Preferences of the side chains in proteins for helix, beta strand, turn, and other conformations. Secondary structures of copper proteins

Statistical preferences of the side chains in proteins for the helical conformation, the beta strand conformation, and the turn conformation were derived from the computer-assigned secondary structures of 55 protein chains reported by Levitt and Greer in 1977 after averaging redundant structures and weighting structures that showed greater than 25% homology by w = square root N/N. Separate preferences are reported for free cysteine side chains and for cystine. These preferences are used to predict the secondary structures of cucumber plastocyanin and cupredoxin, whose crystal structures will be reported soon. The loops in the C-terminal copper-binding regions are discussed.     

A copper-binding site in cytochrome oxidase. The secondary structure of subunit II

A secondary structure is assigned to subunit II of bovine mitochondrial cytochrome oxidase by the method of Chou-Fasman. On the basis of the structural assignments a copper-binding site close to the CO₂-terminal end of the polypeptide chain consisting ofcysteine-196, cysteine-200, histidine-204, and a fourth ligand that may be a histidine or methionnie-207 is proposed The structural assignments are supportive of homology between blue single-copper proteins such as azurin and plastocyanin and Cu_a ion site of cytochrome oxidase [G.J. Steffens and G. Buse, Hoppe-Seylers Z. Physiol.Chem.360,613(1979)]     

Validating functional data analysis measures from 24-h actigraphy data

The timing of sleep and wakefulness are under the influence of the circadian pacemaker in the suprachiasmatic nucleus, and the set-point for the circadian pacemaker is revealed by the time of onset of the secretion of melatonin under dim light conditions (DLMO). Measuring DLMO is time intensive and requires biochemical assays; hence it would be desirable to develop simpler alternatives to DLMO measurement that would otherwise provide similar information about health and illness. Continuous, multi-day measurement of actigraphy can be processed to reveal underlying features such as the time of greatest activity (acrophase), or the time of least activity (bathyphase). In this paper, we explore the calculation of the acrophase and bathyphase using a statistical approach called functional data analysis (FDA), and validated the FDA-calculated bathyphase by correlating it with morningness–eveningness self-reports from 47 depressed adults.     

Intracellular Levels of Cyclic Nucleotides during Cell Enlargement and Cell Division in Excised Tobacco Pith Tissues

Two lines of evidence, one of which is based on the radioimmunoassay and the other on adenosine 3', 5'-cyclic monophosphate (cyclic AMP)-dependent histone phosphorylation, are presented to demonstrate the presence of cyclic AMP in excised tissues of higher plant species. Intracellular levels of this cyclic nucleotide appear to be determined by auxin and a positive correlation has been found to exist between cell enlargement and chromosomal DNA replication, both auxin-dependent processes, and the level of cyclic AMP in tobacco pith cells. Intracellular guanosine 3', 5'-cyclic monophosphate (cyclic GMP) levels, while measurable, did not appear to be affected by either auxin or kinetin, or both, during the cell enlargement or cell division phases of the cell cycle in the tobacco pith system.     

Diversity of free-living ‘naked’ amoeboid organisms

Amoeboid organisms are phylogenetically diverse, some being more closely related to plants or metazoans than to each other. Amoeboid organisms are ecologically successful, having been isolated on all continents, including Antarctica, as well as being the main predators controlling bacterial populations in soil. The classification of these organisms has historically relied upon morphological characteristics. The application of electron microscopy, comparison of enzymic profiles after electrophoretic separation, and analysis of nucleic acid fractions have provided reliable bases for classifying amoeboid organisms. The extent of diversity of these organisms has been recognized, as methods to detect, culture, characterize and identify them has increased. It is reasonable to anticipate that the current 40 000 species of protists will increase substantially as amoeboid organisms are cultivated from poorly accessible niches and from extreme environs.     

Blue copper sites and analogous sites in copper-containing oxidases: a structural description

The secondary structure of the C-terminal region of all blue copper proteins can be assigned to two beta strands and a connecting segment that contains a potential histidine ligand. A similar assignment is made for the second probable blue (Type 1) site that is located in the middle fragment of ceruloplasmin also. The secondary structure regions for stellacyanin and subunit II of cytochrome oxidase predicted by the Chou-Fasman method are compared to those found in the crystal structures of plastocyanin and azurin.     

Characterization of an extracellular factor that stimulates bile salt hydrolase activity in Lactobacillus sp. strain 100–100

Bile salt hydrolase activity in Lactobacillus sp. strain 100-100 is strictly intracellular. The strain produces an extracellular factor that stimulates the intracellular hydrolase activity. The factor is inducible by conjugated bile salts, has an apparent molecular mass over 12 kDa but less than 25 kDa, is stable in air, and resistant to pronase and heat. It is partially extractable into organic solvents and inactivated by a sulphydryl group inhibitor. We postulate that the factor functions by a novel mechanism to facilitate entry of conjugated bile salts into the bacterial cells.