PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces

SUMMARY: PreDs is a WWW server that predicts the dsDNA-binding sites on protein molecular surfaces generated from the atomic coordinates in a PDB format. The prediction was done by evaluating the electrostatic potential, the local curvature and the global curvature on the surfaces. Results of the prediction can be interactively checked with our original surface viewer. AVAILABILITY: PreDs is available free of charge from http://pre-s.protein.osaka-u.ac.jp/~preds/ CONTACT: kino@ims.u-tokyo.ac.jp.     

Thioredoxin suppresses airway hyperresponsiveness and airway inflammation in asthma

Thioredoxin (TRX) is a 12-kDa redox (reduction/oxidation)-active protein that has a highly conserved site (-Cys-Gly-Pro-Cys-) and scavenges reactive oxygen species. Here we examined whether exogenously administered TRX modulated airway hyperresponsiveness (AHR) and airway inflammation in a mouse asthma model. Increased AHR to inhaled acetylcholine and airway inflammation accompanied by eosinophilia were observed in OVA-sensitized mice. Administration of wild-type but not 32S/35S mutant TRX strongly suppressed AHR and airway inflammation, and upregulated expression of mRNA of several cytokines (e.g., IL-1alpha, IL-1beta, IL-1 receptor antagonist, and IL-18) in the lungs of OVA-sensitized mice. In contrast, TRX treatment at the time of OVA sensitization did not improve AHR or airway inflammation in OVA-sensitized mice. Thus, TRX inhibited the asthmatic response after sensitization, but did not prevent sensitization itself. TRX and redox-active protein may have clinical benefits in patients with asthma.     

Isolation and characterization of psychotrophic bacteria from oil-reservoir water and oil sands

Four psychrotrophic strains, which grew at 4 degrees C but not at 37 degrees C, were isolated from Japanese oil-reservoir water (strains SIB1, SIC1, SIS1) and Canadian oil sands (strain CAB1). Strains SIB1, SIS1, and CAB1 had a maximum growth rate at 20 degrees C and grew to the highest cell densities at the cultivation temperature of 0-4 degrees C. Strain SIS1 was capable of growing even at -5 degrees C. The growth profile of strain SIC1 was rather similar to that of a mesophilic bacterium. Strains SIB1, SIC1, and SIS1 were identified as members of the genus Shewanella, and strain CAB1 was a member of the genus Arthrobacter. All these strains exhibited weak degradation ability against catechol, a hydroxylated aromatic hydrocarbon, and tributyrin. These strains are expected to be of potential use in the in situ bioremediation technology of hazardous hydrocarbons and esters under low-temperature conditions.     

Physicochemical evaluation of protein folds predicted by threading

Protein structure prediction remains an unsolved problem. Since prediction of the native structure seems very difficult, one usually tries to predict the correct fold of a protein. Here the "fold" is defined by the approximate backbone structure of the protein. However, physicochemical factors that determine the correct fold are not well understood. It has recently been reported that molecular mechanics energy functions combined with effective solvent terms can discriminate the native structures from misfolded ones. Using such a physicochemical energy function, we studied the factors necessary for discrimination of correct and incorrect folds. We first selected correct and incorrect folds by a conventional threading method. Then, all-atom models of those folds were constructed by simply minimizing the atomic overlaps. The constructed correct model representing the native fold has almost the same backbone structure as the native structure but differs in side-chain packing. Finally, the energy values of the constructed models were compared with that of the experimentally determined native structure. The correct model as well as the native structure showed lower energy than misfolded models. However, a large energy gap was found between the native structure and the correct model. By decomposing the energy values into their components, it was found that solvent effects such as the hydrophobic interaction or solvent shielding and the Born energy stabilized the correct model rather than the native structure. The large energetic stabilization of the native structure was attained by specific side-chain packing. The stabilization by solvent effects is small compared to that by side-chain packing. Therefore, it is suggested that in order to confidently predict the correct fold of a protein, it is also necessary to predict correct side-chain packing.     

Two new species ofMarasmiellus from eastern Honshu, Japan

Two new species ofMarasmiellus are described from eastern Honshu, Japan:Marasmiellus atrostipitatus sp. nov. (sectionRameales subsectionOpacini) is characterized by a white pileus and a blackish stipe covered with white pruinose to flocculos scales.Marasmiellus brunneocarpus sp. nov. (sectionTricolores) has small brownish basidiomata. Both species occur on dead leaves and twigs inQuercus-Eurya forests.