Motivated Proteins: A web application for studying small three-dimensional protein motifs

Background  

Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns.     

Changes in fluid secretion rate alter net transepithelial transport of MRP2 and P-glycoprotein substrates in Malpighian tubules of Drosophila melanogaster

The effects of stimulants of fluid secretion on net transepithelial transport of the MRP2 substrate Texas Red and the p-glycoprotein substrate daunorubicin were examined in Malpighian tubules of Drosophila melanogaster. Fluid secretion rates were determined using the Ramsay assay and secreted fluid concentrations of Texas Red and daunorubicin were determined using a microfluorometric technique. Nanoliter droplets of secreted fluid were collected in optically flat glass capillaries and dye concentration was determined from fluorescence intensity measured by confocal laser scanning microscopy. Net transepithelial flux of each compound was then calculated as the product of its concentration in the secreted fluid and the fluid secretion rate. Net transepithelial flux of Texas Red increased when fluid secretion was stimulated by tyramine, cyclic AMP or hypoosmotic saline. Net flux decreased when fluid secretion rate of cAMP-stimulated tubules was reduced by elevating saline osmolality with sucrose. Net transepithelial flux of daunorubicin increased when fluid secretion was stimulated by cAMP. Significant increases in dye flux were seen only when the dyes were present at concentrations close to or greater than the concentration required for half maximal transport. Regression analyses showed that 57- 88% of the change in dye flux was attributable to the change in fluid secretion rate when tubules were stimulated with cAMP, cGMP, or tyramine. The results do not suggest that the effects of tyramine and cAMP are mediated through changes in transepithelial potential, nor do they indicate the direct effects of the stimulants on MRP2-like or p-glycoprotein-like transporters (e.g., via protein kinases). Instead, the results suggest that increases in fluid secretion rate minimize diffusive backflux of these dyes and, thus, facilitate higher rates of net transepithelial transport indirectly.     

The Influence of Radiographic Phenotype and Smoking Status on Peripheral Blood Biomarker Patterns in Chronic Obstructive Pulmonary Disease

Background

Chronic obstructive pulmonary disease (COPD) is characterized by both airway remodeling and parenchymal destruction. The identification of unique biomarker patterns associated with airway dominant versus parenchymal dominant patterns would support the existence of unique phenotypes representing independent biologic processes. A cross-sectional study was performed to examine the association of serum biomarkers with radiographic airway and parenchymal phenotypes of COPD.

Methodology/Principal Findings

Serum from 234 subjects enrolled in a CT screening cohort was analyzed for 33 cytokines and growth factors using a multiplex protein array. The association of serum markers with forced expiratory volume in one second percent predicted (FEV1%) and quantitative CT measurements of airway thickening and emphysema was assessed with and without stratification for current smoking status. Significant associations were found with several serum inflammatory proteins and measurements of FEV1%, airway thickening, and parenchymal emphysema independent of smoking status. The association of select analytes with airway thickening and emphysema was independent of FEV1%. Furthermore, the relationship between other inflammatory markers and measurements of physiologic obstruction or airway thickening was dependent on current smoking status.

Conclusions/Significance

Airway and parenchymal phenotypes of COPD are associated with unique systemic serum biomarker profiles. Serum biomarker patterns may provide a more precise classification of the COPD syndrome, provide insights into disease pathogenesis and identify targets for novel patient-specific biological therapies.     

Harvesting the potential of induced biological diversity

For most of the past century, chemical and physical mutagens have been used in plant genetic research to introduce novel genetic variation. In crop improvement, more than 2000 plant varieties that contain induced mutations have been released for cultivation having faced none of the regulatory restrictions imposed on genetically modified material. In plant science, mutational approaches have found extensive use in forward genetics and for enhancer and suppressor screens - particularly in model organisms where positional cloning is easily achieved. However, new approaches that combine mutagenesis with novel and sensitive methods to detect induced DNA sequence variation are establishing a new niche for mutagenesis in the expanding area of (crop) plant functional genomics and providing a bridge that links discovery in models to application in crops.     

Multi-functional T-DNA/Ds tomato lines designed for gene cloning and molecular and physical dissection of the tomato genome

In order to make the tomato genome more accessible for molecular analysis and gene cloning, we have produced 405 individual tomato (Lycopersicon esculentum) lines containing a characterized copy of pJasm13, a multifunctional T-DNA/modifiedDs transposon element construct. Both the T-DNA and the Ds element in pJasm13 harbor a set of selectable marker genes to monitor excision and reintegration of Ds and additionally, target sequences for rare cutting restriction enzymes (I-PpoI, SfiI, NotI) and for site-specific recombinases (Cre, FLP, R). Blast analysis of flanking genomic sequences of 174 T-DNA inserts revealed homology to transcribed genes in 69 (40%), of which about half are known or putatively identified as genes and ESTs. The map position of 140 individual inserts was determined on the molecular genetic map of tomato. These inserts are distributed over the 12 chromosomes of tomato, allowing targeted and non-targeted transposon tagging, marking of closely linked genes of interest and induction of chromosomal rearrangements including translocations or creation of saturation-deletions or inversions within defined regions linked to the T-DNA insertion site. The different features of pJasm13 were successfully tested in tomato and Arabidopsis thaliana, thus providing a new tool for molecular/genetic dissection studies, including molecular and physical mapping, mutation analysis and cloning strategies in tomato and potentially, in other plants as well.Equal contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this work     

Mandibular kinematics represented by a non-orthogonal floating axis joint coordinate system

There are many methods used to represent joint kinematics (e.g., roll, pitch, and yaw angles; instantaneous center of rotation; kinematic center; helical axis). Often in biomechanics internal landmarks are inferred from external landmarks. This study represents mandibular kinematics using a non-orthogonal floating axis joint coordinate system based on 3-D geometric models with parameters that are "clinician friendly" and mathematically rigorous. Kinematics data for two controls were acquired from passive fiducial markers attached to a custom dental clutch. The geometric models were constructed from MRI data. The superior point along the arc of the long axis of the condyle was used to define the coordinate axes. The kinematic data and geometric models were registered through fiducial markers visible during both protocols. The mean absolute maxima across the subjects for sagittal rotation, coronal rotation, axial rotation, medial-lateral translation, anterior-posterior translation, and inferior-superior translation were 34.10 degrees, 1.82 degrees, 1.14 degrees, 2.31, 21.07, and 6.95 mm, respectively. All the parameters, except for one subject's axial rotation, were reproducible across two motion recording sessions. There was a linear correlation between sagittal rotation and translation, the dominant motion plane, with approximately 1.5 degrees of rotation per millimeter of translation. The novel approach of combining the floating axis system with geometric models succinctly described mandibular kinematics with reproducible and clinician friendly parameters.     

The activity of protein kinases from hamster fibroblasts towards a synthetic peptide based on a carboxy-terminal portion of ribosomal protein S6

A synthetic decapeptide, S6(231-240), based on a region near the C-terminus of eukaryotic ribosomal protein S6, was used as a substrate for protein kinases (EC 2.7.1.37) from hamster fibroblasts stimulated with fresh medium. Consistent with the results of others using shorter peptides from this region, it was found that the cyclic AMP-dependent protein kinase preferentially phosphorylated the residue corresponding to Ser-235, whereas protein kinase C preferentially phosphorylated the residue corresponding to Ser-236 in this peptide. The peptide did not serve as a substrate for the growth-associated protein kinase from hamster fibroblasts that phosphorylated ribosomal protein S6 in 40S ribosomal subunits, but did serve as a substrate for a previously undetected protein kinase activity that was resolved from the latter by DEAE-cellulose chromatography. This S6(231-240) protein kinase activity did not phosphorylate ribosomal protein S6 in 40S ribosomal subunits, but is possibly a proteolytic fragment of the 40S ribosomal subunit S6 kinase as the latter activity acquired the ability to phosphorylate the decapeptide after partial tryptic proteolysis. The S6(231-240) protein kinase activity preferentially phosphorylated the residue corresponding to Ser-236 with an apparent Km of 15 microM. These results suggest that specific interactions with the ribosome may be required to activate the growth-associated ribosomal protein S6 kinase.     

31P and 1H NMR studies of the effect of the counteracting osmolyte trimethylamine-N-oxide on interactions of urea with ribonuclease A

31P NMR spectroscopy has been used to show that the activity of RNase A, which is lowered in the presence of urea, can be recovered with trimethylamine-N-oxide (TMAO). A 1:1 ratio of TMAO:urea was sufficient to recover the enzyme activity. (1)H nuclear Overhauser effect spectroscopy NMR studies with RNase A have shown that even at relatively low effective concentrations of TMAO, some modification of the three-dimensional structure of the biomolecule is apparent.     

Formin-2, a novel formin homology protein of the cappuccino subfamily, is highly expressed in the developing and adult central nervous system

Formin-1 is the founding member of a family of genes of emerging biological and medical importance that share specific domains of homology, allowing them to be classified together as the formin homology proteins. Although deficiency mutations in formin-1 lead to profound developmental defects in limb and kidney formation, similar deficiency mutations in more distantly related members of this family (diaphanous and cappuccino in Drosophila and BNI1 in yeast) have ostensibly unrelated phenotypes. Here we describe murine and human formin-2 (Fmn2), a gene which bears a high degree of similarity to formin-1 and cappuccino. The mouse gene, which encodes a putative 1567-amino-acid open reading frame and maps to mouse Chromosome 1, is expressed almost exclusively in the developing and mature central nervous system. Expression begins at embryonic day 9. 5 in the developing spinal cord and brain structures and continues in neonatal and adult brain structures including the olfactory bulb, cortex, thalamus, hypothalamus, hippocampus and cerebellum. Human formin-2 has a similar expression pattern.