Structure of the protein kinase Cb phospholipid-binding C2 domain complexed with Ca 2+

Background: Conventional isoforms (α, β and γ) of protein kinase C (PKC) are synergistically activated by phosphatidylserine and Ca 2+ ; both bind to C2 domains located within the PKC amino-terminal regulatory regions. C2 domains contain a bipartite or tripartite Ca 2+ -binding site formed by opposing loops at one end of the protein. Neither the structural basis for cooperativity between phosphatidylserine and Ca 2+ , nor the binding site for phosphatidylserine are known. Results: The structure of the C2 domain from PKCβ complexed with Ca 2+ and o-phospho-L-serine has been determined to 2.7 Å resolution using X-ray crystallography. The eight-stranded, Greek key β-sandwich fold of PKCβ-C2 is similar to that of the synaptotagmin I type I C2 domain. Three Ca 2+ ions, one at a novel site, were located, each sharing common aspartate ligands. One of these ligands is donated by a dyad-related C2 molecule. A phosphoserine molecule binds to a lysine-rich cluster in C2. Conclusions: Shared ligation among the three Ca 2+ ions suggests that they bind cooperatively to PKCβ-C2. Cooperativity may be compromised by the accumulation of positive charge in the binding site as successive ions are bound. Model building shows that the C1 domain could provide carboxylate and carbonyl ligands for two of the three Ca 2+ sites. Ca 2+ -mediated interactions between the two domains could contribute to enzyme activation as well as to the creation of a positively charged phosphatidylserine-binding site

Functional analysis of the interface between the tandem C2 domains of synaptotagmin-1.

C2 domains are widespread motifs that often serve as Ca(2+)-binding modules; some proteins have more than one copy. An open issue is whether these domains, when duplicated within the same parent protein, interact with one another to regulate function. In the present study, we address the functional significance of interfacial residues between the tandem C2 domains of synaptotagmin (syt)-1, a Ca(2+) sensor for neuronal exocytosis. Substitution of four residues, YHRD, at the domain interface, disrupted the interaction between the tandem C2 domains, altered the intrinsic affinity of syt-1 for Ca(2+), and shifted the Ca(2+) dependency for binding to membranes and driving membrane fusion in vitro. When expressed in syt-1 knockout neurons, the YHRD mutant yielded reductions in synaptic transmission, as compared with the wild-type protein. These results indicate that physical interactions between the tandem C2 domains of syt-1 contribute to excitation-secretion coupling.This study was supported by a grant from the NIH (MH061876). C.S.E. was supported by a PhRMA Foundation predoctoral fellowship and by a UW–Madison Molecular and Cellular Pharmacology Training Grant (5T32-GM008688). R.B.S. was supported by an NIH grant (AR063634). P.J. and J.M.E. were funded by Kidney Research UK, and J.M.E. was funded by the Biotechnology and Biological Sciences Research Council (Grant BB/J018236/1). E.R.C. is an investigator of the Howard Hughes Medical Institute.This is the final version of the article. It first appeared from the American Society for Cell Biology via http://dx.doi.org/10.1091/mbc.E15-07-050

New Tolerance Factor to Predict the Stability of Perovskite Oxides and Halides

Predicting the stability of the perovskite structure remains a longstanding challenge for the discovery of new functional materials for many applications including photovoltaics and electrocatalysts. We developed an accurate, physically interpretable, and one-dimensional tolerance factor, {\tau}, that correctly predicts 92% of compounds as perovskite or nonperovskite for an experimental dataset of 576 $ABX_3$ materials ($\textit{X} =$ $O^{2-}$, $F^-$, $Cl^-$, $Br^-$, $I^-$) using a novel data analytics approach based on SISSO (sure independence screening and sparsifying operator). {\tau} is shown to generalize outside the training set for 1,034 experimentally realized single and double perovskites (91% accuracy) and is applied to identify 23,314 new double perovskites ($A_2$$\textit{BB'}$$X_6$) ranked by their probability of being stable as perovskite. This work guides experimentalists and theorists towards which perovskites are most likely to be successfully synthesized and demonstrates an approach to descriptor identification that can be extended to arbitrary applications beyond perovskite stability predictions

Amplification of Black Vulture (\u3ci\u3eCoragyps atratus\u3c/i\u3e) DNA from regurgitated food pellets

Studies that rely on noninvasive collection of DNA for birds often use feces or feathers. Some birds, such as vultures, regurgitate undigested matter in the form of pellets that are commonly found under roost sites. Our research demonstrates that regurgitated pellets are a viable, noninvasive source of DNA for molecular ecology studies of vultures. Our objectives were to amplify 5 microsatellite loci designed for distinguishing Turkey Vultures (Cathartes aura) and Black Vultures (Coragyps atratus) in a single, multiplexed PCR, and to determine how long the target nuclear DNA persists after a vulture pellet is regurgitated and exposed to the environment. We collected pellets from captive Black Vultures and placed them in an outdoor aviary for a maximum estimated total of 12, 24, 36, or 48 h. We swabbed pellet surfaces for extraction and amplified vulture DNA using the panel of markers. All amplified alleles fell within predicted ranges of Black Vultures for all 5 loci, supporting the use of this microsatellite panel for vulture species identification. Overall amplification success for samples collected 0–12 h after regurgitation was 82.3%. Pellets collected 12–24 h, 24–36 h, and 36–48 h after regurgitation had only 18%, 10.2%, and 4.5% amplification success, respectively, which may have been due to a rain event. Our approach will be useful for noninvasive genetic sampling targeting nuclear DNA. These results should encourage noninvasive genetic sampling studies of other species that regurgitate pellets, such as raptors, water birds, or shorebirds

Optimal Image Reconstruction in Radio Interferometry

We introduce a method for analyzing radio interferometry data which produces maps which are optimal in the Bayesian sense of maximum posterior probability density, given certain prior assumptions. It is similar to maximum entropy techniques, but with an exact accounting of the multiplicity instead of the usual approximation involving Stirling's formula. It also incorporates an Occam factor, automatically limiting the effective amount of detail in the map to that justified by the data. We use Gibbs sampling to determine, to any desired degree of accuracy, the multi-dimensional posterior density distribution. From this we can construct a mean posterior map and other measures of the posterior density, including confidence limits on any well-defined function of the posterior map.Comment: 41 pages, 11 figures. High resolution figures 8 and 9 available at http://www.astro.uiuc.edu/~bwandelt/SuttonWandelt200

Drosophila studies support a role for a presynaptic synaptotagmin mutation in a human congenital myasthenic syndrome.

During chemical transmission, the function of synaptic proteins must be coordinated to efficiently release neurotransmitter. Synaptotagmin 2, the Ca2+ sensor for fast, synchronized neurotransmitter release at the human neuromuscular junction, has recently been implicated in a dominantly inherited congenital myasthenic syndrome associated with a non-progressive motor neuropathy. In one family, a proline residue within the C2B Ca2+-binding pocket of synaptotagmin is replaced by a leucine. The functional significance of this residue has not been investigated previously. Here we show that in silico modeling predicts disruption of the C2B Ca2+-binding pocket, and we examine the in vivo effects of the homologous mutation in Drosophila. When expressed in the absence of native synaptotagmin, this mutation is lethal, demonstrating for the first time that this residue plays a critical role in synaptotagmin function. To achieve expression similar to human patients, the mutation is expressed in flies carrying one copy of the wild type synaptotagmin gene. We now show that Drosophila carrying this mutation developed neurological and behavioral manifestations similar to those of human patients and provide insight into the mechanisms underlying these deficits. Our Drosophila studies support a role for this synaptotagmin point mutation in disease etiology

Decadal prediction of the North Atlantic subpolar gyre in the HiGEM high-resolution climate model

This paper presents an analysis of initialised decadal hindcasts of the North Atlantic subpolar gyre (SPG) using the HiGEM model, which has a nominal grid-spacing of 90 km in the atmosphere, and 1/3 ∘∘ in the ocean. HiGEM decadal predictions (HiGEM-DP) exhibit significant skill at capturing 0–500 m ocean heat content in the SPG, and outperform historically forced transient integrations and persistence for up to a decade ahead. An analysis of case-studies of North Atlantic decadal change, including the 1960s cooling, the mid-1990s warming, and the post-2005 cooling, show that changes in ocean circulation and heat transport dominate the predictions of the SPG. However, different processes are found to dominate heat content changes in different regions of the SPG. Specifically, ocean advection dominates in the east, but surface fluxes dominate in the west. Furthermore, compared to previous studies, we find a smaller role for ocean heat transport changes due to ocean circulation anomalies at the latitudes of the SPG, and, for the 1960s cooling, a greater role for surface fluxes. Finally, HiGEM-DP predicts the observed positive state of the North Atlantic Oscillation in the early 1990s. These results support an important role for the ocean in driving past changes in the North Atlantic region, and suggest that these changes were predictable