Structural and Functional Studies of SLO K+ Channels: Mechanisms of Gating by Intracellular Signaling

Eukaryotic K+ channels from the SLO family (SLO1, SLO2 and SLO3) provide a link between intracellular signaling and the electrical activity of a cell. The opening and closing (gating) of the three different SLO homologs is controlled by the synergistic action of membrane voltage and specific intracellular cues: Ca2+ binding in SLO1, Na+ binding in SLO2 and pH increase in SLO3. It is known that intracellular signals activate SLO channels by acting on the large cytoplasmic domains (CTDs) of these proteins, which follows the transmembrane ionconduction pore. However, a molecular description of the mechanisms of intracellular gating in SLO channels is still lacking. In this thesis, I present biochemical, structural and functional studies aiming at understanding how the activity of SLO1 and SLO3 channels is controlled by intracellular Ca2+ binding and pH increase, respectively. First, I describe recombinant methods for the large-scale expression and purification of functional SLO channels, paving the way for a more complete biochemical and structural analysis of these proteins. Then, I report the crystal structures of the large cytoplasmic domains (CTDs) from two different SLO1 channels. Structures of the Ca2+-bound CTDs from human and zebrafish SLO1 channels define the precise molecular architecture of SLO1’s Ca2+-sensing module: CTDs from the four subunits of a tetrameric SLO1 channel assemble in a so-called gating ring structure at the intracellular face of the membrane. In conjunction with other studies, these results describe how Ca2+ binding affects the conformation of one layer of the SLO1 gating ring, which can explain the Ca2+-driven opening of SLO1’s ion conduction pore. Next, I present the crystal structure of the human SLO3 gating ring. A comparison with the SLO1 structures suggests that the hSLO3 structure represents the open conformation of the hSLO3 gating ring. Finally, I describe functional mutagenesis studies on the mouse SLO3 ortholog, which reveal a possible mechanism for pH sensing in the mouse SLO3 channel. Surprisingly, the mechanism I propose appears not to be conserved in SLO3 channels from other species. This could be a dramatic example of how new functional mechanisms can easily evolve within the very versatile scaffold of a gating ring structure. Altogether, the results presented in this thesis provide a molecular framework to understand the mechanisms of intracellular gating in SLO channels

An efficient mixed variational reduced order model formulation for non-linear analyses of elastic shells

The Koiter-Newton method had recently demonstrated a superior performance for non-linear analyses of structures, compared to traditional path-following strategies. The method follows a predictor-corrector scheme to trace the entire equilibrium path. During a predictor step a reduced order model is constructed based on Koiter's asymptotic post-buckling theory which is followed by a Newton iteration in the corrector phase to regain the equilibrium of forces. In this manuscript, we introduce a robust mixed solid-shell formulation to further enhance the efficiency of stability analyses in various aspects. We show that a Hellinger-Reissner variational formulation facilitates the reduced order model construction omitting an expensive evaluation of the inherent fourth order derivatives of the strain energy. We demonstrate that extremely large step sizes with a reasonable out-of-balance residual can be obtained with substantial impact on the total number of steps needed to trace the complete equilibrium path. More importantly, the numerical effort of the corrector phase involving a Newton iteration of the full order model is drastically reduced thus revealing the true strength of the proposed formulation. We study a number of problems from engineering and compare the results to the conventional approach in order to highlight the gain in numerical efficiency for stability problems

A quasi-static nonlinear analysis for assessing the fire resistance of 3d frames exploiting time-dependent yield surface

In this work an automatic procedure for evaluating the axial force-biaxial bending yield surface of reinforced concrete sections in fire is proposed. It provides an accurate time-dependent expression of the yield condition by a section analysis carried out once and for all, accounting for the strength reduction of the materials, which is a function of the fire duration. The equilibrium state of 3D frames with such yield conditions, once discretized using beam finite elements, is formulated as a nonlinear vectorial equation defining a curve in the hyperspace of the discrete variables and the fire duration. A generalized path-following strategy is proposed for tracing this curve and evaluating, if it exists, the limit fire duration, that is the time of exposure which leads to structural collapse. Compared to the previous proposals on the topic, which are limited to local sectional checks, this work is the first to present a global analysis for assessing the fire resistance of 3D frames, providing a time history of the fire event and taking account of the stress redistribution. Numerical examples are given to illustrate and validate the proposal

Improved split fluorescent proteins for endogenous protein labeling.

Self-complementing split fluorescent proteins (FPs) have been widely used for protein labeling, visualization of subcellular protein localization, and detection of cell-cell contact. To expand this toolset, we have developed a screening strategy for the direct engineering of self-complementing split FPs. Via this strategy, we have generated a yellow-green split-mNeonGreen21-10/11 that improves the ratio of complemented signal to the background of FP1-10-expressing cells compared to the commonly used split GFP1-10/11; as well as a 10-fold brighter red-colored split-sfCherry21-10/11. Based on split sfCherry2, we have engineered a photoactivatable variant that enables single-molecule localization-based super-resolution microscopy. We have demonstrated dual-color endogenous protein tagging with sfCherry211 and GFP11, revealing that endoplasmic reticulum translocon complex Sec61B has reduced abundance in certain peripheral tubules. These new split FPs not only offer multiple colors for imaging interaction networks of endogenous proteins, but also hold the potential to provide orthogonal handles for biochemical isolation of native protein complexes.Split fluorescent proteins (FPs) have been widely used to visualise proteins in cells. Here the authors develop a screen for engineering new split FPs, and report a yellow-green split-mNeonGreen2 with reduced background, a red split-sfCherry2 for multicolour labeling, and its photoactivatable variant for super-resolution use

Co-transport-induced instability of membrane voltage in tip-growing cells

A salient feature of stationary patterns in tip-growing cells is the key role played by the symports and antiports, membrane proteins that translocate two ionic species at the same time. It is shown that these co-transporters destabilize generically the membrane voltage if the two translocated ions diffuse differently and carry a charge of opposite (same) sign for symports (antiports). Orders of magnitude obtained for the time and lengthscale are in agreement with experiments. A weakly nonlinear analysis characterizes the bifurcation

Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to

The fusion oncoprotein Bcr-Abl is an aberrant tyrosine kinase responsible for chronic myeloid leukemia and acute lymphoblastic leukemia. The auto-inhibition regulatory module observed in the progenitor kinase c-Abl is lost in the aberrant Bcr-Abl, because of the lack of the N-myristoylated cap able to bind the myristoyl binding pocket also conserved in the Bcr-Abl kinase domain. A way to overcome the occurrence of resistance phenomena frequently observed for Bcr-Abl orthosteric drugs is the rational design of allosteric ligands approaching the so-called myristoyl binding pocket. The discovery of these allosteric inhibitors although very difficult and extremely challenging, represents a valuable option to minimize drug resistance, mostly due to the occurrence of mutations more frequently affecting orthosteric pockets, and to enhance target selectivity with lower off-target effects. In this perspective, we will elucidate at a molecular level the structural bases behind the Bcr-Abl allosteric control and will show how artificial intelligence can be effective to drive the automated de novo design towards off-patent regions of the chemical space

Optonongenetic enhancement of activity in primary cortical neurons

It has been recently demonstrated that the exposure of naive neuronal cells to light—at the basis of optogenetic techniques and calcium imaging measurements—may alter neuronal firing. Indeed, understanding the effect of light on nongenetically modified neurons is crucial for a correct interpretation of calcium imaging and optogenetic experiments. Here we investigated the effect of continuous visible LED light exposure (490 nm, 0.18−1.3 mW/mm2) on spontaneous activity of primary neuronal networks derived from the early postnatal mouse cortex. We demonstrated, by calcium imaging and patch clamp experiments, that illumination higher than 1.0 mW/mm2 causes an enhancement of network activity in cortical cultures. We investigated the possible origin of the phenomena by blocking the transient receptor potential vanilloid 4 (TRPV4) channel, demonstrating a complex connection between this temperature-dependent channel and the measured effect. The results presented here shed light on an exogenous artifact, potentially present in all calcium imaging experiments, that should be taken into account in the analysis of fluorescence data

Increase in circulating microparticles in inflammatory bowel disease patients induces vascular alterations

Alterations of vascular function participate to the development of the inflammatory bowel disease (IBD). We have previously reported the presence of inflammation-related vasoactive factors in small mesenteric arteries from Crohn’s disease patients (Tabernero et al., Circulation, 2003). Microparticles (MPs) are membrane vesicles released during cell activation and apoptosis whose circulating levels have been shown to be increased in patients with IBD, including MPs from platelets and activated platelets, endothelial, leukocyte and erythrocyte origins (Leonetti et al., Archives of Cardiovascular Diseases, Tome 102-Supplement 1-Mars 2009.).Here, we investigated whether MPs from IBD patients (IBD-MPs) play a role in the regulation of endothelial function and vascular reactivity in this disease. Male Swiss mice were injected intravenously with IBD-MPs or saline solution and sacrificed 24 h after. Endothelial function and vascular reactivity were studied on aortic rings by myography. The involvement of nitric oxide (NO), cyclooxygenase (COX) metabolites and superoxide anion (O2- ) was also assessed using the following inhibitors: NG-L-Nitro-arginine (NO synthase inhibitor, L-NA); indomethacin (non-selective COX inhibitor); SC-560 (selective COX-1 inhibitor), NS-398 (selective COX-2 inhibitor) and MnTMPyP (permeable superoxide dismutase mimetic). In aorta, IBD-MPs significantly reduced both endothelium-dependent induced by acetylcholine and the NO donor, sodium nitroprusside, respectively. IBD-MPs decreased the contraction to serotonin (5-HT) compared to saline that was completely prevented in the presence of L-NA. Moreover, aorta from mice treated with IBD-MPs displayed increase NO production. Interestingly, the ability of NS-398 to reduce 5-HT-induced contraction in control mice was abolished in vessels taken from mice treated with IBD-MPs. Although IBD-MPs decreased O2- production in the aorta, the O2- scavenger MnTMPyP reduced the contraction to 5-HT in an identical manner in aorta from both control and IBD-MPs treated mice. The present study provides evidence of the capacity of IBD-MPs to induce endothelial dysfunction and vascular hyporeactivity. These effects result from a subtle alteration of the balance between NO, reactive oxygen species and metabolites from COX-2. They underscore the participation of MPs in the course of vascular alterations in this disease. (Partially supported by Ferring France Laboratories)