Biological meaning of "habitable zone" in nucleotide composition space.

Organisms generally display two contrasting properties: large biodiversity and a uniform state of "life". In this study, we focused on the question of how genome sequences describe "life" where a large number of biomolecules are harmonized. We analyzed the whole genome sequence of 2664 organisms, paying attention to the nucleotide composition which is an intensive parameter from the genome sequence.

What parameters characterize "life"?

"Life" is a particular state of matter, and matter is composed of various molecules. The state corresponding to "life" is ultimately determined by the genome sequence, and this sequence determines the conditions necessary for survival of the organism. In order to elucidate one parameter characterizing the state of "life", we analyzed the amino acid sequences encoded in the total genomes of 557 prokaryotes and 40 eukaryotes using a membrane protein prediction online tool called SOSUI.

Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics.

Developments in atomic force microscopy have opened up a new path toward single-molecular phenomena; in particular, during the process of pulling a membrane protein out of a lipid bilayer. However, the characteristic features of the force-distance (F-D) curve of a bacteriorhodopsin in purple membrane, for instance, have not yet been fully elucidated in terms of physicochemical principles. To address the issue, we performed a computer simulation of bacteriorhodopsin with, to our knowledge, a novel coarse-grained (C-G) model.

Dependence of purple membrane bump curvature on pH and ionic strength analyzed using atomic force microscopy combined with solvent exchange.

Purple membrane (PM), which is a membrane patch formed by the self-assembly of the membrane protein bacteriorhodopsin (bR) with archaeal lipids, is a good subject for studying the mechanism for the supramolecular structural formation of membrane proteins. Several studies have suggested that PM is not simply planar but that it has a curvature. Atomic force microscopy (AFM) studies also indicate the presence of dome-like structures (bumps) on the cytoplasmic surface of PM.

Biological meaning of DNA compositional biases evaluated by ratio of membrane proteins.

Membrane spanning regions can be used as markers for studying the robustness of biologically important units of proteins against evolutionary change (R. Sawada and S. Mitaku, Genes to Cells, 2010).

Electrostatic effects influence the formation of two-dimensional crystals of bacteriorhodopsin reconstituted into dimyristoylphosphatidylcholine membranes.

We examined how electrostatic shielding affects the formation of two-dimensional (2D) crystals of bacteriorhodopsin (bR) in reconstituted dimyristoylphosphatidylcholine (DMPC) membranes by varying the sodium chloride (NaCl) concentration. The 2D crystalline array of bR formed in the gel phase of DMPC membranes was characterized by a symmetric bipolar pattern in visible circular dichroic spectra collected around 560 nm. The amplitude of the bipolar pattern was systematically enhanced by increasing the NaCl concentration.

How are exons encoding transmembrane sequences distributed in the exon-intron structure of genes?

The exon-intron structure of eukaryotic genes raises a question about the distribution of transmembrane regions in membrane proteins. Were exons that encode transmembrane regions formed simply by inserting introns into preexisting genes or by some kind of exon shuffling? To answer this question, the exon-per-gene distribution was analyzed for all genes in 40 eukaryotic genomes with a particular focus on exons encoding transmembrane segments. In 21 higher multicellular eukaryotes, the percentage of multi-exon genes (those containing at least one intron) within all genes in a genome was high (>70%) and with a mean of 87%.

Effect of lipid phase transition on molecular assembly and structural stability of bacteriorhodopsin reconstituted into phosphatidylcholine liposomes with different acyl-chain lengths.

Previous studies on the correlation between bacteriorhodopsin (bR) disassembly and photobleaching suggested that a weakening of intermolecular interactions is responsible for irreversible photobleaching (Mukai, Y.; Kamo, N.; Mitaku, S.

Structural changes in bacteriorhodopsin in purple membranes induced by irreversible photobleaching with heterogeneous and homogeneous stability.

Kinetic studies of irreversible photobleaching of bacteriorhodopsin (bR) in purple membrane (PM) at neutral pH have previously indicated the existence of two kinds of species which differ in their structural stability. bR was shown to have kinetically slow- and fast-decayed components with the faster one increasing with changes in intra- and intermolecular structures in darkness. However, our recent work reported that photobleaching kinetics above pH 10 were characterized by a single-decay component.

Characteristic amino acid distribution around segments unique to allergens.

Epitopes are located at the surface of allergens with which antibodies specifically bind. On the assumption that fragments unique to allergens have common, characteristic amino acid sequences, we compared the amino acid sequences of allergens with those of non-allergens. Segments around fragments unique to allergens showed wavelet-like distributions for several amino acids.

SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in gram-negative bacteria.

A predictive software system, SOSUI-GramN, was developed for assessing the subcellular localization of proteins in Gram-negative bacteria. The system does not require the sequence homology data of any known sequences; instead, it uses only physicochemical parameters of the N- and C-terminal signal sequences, and the total sequence. The precision of the prediction system for subcellular localization to extracellular, outer membrane, periplasm, inner membrane and cytoplasmic medium was 92.

Reconstitution of bacteriorhodopsin into cyclic lipid vesicles.

Bacteriorhodopsin (bR), a membrane protein that can generate a light-driven proton pump, was successfully reconstituted into vesicles composed of an artificial cyclic lipid that mimics archaeal membrane lipids. Unlike reconstituted bR in 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles, the net topology and structure of bR molecules in cyclic lipid vesicles are identical to those in the native purple membrane of Halobacterium salinarum.

Sesquiterpene lactones from Staehelina fruticosa.

The phytochemical analysis of Staehelina fruticosa led to the isolation of four germacranolide-type sesquiterpene lactones (1- 4), including two new glycosides. The structures of these sesquiterpene lactones were elucidated using spectroscopic techniques, and enzymatic hydrolysis was carried out to confirm the nature of the two glycoside derivatives. Molecular modeling was incorporated to substantiate their relative configuration.

Vertebrate genomes code excess proteins with charge periodicity of 28 residues.

All amino acid sequences derived from 248 prokaryotic genomes, 10 invertebrate genomes (plants and fungi) and 10 vertebrate genomes were analysed by the autocorrelation function of charge sequences. The analysis of the total amino acid sequences derived from the 268 biological genomes showed that a significant periodicity of 28 residues is observable for the vertebrate genomes, but not for the other genomes. When proteins with a charge periodicity of 28 residues (PCP28) were selected from the total proteomes, we found that PCP28 in fact exists in all proteomes, but the number of PCP28 is much larger for the vertebrate proteomes than for the other proteomes.

Ratio of membrane proteins in total proteomes of prokaryota.

The numbers of membrane proteins in the current genomes of various organisms provide an important clue about how the protein world has evolved from the aspect of membrane proteins. Numbers of membrane proteins were estimated by analyzing the total proteomes of 248 prokaryota, using the SOSUI system for membrane proteins (Hirokawa , , 1998) and SOSUI-signal for signal peptides (Gomi , , 2004). The results showed that the ratio of membrane proteins to total proteins in these proteomes was almost constant: 0.

Structural change of bacteriorhodopsin in the purple membrane above pH 10 decreases heterogeneity of the irreversible photobleaching components.

Kinetic investigations of irreversible photobleaching of bacteriorhodopsin (bR) in purple membrane (PM) at high temperature have previously shown two kinds of bR species upon light illumination. The bR species consist of kinetically fast- and slow-denatured components, whose proportions were dependent upon structural changes in dark, as shown by CD. In order to elucidate electrostatic contribution on the heterogeneous stability and the bR structure in PM, photobleaching behaviour and structural changes over a wide pH range were investigated by kinetics as well as various spectroscopic techniques.

Alkaloids from Sarcomelicope megistophylla.

Two new alkaloids were isolated from the bark of Sarcomelicope megistophylla. Cyclomegistine B (1), a new quinolone alkaloid, that possesses a rare cyclobuta[b]quinoline ring system and sarcomejine B (2) which is a quinolone alkaloid with an unusual side chain. The structure of both compounds was elucidated on the basis of MS data and extensive NMR studies.

seco-Cycloartane triterpenes from Gardenia aubryi.

Three new 3,4-seco-cycloartanes, secaubryenol (1), secaubrytriol (2), and secaubryolide (3), were isolated from an exudate collected on the aerial parts of Gardenia aubryi, in addition to the known (24S)-cycloartane-24,25-diol-3-one, coccinetane A, herbacetin 3,8-dimethyl ether, hibiscetin 3,8,3',4'-tetramethyl ether, and conyzatin. The structures of 1 and 2 were established by mass spectrometry and NMR experiments, while the relative configuration of 2 was defined unequivocally using X-ray crystallography. The in vitro cytotoxic activity of compounds 1-3 was evaluated against four human solid tumor cell lines.

New lignans from the perisperm of Sesamum indicum.

A procedure, based on XAD-4 adsorption resin, which permits the obtainment of enriched polyphenolic extracts from Sesamum indicum perisperm (coat) has been developed. Chemical analysis of the obtained extracts led to the identification of 16 lignans. Among them, two new lignans, (+)-saminol and (+)-episesaminone-9-O-beta-D-sophoroside, have been isolated.

Activity of grape extracts from Greek varieties of Vitis vinifera against mutagenicity induced by bleomycin and hydrogen peroxide in Salmonella typhimurium strain TA102.

Several in vivo and in vitro studies have shown that grape extracts could prevent certain steps in carcinogenesis and a few mechanisms have been proposed for this activity. In this study, the potential antimutagenic activity of methanolic and aqueous extracts from two Greek grape varieties of Vitis vinifera against DNA damage induced by reactive oxygen species (ROS) was assessed as a potential novel chemopreventive mechanism, using Salmonella typhimurium strain TA102. The two grape varieties were Assyrtiko (white grapes) and Mandilaria (red grapes), while the oxidant mutagens used were bleomycin (BLM) and hydrogen peroxide (H(2)O(2)).

Heterogeneity in regeneration of bacteriorhodopsin from bacterio-opsin and all-trans retinal at high temperatures: implications for dynamic structural fluctuations.

Measurements of regeneration kinetics were performed in order to investigate the regeneration mechanisms of bacteriorhodopsin (bR) from thermally unfolded bacterio-opsin (bO) and all-trans retinal. Regeneration kinetics data were successfully fitted to a single exponential function when regeneration was performed at 25 degrees C after incubation at high temperatures. Conversely, the process of regeneration after the addition of retinal to bO at high temperatures occurred at two different rate constants.

Genome sequence of the cat pathogen, Chlamydophila felis.

Chlamydophila felis (Chlamydia psittaci feline pneumonitis agent) is a worldwide spread pathogen for pneumonia and conjunctivitis in cats. Herein, we determined the entire genomic DNA sequence of the Japanese C. felis strain Fe/C-56 to understand the mechanism of diseases caused by this pathogen.

Acretoside, a new sucrose ester from Aristolochia cretica.

A new sucrose ester, acretoside, has been isolated from the roots of the Greek endemic species Aristolochia cretica and identified as 6-O-p-coumaroyl-beta-D-fructofuranosyl-(2 --> 1)-alpha-D-glucopyranoside (1). In addition, a known sucrose ester, identified as arillatose B, two phenylpropanoid glucose esters, and five derivatives of aristolochic acids have been isolated. Their structures have been elucidated on the basis of MS and NMR data.

Mechanisms of secondary structure breakers in soluble proteins.

Breaking signals of secondary structure put strong limitations on the tertiary structures of proteins. In addition to proline and glycine clusters, which are well-known secondary structure breakers, clusters of amphiphilic residues were found to be a novel type of secondary structure breaker. These secondary structure breakers were found to depend on specific environmental factors.

Acretoside, a new sucrose ester from Aristolochia cretica.

A new sucrose ester, acretoside, was isolated from the roots of the Greek endemic species Aristolochia cretica and identified as 6-O-p-coumaroyl-beta-D-fructofuranosyl-(2 --> 1)-alpha-D-glucopyranoside (1). In addition, a known sucrose ester, identified as arillatose B, two phenylpropanoid glucose esters, and five derivatives of aristolochic acid were isolated. Their structures were elucidated on the basis of MS and NMR data.