Calcium regulates acid-sensing ion channel 3 activation by competing with protons in the channel pore and at an allosteric binding site.

The extracellular Ca concentration changes locally under certain physiological and pathological conditions. Such variations affect the function of ion channels of the nervous system and consequently also neuronal signalling. We investigated here the mechanisms by which Ca controls the activity of acid-sensing ion channel (ASIC) 3.

ProMod3-A versatile homology modelling toolbox.

Computational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad spectrum of scientific questions in biomedical research. The most accurate methods today are based on homology modelling, i.e.

An Amphipathic Helix Directs Cellular Membrane Curvature Sensing and Function of the BAR Domain Protein PICK1.

BAR domains are dimeric protein modules that sense, induce, and stabilize lipid membrane curvature. Here, we show that membrane curvature sensing (MCS) directs cellular localization and function of the BAR domain protein PICK1. In PICK1, and the homologous proteins ICA69 and arfaptin2, we identify an amphipathic helix N-terminal to the BAR domain that mediates MCS.

Conformational dynamics and role of the acidic pocket in ASIC pH-dependent gating.

Acid-sensing ion channels (ASICs) are proton-activated Na channels expressed in the nervous system, where they are involved in learning, fear behaviors, neurodegeneration, and pain sensation. In this work, we study the role in pH sensing of two regions of the ectodomain enriched in acidic residues: the acidic pocket, which faces the outside of the protein and is the binding site of several animal toxins, and the palm, a central channel domain. Using voltage clamp fluorometry, we find that the acidic pocket undergoes conformational changes during both activation and desensitization.

Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations.

Background: The importance of the material properties of membranes for diverse cellular processes is well established. Notably, the elastic properties of the membrane, which depend on its composition, can directly influence membrane reshaping and fusion processes as well as the organisation and function of membrane proteins. Determining these properties is therefore key for a mechanistic understanding of how the cell functions.

Curvature and Lipid Packing Modulate the Elastic Properties of Lipid Assemblies: Comparing HII and Lamellar Phases.

Accumulating evidence indicates that membrane reshaping and fusion processes, as well as regulation of membrane protein function, depend on lipid composition. Although it is widely accepted that cell membranes are under considerable stress and frustration and can be locally highly curved, experimental approaches to determine the material properties of lipids usually rely on their study in a relaxed environment or in flat bilayers. Here, we propose a computational method to determine the elastic properties of lipid assemblies of arbitrarily shaped interfaces and apply it to lipidic mixtures in the inverted hexagonal and lamellar phases.

Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering.

PICK1 is a neuronal scaffolding protein containing a PDZ domain and an auto-inhibited BAR domain. BAR domains are membrane-sculpting protein modules generating membrane curvature and promoting membrane fission. Previous data suggest that BAR domains are organized in lattice-like arrangements when stabilizing membranes but little is known about structural organization of BAR domains in solution.

Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes.

The dopamine transporter (DAT) is a transmembrane protein belonging to the family of neurotransmitter:sodium symporters (NSS). Members of the NSS are responsible for the clearance of neurotransmitters from the synaptic cleft, and for their translocation back into the presynaptic nerve terminal. The DAT contains long intracellular N- and C-terminal domains that are strongly implicated in the transporter function.

Protein and lipid interactions driving molecular mechanisms of in meso crystallization.

The recent advances in the in meso crystallization technique for the structural characterization of G-protein coupled receptor (GPCR) proteins have established the usefulness of the lipidic-cubic phases (LCPs) in the field of crystallography of membrane proteins. It is surprising that despite the success of the approach, the molecular mechanisms of the in meso method are still not well understood. Therefore, the approach must rely on extensive screening for a suitable protein construct, for host and additive lipids, and for the appropriate precipitants and temperature.

How the dynamic properties and functional mechanisms of GPCRs are modulated by their coupling to the membrane environment.

Experimental observations of the dependence of function and organization of G protein-coupled receptors (GPCRs) on their lipid environment have stimulated new quantitative studies of the coupling between the proteins and the membrane. It is important to develop such a quantitative understanding at the molecular level because the effects of the coupling are seen to be physiologically and clinically significant. Here we review findings that offer insight into how membrane-GPCR coupling is connected to the structural characteristics of the GPCR, from sequence to 3D structural detail, and how this coupling is involved in the actions of ligands on the receptor.

Why GPCRs behave differently in cubic and lamellar lipidic mesophases.

Recent successes in the crystallographic determination of structures of transmembrane proteins in the G protein-coupled receptor (GPCR) family have established the lipidic cubic phase (LCP) environment as the medium of choice for growing structure-grade crystals by the method termed "in meso". The understanding of in meso crystallogenesis is currently at a descriptive level. To enable an eventual quantitative, energy-based description of the nucleation and crystallization mechanism, we have examined the properties of the lipidic cubic phase system and the dynamics of the GPCR rhodopsin reconstituted into the LCP with coarse-grained molecular dynamics simulations with the Martini force-field.

Synergistic substrate binding determines the stoichiometry of transport of a prokaryotic H(+)/Cl(-) exchanger.

Active exchangers dissipate the gradient of one substrate to accumulate nutrients, export xenobiotics and maintain cellular homeostasis. Mechanistic studies have suggested that two fundamental properties are shared by all exchangers: substrate binding is antagonistic, and coupling is maintained by preventing shuttling of the empty transporter. The CLC H(+)/Cl(-) exchangers control the homeostasis of cellular compartments in most living organisms, but their transport mechanism remains unclear.

Optimal percolation of disordered segregated composites.

We evaluate the percolation threshold values for a realistic model of continuum segregated systems, where random spherical inclusions forbid the percolating objects, modeled by hardcore spherical particles surrounded by penetrable shells, to occupy large regions inside the composite. We find that the percolation threshold is generally a nonmonotonous function of segregation, and that an optimal (i.e.

Percolative properties of hard oblate ellipsoids of revolution with a soft shell.

We present an in-depth analysis of the geometrical percolation behavior in the continuum of random assemblies of hard oblate ellipsoids of revolution. Simulations were carried out by considering a broad range of aspect ratios, from spheres up to aspect-ratio-100 platelike objects, and with various limiting two-particle interaction distances, from 0.05 times the major axis up to 4.