Amino-terminal cysteine residues of RGS16 are required for palmitoylation and modulation of G(i)- and G(q)-mediated signaling

RGS proteins (Regulators of G protein Signaling) are a recently discovered family of proteins that accelerate the GTPase activity of heterotrimeric G protein α subunits of the i, q, and 12 classes. The proteins share a homologous core domain but have divergent amino-terminal sequences that are the site of palmitoylation for RGS-GAIP and RGS4. We investigated the function of palmitoylation for RGS16, which shares conserved amino-terminal cysteines with RGS4 and RGS5. Mutation of cysteine residues at residues 2 and 12 blocked the incorporation of [3H]palmitate into RGS16 in metabolic labeling studies of transfected cells or into purified RGS proteins in a cell-free palmitoylation assay. The purified RGS16 proteins with the cysteine mutations were still able to act as GTPase-activating protein for Giα. Inhibition or a decrease in palmitoylation did not significantly change the amount of protein that was membrane-associated. However, palmitoylation-defective RGS16 mutants demonstrated impaired ability to inhibit both Gi- and Gq-linked signaling pathways when expressed in HEK293T cells. These findings suggest that the amino-terminal region of RGS16 may affect the affinity of these proteins for Gα subunits in vivo or that palmitoylation localizes the RGS protein in close proximity to Gα subunits on cellular membranes

Subtle pH differences trigger single residue motions for moderating conformations of calmodulin

This study reveals the essence of ligand recognition mechanisms by which calmodulin (CaM) controls a variety of Ca2+ signaling processes. We study eight forms of calcium-loaded CaM each with distinct conformational states. Reducing the structure to two degrees of freedom conveniently describes main features of the conformational changes of CaM via simultaneous twist-bend motions of the two lobes. We utilize perturbation-response scanning (PRS) technique, coupled with molecular dynamics simulations. PRS is based on linear response theory, comprising sequential application of directed forces on selected residues followed by recording the resulting protein coordinates. We analyze directional preferences of the perturbations and resulting conformational changes. Manipulation of a single residue reproduces the structural change more effectively than that of single/pairs/triplets of collective modes of motion. Our findings also give information on how the flexible linker acts as a transducer of binding information to distant parts of the protein. Furthermore, by perturbing residue E31 located in one of the EF hand motifs in a specific direction, it is possible to induce conformational change relevant to five target structures. Independently, using four different pKa calculation strategies, we find this particular residue to be the charged residue (out of a total of 52), whose ionization state is most sensitive to subtle pH variations in the physiological range. It is plausible that at relatively low pH, CaM structure is less flexible. By gaining charged states at specific sites at a pH value around 7, such as E31 found in the present study, local conformational changes in the protein will lead to shifts in the energy landscape, paving the way to other conformational states. These findings are in accordance with Fluorescence Resonance Energy Transfer (FRET) measured shifts in conformational distributions towards more compact forms with decreased pH. They also corroborate mutational studies and proteolysis results which point to the significant role of E31 in CaM dynamics

Interaction between Group Work, Motivation and Instructional Feedback in Project-Based Courses

This study aimed to define the relationships between the factors affecting the learning processes of participants in project-based courses. The study sample consisted of 132 participants who had taken in the instructional design course offered at the undergraduate level. The MSLQ, SAGE, and SPIF were used as data collection tools. The findings showed that the conflicts caused by the individuals with negative affect about instructional feedback diminished the quality of product and process during group work. Positive affect was found to be directly affected by ‘extrinsic goal orientation’, which is one of the motivation variables

A Bifunctional B,N-Based Asymmetric Catalytic Nitrostyrene-Michael Addition Acting through a 10-Membered Ring Cyclic Transition State

The B,N-bifunctional catalyst homoboroproline has been applied to a catalytic asymmetric nitroalkene-Michael addition to β-nitrostyrene analogues, showing broad substrate tolerance, high conversions and moderate to good asymmetric induction. The ability of homoboroproline to act as an efficient catalyst based on enamine-formation of the secondary amine, coupled with intramolecular Lewis-acid chelation of the nitro function, in a non-FLP manner, to effect efficient and enantioselective catalysis via a proposed large 10-membered ring transition state is remarkable and reinforced by theoretical calculations

The Expected Perimeter in Eden and Related Growth Processes

Following Richardson and using results of Kesten on First-passage percolation, we obtain an upper bound on the expected perimeter in an Eden Growth Process. Using results of the author from a problem in Statistical Mechanics, we show that the average perimeter of the lattice animals resulting from a very natural family of "growth histories" does not obey a similar bound.Comment: 11 page

Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies

Thinking outside the silicon box: Molecular and logic as an additional layer of selectivity in singlet oxygen generation for photodynamic therapy

A simple derivative of a well-known dye bodipy appears to be a satisfactory sensitizer for singlet oxygen. Moreover, the rate of singlet oxygen generation can be modulated by two cancer-related cellular parameters, sodium ion concentration and acidity. Singlet oxygen generation rate is maximal when sodium ions and an organic acid were added. The operation of this molecular automaton follows AND logic, which introduces an additional layer of selectivity in the photodynamic action of the reagent. It should also be noted that in this system sensing, computing and actuating functions are realized within a single molecule. Copyright © 2008 American Chemical Society

Bilateral symmetrical cortical osteolytic lesions in two patients with Gaucher disease

Gaucher disease (GD) is an autosomal recessive lysosomal storage disorder characterized by the reduced or absent activity of glucocerebrosidase. The disease is split into three types. Type 3, or chronic neuronopathic GD, manifests with heterogeneous clinical presentations. Skeletal manifestations of GD can include abnormal bone remodeling resulting in the characteristic Erlenmeyer flask deformities, painful bone crises, osteopenia, and an increased frequency of fractures. Osteolytic lesions can also occur but are rare and tend to be large, expanding intramedullary lesions with cortical thinning. We present two adolescent patients with type 3 GD who developed bilateral symmetrical cortical osteolytic lesions. The lesions in both cases demonstrate predominant cortical scalloping with fairly indolent growth. Neither patient manifests some of the more common bony manifestations of GD—bone crises or osteonecrosis. These atypical and unique skeletal findings in two unrelated probands with type 3 GD further expand the extent of phenotypic variation encountered in this single gene disorder

Subtle pH differences trigger single residue motions for moderating conformations of calmodulin

This study reveals the essence of ligand recognition mechanisms by which calmodulin (CaM) controls a variety of Ca2+ signaling processes. We study eight forms of calcium-loaded CaM each with distinct conformational states. Reducing the structure to two degrees of freedom conveniently describes main features of conformational changes of CaM via simultaneous twist-bend motions of the two lobes. We utilize perturbation-response scanning (PRS) technique, coupled with molecular dynamics simulations to analyze conformational preferences of calcium-loaded CaM, initially in extended form. PRS is comprised of sequential application of directed forces on residues followed by recording the resulting coordinates. We show that manipulation of a single residue, E31 located in one of the EF hand motifs, reproduces structural changes to compact forms, and the flexible linker acts as a transducer of binding information to distant parts of the protein. Independently, using four different pKa calculation strategies, we find E31 to be the charged residue (out of 52), whose ionization state is most sensitive to subtle pH variations in the physiological range. It is proposed that at relatively low pH, CaM structure is less flexible. By gaining charged states at specific sites at a pH value around 7, local conformational changes in the protein will lead to shifts in the energy landscape, paving the way to other conformational states. These findings are in accordance with FRET measured shifts in conformational distributions towards more compact forms with decreased pH. They also corroborate mutational studies and proteolysis results which point to the significant role of E31 in CaM dynamics.Comment: 47 pages, 4 figure