An anti-apoptotic viral protein that recruits Bax to mitochondria

The viral mitochondria-localized inhibitor of apoptosis (vMIA), encoded by the UL37 gene of human cytomegalovirus, inhibits apoptosis-associated mitochondrial membrane permeabilization by a mechanism different from that of Bcl-2. Here we show that vMIA induces several changes in Bax that resemble those found in apoptotic cells yet take place in unstimulated, non-apoptotic vMIA-expressing cells. These changes include the constitutive localization of Bax at mitochondria, where it associates tightly with the mitochondrial membrane, forming high molecular weight aggregates that contain vMIA. vMIA recruits Bax to mitochondria but delays relocation of caspase-8-activated truncated Bid-green fluorescent protein (GFP) (t-Bid-GFP) to mitochondria. The ability of vMIA and its deletion mutants to associate with Bax and to induce relocation of Bax to mitochondria correlates with their anti-apoptotic activity and with their ability to suppress mitochondrial membrane permeabilization. Taken together, our data indicate that vMIA blocks apoptosis via its interaction with Bax. vMIA neutralizes Bax by recruiting it to mitochondria and "freezing" its pro-apoptotic activity. These data unravel a novel strategy of subverting an intrinsic pathway of apoptotic signaling.     

Pavement Ant Workers (<Emphasis Type="Italic">Tetramorium caespitum</Emphasis>) Assess Cues Coded in Cuticular Hydrocarbons to Recognize Conspecific and Heterospecific Non-Nestmate Ants

Most ants live in closed societies from which non-members are excluded through fighting or ritualized displays to protect colony resources. Nestmate recognition is the process by which ants discriminate nestmate from non-nestmate ants. Ants use cues coded in mixtures of long-chain hydrocarbon compounds on the cuticle as nestmate recognition cues. Pavement ants (Tetramorium caespitum) form conspicuous wars between neighboring colonies that are organized after workers meet and make the decision to fight after assessing nestmate recognition cues. These wars involve thousands of individuals. Fighting is ritualized and few ants die in the process. We identified 24 cuticular hydrocarbon compounds, above 1% in relative abundance, in the profile of pavement ants with chain lengths ranging from 15 to 31 carbon atoms. Cuticular lipids contained, in order of abundance: mono-methyl alkanes (45–56%), n-alkanes (range: 16–40% relative abundance), and alkenes (10–20%), with small or trace amounts of di-methyl, tri-methyl alkanes and fatty acids. Results from behavioral tests show that pavement ants assess information in cuticular hydrocarbon profiles to recognize both conspecific and heterospecfic (Pogonomyrmex occidentalis and Camponotus modoc) non-nestmate ants and that the relative abundance of methyl-branched alkanes and alkenes codes for nestmate status, at least for conspecific interactions. Our data add to a growing body of knowledge about how ants use cuticular hydrocarbon based nestmate recognition cues to prevent the intrusion of non-nestmates in to colony space.     

Residence Times of Receptors in Dendritic Spines Analyzed by Stochastic Simulations in Empirical Domains

Analysis of high-density superresolution imaging of receptors reveals the organization of dendrites at nanoscale resolution. We present here an apparently novel method that uses local statistics extracted from short-range trajectories for the simulations of long-range trajectories in empirical live cell images. Based on these empirical simulations, we compute the residence time of a receptor in dendritic spines that accounts for receptors’ local interactions and geometrical membrane organization. We report here that depending on the type of the spine, the residence time varies from 1 to 5 min. Moreover, we show that there exists transient organized structures, previously described as potential wells that can regulate the trafficking of receptors to dendritic spine: the simulation results suggest that receptor trafficking is regulated by transient structures.     

Structural Mechanisms Determining Inhibition of the Collagen Receptor DDR1 by Selective and Multi-Targeted Type II Kinase Inhibitors

The discoidin domain receptors (DDRs), DDR1 and DDR2, form a unique subfamily of receptor tyrosine kinases that are activated by the binding of triple-helical collagen. Excessive signaling by DDR1 and DDR2 has been linked to the progression of various human diseases, including fibrosis, atherosclerosis and cancer. We report the inhibition of these unusual receptor tyrosine kinases by the multi-targeted cancer drugs imatinib and ponatinib, as well as the selective type II inhibitor DDR1-IN-1. Ponatinib is identified as the more potent molecule, which inhibits DDR1 and DDR2 with an IC₅₀ of 9 nM. Co-crystal structures of human DDR1 reveal a DFG-out conformation (DFG, Asp-Phe-Gly) of the kinase domain that is stabilized by an unusual salt bridge between the activation loop and αD helix. Differences to Abelson kinase (ABL) are observed in the DDR1 P-loop, where a β-hairpin replaces the cage-like structure of ABL. P-loop residues in DDR1 that confer drug resistance in ABL are therefore accommodated outside the ATP pocket. Whereas imatinib and ponatinib bind potently to both the DDR and ABL kinases, the hydrophobic interactions of the ABL P-loop appear poorly satisfied by DDR1-IN-1 suggesting a structural basis for its DDR1 selectivity. Such inhibitors may have applications in clinical indications of DDR1 and DDR2 overexpression or mutation, including lung cancer.     

Seed fate and decision‐making processes in scatter‐hoarding rodents

A mechanistic understanding of seed movement and survival is important both for the development of theoretical models of plant population dynamics, spatial spread, and community assembly, and for the conservation and management of plant communities under global change. While models of wind‐borne seed dispersal have advanced rapidly over the past two decades, models for animal‐mediated dispersal have failed to make similar progress due to their dependence on interspecific interactions and complex, context‐dependent behaviours. In this review, we synthesize the literature on seed dispersal and consumption by scatter‐hoarding, granivorous rodents and outline a strategy for development of a general mechanistic seed‐fate model in these systems. Our review decomposes seed dispersal and survival into six distinct sub‐processes (exposure, harvest, allocation, preparation, placement, and recovery), and identifies nine intermediate (latent) variables that link physical state variables (e.g. seed and animal traits, habitat structure) to decisions regarding seed allocation to hoarding or consumption, cache placement and management, and deployment of radicle‐pruning or embryo excision behaviours. We also highlight specific areas where research on these intermediate relationships is needed to improve our mechanistic understanding of scatter‐hoarder behaviour. Finally, we outline a strategy to combine detailed studies on individual functional relationships with seed‐tracking experiments in an iterative, hierarchical Bayesian framework to construct, refine, and test mechanistic models for context‐dependent, scatter‐hoarder‐mediated seed fate.     

Bacterial adaptation to cold: Conservation of a short J-domain co-chaperone and its protein partners in environmental proteobacteria

Bacterial genomes are a huge reservoir of genes encoding J-domain protein co-chaperones that recruit the molecular chaperone DnaK to assist protein substrates involved in survival, adaptation, or fitness. The atc operon of the aquatic mesophilic bacterium Shewanella oneidensis encodes the proteins AtcJ, AtcA, AtcB, and AtcC, and all of them, except AtcA, are required for growth at low temperatures. AtcJ is a short J-domain protein that interacts with DnaK, but also with AtcC through its 21 amino acid C-terminal domain. This interaction network is critical for cold growth. Here, we show that AtcJ represents a subfamily of short J-domain proteins that (i) are found in several environmental, mostly aquatic, β- or ɣ-proteobacteria and (ii) contain a conserved PX₇W motif in their C-terminal extension. Using a combination of NMR, biochemical and genetic approaches, we show that the hydrophobic nature of the tryptophan of the S. oneidensis AtcJ PX₇W motif determines the strong AtcJ–AtcC interaction essential for cold growth. The AtcJ homologues are encoded by operons containing at least the S. oneidensis atcA, atcB, and atcC homologues. These findings suggest a conserved network of DnaK and Atc proteins necessary for low-temperature growth and, given the variation in the atc operons, possibly for other biological functions.     

Molecular dynamics simulations of apo and holo forms of fatty acid binding protein 5 and cellular retinoic acid binding protein II reveal highly mobile protein,retinoic acid ligand,and water molecules

Structural and dynamic properties from a series of 300 ns molecular dynamics, MD, simulations of two intracellular lipid binding proteins, iLBPs, (Fatty Acid Binding Protein 5, FABP5, and Cellular Retinoic Acid Binding Protein II, CRABP-II) in both the apo form and when bound with retinoic acid reveal a high degree of protein and ligand flexibility. The ratio of FABP5 to CRABP-II in a cell may determine whether it undergoes natural apoptosis or unrestricted cell growth in the presence of retinoic acid. As a result, FABP5 is a promising target for cancer therapy. The MD simulations presented here reveal distinct differences in the two proteins and provide insight into the binding mechanism. CRABP-II is a much larger, more flexible protein that closes upon ligand binding, where FABP5 transitions to an open state in the holo form. The traditional understanding obtained from crystal structures of the gap between two β-sheets of the β-barrel common to iLBPs and the α-helix cap that forms the portal to the binding pocket is insufficient for describing protein conformation (open vs. closed) or ligand entry and exit. When the high degree of mobility between multiple conformations of both the ligand and protein are examined via MD simulation, a new mode of ligand motion that improves understanding of binding dynamics is revealed.