aim, we have developed procedures for preparation of an additive-free cell extract (AFCE) and for concentrating biomacromolecules in artificial cells. In this review, we introduce our recent progress to reconstitute intracellular environments in vitro and in artificial cells.

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An ultrasensitive method for the determination of proteins is described that combines an enzyme-linked immunosorbent assay (ELISA) and a thionicotinamide-adenine dinucleotide (thio-NAD) cycling method. A sandwich method using a primary and a secondary antibody for antigens is employed in an ELISA. An androsterone derivative, 3α-hydroxysteroid, is produced by the hydrolysis of 3α-hydroxysteroid 3-phosphate with alkaline phosphatase linked to the secondary antibody. This 3α-hydroxysteroid is oxidized to a 3-ketosteroid by 3α-hydroxysteroid dehydrogenase (3α-HSD) with a cofactor thio-NAD. By the opposite reaction, the 3-ketosteroid is reduced to a 3α-hydroxysteroid by 3α-HSD with a cofactor NADH. During this cycling reaction, thio-NADH accumulates in a quadratic function-like fashion. Accumulated thio-NADH can be measured directly at an absorbance of 400 nm without any interference from other cofactors. These features enable us to detect a target protein with ultrasensitivity (10^–19 mol/assay) by measuring the cumulative quantity of thio-NADH. Our ultrasensitive determination of proteins thus allows for the detection of small amounts of proteins only by the application of thio-NAD cycling reagents to the usual ELISA system.

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Familial clustering without any prerequisite knowledge becomes often necessary in Behavioral Science, and forensic studies in case of great disasters like Tsunami and earthquake requiring body-identification without any usable information. However, there has been no well-established method for this purpose although conventional ones such as short tandem repeats (STR) and single nucleotide polymorphism (SNP), which might be applied with toil and moil to some extent. In this situation, we could find that the universal genome distance-measuring method genome profiling (GP), which is made up of three elemental techniques; random PCR, micro-temperature gradient gel electrophoresis (μTGGE), and computer processing for normalization, can do this purpose with ease when applied to mouse families. We also confirmed that the sequencing approach based on the ccgf (commonly conserved genetic fragment appearing in the genome profile) was not completely discriminative in this case. This is the first demonstration that the familial clustering can be attained without a priori sequence information to the level of discriminating strains and sibling relationships. This method can complement the conventional approaches in preliminary familial clustering.

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Two mammalian DNA glycosylases, methyl-CpG binding domain protein 4 (MBD4) and thymine DNA glycosylase (TDG), are involved in active DNA demethylation via the base excision repair pathway. Both MBD4 and TDG excise the mismatch base from G:X, where X is uracil, thymine, and 5-hydroxymethyluracil (5hmU). In addition, TDG excises 5mC oxidized bases i.e. when X is 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) not 5-hydroxymethylcytosine (5hmC). A MBD4 inactive mutant and substrate crystal structure clearly explains how MBD4 glycosylase discriminates substrates: 5mC are not able to be directly excised, but a deamination process from 5mC to thymine is required. On the other hand, TDG is much more complicated; in this instance, crystal structures show that TDG recognizes G:X mismatch DNA containing DNA and G:5caC containing DNA from the minor groove of DNA, which suggested that TDG might recognize 5mC oxidized product 5caC like mismatch DNA. In mutation studies, a N157D mutation results in a more 5caC specific glycosylase, and a N191A mutation inhibits 5caC activity while that when X=5fC or T remains. Here I revisit the recent MBD4 glycosylase domain co-crystal structures with DNA, as well as TDG glycosylase domain co-crystal structures with DNA in conjunction with its mutation studies.

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Myosin V is a vesicle transporter that unidirectionally walks along cytoskeletal actin filaments by converting the chemical energy of ATP into mechanical work. Recently, it was found that myosin V force generation is a composition of two processes: a lever-arm swing, which involves a conformational change in the myosin molecule, and a Brownian search-and-catch, which involves a diffusive “search” by the motor domain that is followed by an asymmetric “catch” in the forward actin target such that Brownian motion is rectified. Here we developed a system that combines optical tweezers with DNA nano-material to show that the Brownian search-and-catch mechanism is the energetically dominant process at near stall force, providing 13 k_BT of work compared to just 3 k_BT by the lever-arm swing. Our result significantly reconsiders the lever-arm swinging model, which assumes the swing dominantly produces work (>10 k_BT), and sheds light on the Brownian search-and-catch as a driving process.

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Dermal photoreceptors located in the mantle of Lymnaea stagnalis were histologically and physiologically characterized. Our previous study demonstrated that the shadow response from dermal photoreceptors induces the whole-body withdrawal response. Through the interneuron, RPeD11, we detected that the light-off response indirectly originated from a dermal photoreceptor. Previous observations, based on behavioral pharmacology, revealed that cyclic guanosine monophosphate acts as a second messenger in the dermal photoreceptor. Furthermore, gastropods possess dermal photoreceptors containing rhodopsin, as a photopigment, and another photo-sensitive protein, arrestin, responsible for terminating the light response. Thus, we chose three antibodies, anti-cGMP, anti-rhodopsin, and anti-β-arrestin, to identify the dermal photoreceptor molecules in Lymnaea mantle. Extracellular recording, using a suction electrode on the mantle, revealed a light off-response from the right parietal nerve. Overlapping structures, positive against each of the antibodies, were also observed. Numerous round, granular particles of 3–47 μm in diameter with one nucleus were distributed around pneumostome and/or inside the mantle. The cells surrounding the pneumostome area, located 10 μm beneath the surface, tended to have smaller cell soma ranging from 3 to 25 μm in diameter, while cells located in other areas were distributed uniformly inside the mantle, with a larger diameter ranging from 12 to 47 μm. The histological examination using back-filing Lucifer Yellow staining of the right parietal nerve with the three dermal photoreceptor antibodies confirmed that these overlapping-stained structures were dermal photoreceptors in Lymnaea.

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Skeletal myosin S1 consists of two functional segments, a catalytic-domain and a lever-arm. Since the crystal structure of ADP/Vi-bound S1 exhibits a strong intramolecular flexure between two segments, inter-conversion between bent and extended forms; i.e. “tilting of the lever-arm” has been accepted as the established molecular mechanism of skeletal muscle contraction. We utilized quick-freeze deep-etch replica electron microscopy to directly visualize the structure of in vitro actin-sliding myosin, and found the existence of a novel oppositely-bent configuration, instead of the expected ADP/Vi-bound form. We also noticed that SH1–SH2 cross-linked myosin gives an aberrant appearance similar to the above structure. Since SH1–SH2-cross-linked myosin is a well-studied analogue of the transient intermediate of the actomyosin cross-bridge cycle, we devised a new image-processing procedure to define the relative view-angles between the catalytic-domain and the lever-arm from those averaged images, and built a 3-D model of the new conformer. The lever-arm in that model was bent oppositely to the ADP/Vi-bound form, in accordance with observed actin-sliding cross-bridge structure. Introducing this conformer as the crucial intermediate that transiently appears during sliding, we propose a revised scheme of the cross-bridge cycle. In the scenario, the novel conformer keeps actin-binding in two different modes until it forms a primed configuration. The final extension of the lever-arm back to the original rigor-state constitutes the “power-stroke”. Various images observed during sliding could be easily interpreted by the new conformer. Even the enigmatic behavior of the cross-bridges reported as “loose chemo-mechanical coupling” might be adequately explained under some assumptions.

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We propose the cooperative model of phenotype-driven evolution, in which natural selection operates on a phenotype caused by both genetic and epigenetic factors. The conventional theory of evolutionary synthesis assumes that a phenotypic value (P) is the sum of genotypic value (G) and environmental deviation (E), P=G+E, where E is the fluctuations of the phenotype among individuals in the absence of environmental changes. In contrast, the cooperative model assumes that an evolution is triggered by an environmental change and individuals respond to the change by phenotypic plasticity (epigenetic changes). The phenotypic plasticity, while essentially qualitative, is denoted by a quantitative value F which is modeled as a normal random variable like E, but with a much larger variance. Thus, the fundamental equation of the cooperative model is given as P=G+F where F includes the effect of E. Computer simulations using a genetic algorithm demonstrated that the cooperative model realized much faster evolution than the evolutionary synthesis. This accelerated evolution was found to be due to the cumulative evolution made possible by a ratchet mechanism due to the epigenetic contribution to the phenotypic value. The cooperative model can well account for the phenomenon of genetic assimilation, which, in turn, suggests the mechanism of cumulative selection. The cooperative model may also serve as a theoretical basis to understand various ideas and phenomena of the phenotypedriven evolution such as genetic assimilation, the theory of facilitated phenotypic variation, and epigenetic inheritance over generations.

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Temperature-sensitive Ca²⁺ dynamics occur primarily through transient receptor potential channels, but also by means of Ca²⁺ channels and pumps on the endoplasmic reticulum membrane. As such, cytoplasmic Ca²⁺ concentration ([Ca²⁺]_cyt) is re-equilibrated by changes in ambient temperature. The present study investigated the effects of heat pulses (heating duration: 2 s or 150 s) on [Ca²⁺]_cyt in single WI-38 fibroblasts, which are considered as normal cells. We found that Ca²⁺ burst occurred immediately after short (2 s) heat pulse, which is similar to our previous report on HeLa cells, but with less thermosensitivity. The heat pulses originated from a focused 1455-nm infrared laser light were applied in the vicinity of cells under the optical microscope. Ca²⁺ bursts induced by the heat pulse were suppressed by treating cells with inhibitors for sarco/endoplasmic reticulum Ca²⁺ ATPase (SERCA) or inositol trisphosphate receptor (IP₃R). Long (150 s) heat pulses also induced Ca²⁺ bursts after the onset of heating and immediately after re-cooling. Cells were more thermosensitive at physiological (37°C) than at room (25°C) temperature; however, at 37°C, cells were responsive at a higher temperature (ambient temperature+heat pulse). These results strongly suggest that the heat pulse-induced Ca²⁺ burst is caused by a transient imbalance in Ca²⁺ flow between SERCA and IP₃R, and offer a potential new method for thermally controlling Ca²⁺-regulated cellular functions.

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Taste avoidance conditioning (TAC) was carried out on the pond snail, Lymnaea stagnalis. The conditional stimulus (CS) was sucrose which elicits feeding behavior; while the unconditional stimulus (US) was a tactile stimulus to the head which causes feeding to be suppressed. The neuronal circuit that drives feeding behavior in Lymnaea is well worked out. We therefore compared the physiological characteristics on 3 classes of neurons involved with feeding behavior especially in response to the CS in conditioned vs. control snails. The cerebral giant cell (CGC) modulates feeding behavior, N1 medial neuron (N1M) is one of the central pattern generator neurons that organizes feeding behavior, while B3 is a motor neuron active during the rasp phase of feeding. We found the resting membrane potential in CGC was hyperpolarized significantly in conditioned snails but impulse activity remained the same between conditioned vs. control snails. There was, however, a significant increase in spontaneous activity and a significant depolarization of N1M’s resting membrane potential in conditioned snails. These changes in N1M activity as a result of training are thought to be due to withdrawal interneuron RPeD11 altering the activity of the CGCs. Finally, in B3 there was: 1) a significant decrease in the amplitude and the frequency of the post-synaptic potentials; 2) a significant hyperpolarization of resting membrane potential in conditioned snails; and 3) a disappearance of bursting activity typically initiated by the CS. These neuronal modifications are consistent with the behavioral phenotype elicited by the CS following conditioning.

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