Data Article - Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface
Contributors: Patrik Schadzek, Barbara Schlingmann, Frank Schaarschmidt, Julia Lindner, Michael Koval, Alexander Heisterkamp, Anaclet Ngezahayo, Matthias Preller
... The structure of hCx26 derived from the X-ray analysis was used to generate a homology model for hCx46. Interacting connexin molecules were used as starting model for the molecular dynamics (MD) simulation using NAMD and allowed us to predict the dynamic behavior of hCx46wt and the cataract related mutant hCx46N188T as well as two artificial mutants hCx46N188Q and hCx46N188D. Within the 50ns simulation time the docked complex composed of the mutants dissociate while hCx46wt remains stable. The data indicates that one hCx46 molecule forms 5–7 hydrogen bonds (HBs) with the counterpart connexin of the opposing connexon. These HBs appear essential for a stable docking of the connexons as shown by the simulation of an entire gap junction channel and were lost for all the tested mutants.
Data Article - Mass spectrometry analysis of PPIP5K1 interactions and data on cell motility of PPIP5K1-deficient cells
Contributors: Gayane Machkalyan, Phan Trieu, Darlaine Pétrin, Terence E. Hébert, Gregory J. Miller
... Inositol pyrophosphates are cellular signals that are created by the actions of inositol kinases and are degraded by highly active inositol phosphatases. The potent actions of these phosphatases suggest these signals must be created near their sites of action. To identify sites where the inositol kinase, PPIP5K1 acts, we performed affinity purification of PPIP5K1 from HEK293 cells and analyzed these samples using mass spectrometry to identify the proteins pesent (10.1016/j.cellsig.2016.02.002) . We further decreased PPIP5K1 levels in HeLa cells and treated these with PPIP5K1 siRNA. We then monitored the motility of these cells in Scratch assays.
Original research article - Control of the collective migration of enteric neural crest cells by the Complement anaphylatoxin C3a and N-cadherin
Contributors: Florence Broders-Bondon, Perrine Paul-Gilloteaux, Elodie Gazquez, Julie Heysch, Matthieu Piel, Roberto Mayor, John D. Lambris, Sylvie Dufour
... We analyzed the cellular and molecular mechanisms governing the adhesive and migratory behavior of enteric neural crest cells (ENCCs) during their collective migration within the developing mouse gut. We aimed to decipher the role of the complement anaphylatoxin C3a during this process, because this well-known immune system attractant has been implicated in cephalic NCC co-attraction, a process controlling directional migration.
Contributors: Marc Krüger, Hubert Kalbacher, Panagiotis L. Kastritis, Joachim Bischof, Holger Barth, Doris Henne-Bruns, Constantinos Vorgias, Stefania Sarno, Lorenzo A. Pinna, Uwe Knippschild
... Members of the CK1 family are highly conserved serine/threonine specific kinases being expressed in all eukaryotes. They are involved in many cellular processes and therefore tightly regulated. A central mechanism to modulate CK1 activity is via interaction with cellular proteins. CK1δ interacts with α-/β-tubulin and is involved in the regulation of microtubule dynamics. Therefore, it is important to identify the structural elements responsible for the interaction between these proteins. Using a peptide library covering the human CK1δ amino acid sequence in SPR and ELISA analyses, we identified peptide 39 (P39), encompassing aa361–aa375 of CK1δ, as a prominent binding partner of α-tubulin. P39 decreases α-tubulin phosphorylation by CK1δ and reduces the thermodynamic stability of α-tubulin in fluorescence thermal shift assays. Furthermore, P39 induces an inhibition of mitotic progression and a disruption of cells entering mitosis in CV-1 cells. Taken together our data provide valuable information regarding the interaction of CK1δ and α-tubulin and a novel approach for the development of pharmacological tools to inhibit proliferation of cancer cells.
Membrane permeability during pressure ulcer formation: A computational model of dynamic competition between cytoskeletal damage and repair
Contributors: N. Suhas Jagannathan, Lisa Tucker-Kellogg
... Pressure ulcers are debilitating wounds that arise frequently in people who have lost mobility. Mechanical stress, oxidative stress and ischemia–reperfusion injury are potential sources of damage during pressure ulcer formation, but cross-talk between these sources has rarely been investigated. In vitro experiments with mechanically-induced cell damage previously demonstrated that non-lethal amounts of static cell deformation could induce myoblast membrane permeabilization. Permeabilization, in turn, has the potential to induce oxidative stress via leakage of calcium, myoglobin or alarmins. In this work, we constructed a hypothetical causal network of cellular-scale effects resulting from deformation and permeabilization, and we investigated the theoretical sensitivity of cell death toward various parameters and pathways of the model. Simulations showed that the survival/death outcome was particularly sensitive to the speed of membrane repair. The outcome was also sensitive to whether oxidative stress could decrease the speed of membrane repair. Finally, using the assumption that apoptosis and necrosis would have opposite effects on membrane leakage in dying cells, we showed that promoting apoptosis might under certain conditions have the paradoxical effect of decreasing, rather than increasing, total cell death. Our work illustrates that apoptosis may have hidden benefits at preventing spatial spread of death. More broadly, our work shows the importance of membrane repair dynamics and highlights the need for experiments to measure the effects of ischemia, apoptosis induction, and other co-occurring sources of cell stress toward the speed of membrane repair.
Contributors: Kai Gao, Yong Zhang, Jizhong Lou
... Enveloped virus, such as HIV-1, employs membrane fusion mechanism to invade into host cell. HIV-1 gp41 ectodomain uses six-helix bundle configuration to accomplish this process. Using molecular dynamic simulations, we confirmed the stability of this six-helix bundle by showing high occupancy of hydrogen bonds and hydrophobic interactions. Key residues and interactions important for the bundle integration were characterized by force-induced unfolding simulations of six-helix bundle, exhibiting the collapse order of these groups of interactions. Moreover, our results in some way concerted with a previous theory that the formation of coiled-coil choose a route which involved cooperative interactions between the N-terminal and C-terminal helix.
Contributors: Cécile Dau, Manfred Fliegauf, Heymut Omran, Martin Schlensog, Edgar Dahl, Claudia R. van Roeyen, Wilhelm Kriz, Marcus J. Moeller, Gerald S. Braun
... Mucociliary clearance requires the distinct orientation and coordinated movement of airway cilia, which is established through planar cell polarity signaling (PCP). The atypical cadherin Dachsous1 (Dchs1) is a transmembrane protein that regulates PCP in D. melanogaster. However, little is known about Dchs1 expression and its potential role in PCP in mammalian adult tissues. Here, we show that Dchs1 is ubiquitously expressed in mouse embryos, but exhibits a highly restricted expression to lung tissues in the adult stage. Strikingly, human Dchs1 localized exclusively to the base of the ciliary apparatus in cultured human respiratory epithelial cells with differentiated motile 9 + 2 cilia. This localization could be functionally important as we observed aberrant DCHS1 mRNA expression in human non-small cell lung cancer tissue. In sum, we establish Dchs1 as a component of the membrane domain surrounding the ciliary base. This suggests a specific role of Dchs1 in PCP-dependent organization of ciliary function and a possible role in lung disease.
Contributors: S.G. Roy, P.O. Koons, B. Osti, P. Upton, G.E. Tucker
... We present the every-direction variogram analysis (EVA) method for quantifying orientation and scale dependence of topographic anisotropy to aid in differentiation of the fluvial and tectonic contributions to surface evolution. Using multi-directional variogram statistics to track the spatial persistence of elevation values across a landscape, we calculate anisotropy as a multiscale, direction-sensitive variance in elevation between two points on a surface. Tectonically derived topographic anisotropy is associated with the three-dimensional kinematic field, which contributes (1) differential surface displacement and (2) crustal weakening along fault structures, both of which amplify processes of surface erosion. Based on our analysis, tectonic displacements dominate the topographic field at the orogenic scale, while a combination of the local displacement and strength fields are well represented at the ridge and valley scale. Drainage network patterns tend to reflect the geometry of underlying active or inactive tectonic structures due to the rapid erosion of faults and differential uplift associated with fault motion. Regions that have uniform environmental conditions and have been largely devoid of tectonic strain, such as passive coastal margins, have predominantly isotropic topography with typically dendritic drainage network patterns. Isolated features, such as stratovolcanoes, are nearly isotropic at their peaks but exhibit a concentric pattern of anisotropy along their flanks. The methods we provide can be used to successfully infer the settings of past or present tectonic regimes, and can be particularly useful in predicting the location and orientation of structural features that would otherwise be impossible to elude interpretation in the field. Though we limit the scope of this paper to elevation, EVA can be used to quantify the anisotropy of any spatially variable property.
Imaging analysis of nuclear antiviral factors through direct detection of incoming adenovirus genome complexes
Contributors: Tetsuro Komatsu, Hans Will, Kyosuke Nagata, Harald Wodrich
... Recent studies involving several viral systems have highlighted the importance of cellular intrinsic defense mechanisms through nuclear antiviral proteins that restrict viral propagation. These factors include among others components of PML nuclear bodies, the nuclear DNA sensor IFI16, and a potential restriction factor PHF13/SPOC1. For several nuclear replicating DNA viruses, it was shown that these factors sense and target viral genomes immediately upon nuclear import. In contrast to the anticipated view, we recently found that incoming adenoviral genomes are not targeted by PML nuclear bodies. Here we further explored cellular responses against adenoviral infection by focusing on specific conditions as well as additional nuclear antiviral factors. In line with our previous findings, we show that neither interferon treatment nor the use of specific isoforms of PML nuclear body components results in co-localization between incoming adenoviral genomes and the subnuclear domains. Furthermore, our imaging analyses indicated that neither IFI16 nor PHF13/SPOC1 are likely to target incoming adenoviral genomes. Thus our findings suggest that incoming adenoviral genomes may be able to escape from a large repertoire of nuclear antiviral mechanisms, providing a rationale for the efficient initiation of lytic replication cycle.
Contributors: Bingfang Xu, Angela M. Washington, Raquel Fantin Domeniconi, Ana Cláudia Ferreira Souza, Xiaowei Lu, Ann Sutherland, Barry T. Hinton
... The Wolffian duct, the proximal end of the mesonephric duct, undergoes non-branching morphogenesis to achieve an optimal length and size for sperm maturation. It is important to examine the mechanisms by which the developing mouse Wolffian duct elongates and coils for without proper morphogenesis, male infertility will result. Here we show that highly proliferative epithelial cells divide in a random orientation relative to the elongation axis in the developing Wolffian duct. Convergent extension (CE)-like of cell rearrangements is required for elongating the duct while maintaining a relatively unchanged duct diameter. The Wolffian duct epithelium is planar polarized, which is characterized by oriented cell elongation, oriented cell rearrangements, and polarized activity of regulatory light chain of myosin II. Conditional deletion of protein tyrosine kinase 7 (PTK7), a regulator of planar cell polarity (PCP), from mesoderm results in loss of the PCP characteristics in the Wolffian duct epithelium. Although loss of Ptk7 does not alter cell proliferation or division orientation, it affects CE and leads to the duct with significantly shortened length, increased diameter, and reduced coiling, which eventually results in loss of sperm motility, a key component of sperm maturation. In vitro experiments utilizing inhibitors of myosin II results in reduced elongation and coiling, similar to the phenotype of Ptk7 knockout. This data suggest that PTK7 signaling through myosin II regulates PCP, which in turn ensures CE-like of cell rearrangements to drive elongation and coiling of the Wolffian duct. Therefore, PTK7 is essential for Wolffian duct morphogenesis and male fertility.