Molecular dynamics simulations of Piezo1 channel opening by increases in membrane tension

Piezo1 is a mechanosensitive channel involved in many cellular functions and responsible for sensing shear stress and pressure forces in cells. Piezo1 has a unique trilobed topology with a curved membrane region in the closed state. It has been suggested that upon activation Piezo1 adopts a flattened conformation, but the molecular and structural changes underpinning the Piezo1 gating and opening mechanisms and how the channel senses forces in the membrane remain elusive. Here, we used molecular dynamics simulations to reveal the structural rearrangements that occur when Piezo1 moves from a closed to an open state in response to increased mechanical tension applied to a model membrane. We find that membrane stretching causes Piezo1 to flatten and expand its blade region, resulting in tilting and lateral movement of the pore-lining transmembrane helices 37 and 38. This is associated with the opening of the channel and movement of lipids out of the pore region. Our results reveal that because of the rather loose packing of Piezo1 pore region, movement of the lipids outside the pore region is critical for the opening of the pore. Our simulations also suggest synchronous flattening of the Piezo1 blades during Piezo1 activation. The flattened structure lifts the C-terminal extracellular domain up, exposing it more to the extracellular space. Our studies support the idea that it is the blade region of Piezo1 that senses tension in the membrane because pore opening failed in the absence of the blades. Additionally, our simulations reveal that upon opening, water molecules occupy lateral fenestrations in the cytosolic region of Piezo1, which might be likely paths for ion permeation. Our results provide a model for how mechanical force opens the Piezo1 channel and thus how it might couple mechanical force to biological response

Modelling of full-length Piezo1 suggests importance of the proximal N-terminus for dome structure

Piezo1 forms a mechanically activated calcium-permeable nonselective cation channel that is functionally important in many cell types. Structural data exist for C-terminal regions, but we lack information about N-terminal regions and how the entire channel interacts with the lipid bilayer. Here, we use computational approaches to predict the three-dimensional structure of the full-length Piezo1 and simulate it in an asymmetric membrane. A number of novel insights are suggested by the model: 1) Piezo1 creates a trilobed dome in the membrane that extends beyond the radius of the protein, 2) Piezo1 changes the lipid environment in its vicinity via preferential interactions with cholesterol and phosphatidylinositol 4,5-bisphosphate (PIP2) molecules, and 3) cholesterol changes the depth of the dome and PIP2 binding preference. In vitro alteration of cholesterol concentration inhibits Piezo1 activity in a manner complementing some of our computational findings. The data suggest the importance of N-terminal regions of Piezo1 for dome structure and membrane cholesterol and PIP2 interactions

Computer Simulations Provide Guidance for Molecular Medicine through Insights on Dynamics and Mechanisms at the Atomic Scale

International audienceComputer simulations provide crucial insights and rationales for the design of molecular approaches in medicine. Several case studies illustrate how molecular model building and molecular dynamics simulations of complex molecular assemblies such as membrane proteins help in that process. Important aspects relate to build relevant molecular models with and without a crystal structure, to model membrane aggregates, then to link (dynamic) models to function, and finally to understand key disease-triggering phenomena such as aggregation. Through selected examples-including key signaling pathways in neurotransmission-the links between a molecular-level understanding of biological mechanisms and original approaches to treat disease conditions will be illuminated. Such treatments may be symptomatic, e.g. by better understanding the function and pharmacology of macromolecular key players, or curative, e.g. through molecular inhibition of disease-inducing molecular processes

Molecular Simulations of Intact Anion Exchanger 1 Reveal Specific Domain and Lipid Interactions

Anion exchanger 1 (AE1) is responsible for the exchange of bicarbonate and chloride across the erythrocyte plasma membrane. Human AE1 consists of a cytoplasmic and a membrane domain joined by a 33-residue flexible linker. Crystal structures of the individual domains have been determined, but the intact AE1 structure remains elusive. In this study, we use molecular dynamics simulations and modeling to build intact AE1 structures in a complex lipid bilayer that resembles the native erythrocyte plasma membrane. AE1 models were evaluated using available experimental data to provide an atomistic view of the interaction and dynamics of the cytoplasmic domain, the membrane domain, and the connecting linker in a complete model of AE1 in a lipid bilayer. Anionic lipids were found to interact strongly with AE1 at specific amino acid residues that are linked to diseases and blood group antigens. Cholesterol was found in the dimeric interface of AE1, suggesting that it may regulate subunit interactions and anion transport

Geography in Italian schools (An example of a cross-curricular project using geospatial technologies for a practical contribution to educators)

During the last few years the Italian school system has seen significant changes but geography continues to be considered a boring and un-useful discipline by public institutions. The main problem is the widespread geographic illiteracy and the fact that very often people do not know the objectives, methodology and tools of geographical studies. In this paper, we provide a framework of the recent modifications concerning geography, recalling the appeal promoted some months ago by the Associazione Italiana Insegnanti di Geografia (AIIG) to avoid a further weakening of the role of geography in senior high schools. We then underline the importance of geography in cross-curricular projects and focus attention on the “Valorinvilla” project in order to make a concrete example of an approach which arouses enthusiasm in the students, fulfils interesting purposes and facilitates dialogue with other disciplines. Specifically, the “Valorinvilla” project has been created by AIIG for schools of every level and type present in Rome in order to safeguard and enhance the Villa Ada Park, important for its biodiversity and significant historical features. Finally, we show how geospatial technologies, above all virtual globes and world maps, can provide added value both during the preparation phase and during the planning and operational phase of educational projects, generally, and of “Valorinvilla” project, particularly. The main aim is to furnish guidelines and a practical contribution to educators and to make geographical research useful, dynamic and pleasant

A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin

Mitochondria are dynamic organelles characterized by an ultrastructural organization which is essential in maintaining their quality control and ensuring functional efficiency. The complex mitochondrial network is the result of the two ongoing forces of fusion and fission of inner and outer membranes. Understanding the functional details of mitochondrial dynamics is physiologically relevant as perturbations of this delicate equilibrium have critical consequences and involved in several neurological disorders. Molecular actors involved in this process are large GTPases from the dynamin-related protein family. They catalyze nucleotide-dependent membrane remodeling and are widely conserved from bacteria to higher eukaryotes. Although structural characterization of different family members has contributed in understanding molecular mechanisms of mitochondrial dynamics in more detail, the complete structure of some members as well as the precise assembly of functional oligomers remains largely unknown. As increasing structural data become available, the domain modularity across the dynamin superfamily emerged as a foundation for transfering the knowledge towards less characterized members. In this review, we will first provide an overview of the main actors involved in mitochondrial dynamics. We then discuss recent example of computational methodologies for the study of mitofusin oligomers, and present how the usage of integrative modeling in conjunction with biochemical data can be an asset in progressing the still challenging field of membrane dynamics

Genetic variants of PIEZO1 associate with COVID-19 fatality

Fatality from coronavirus disease 19 (COVID-19) is a major problem globally and so identification of its underlying molecular mechanisms would be helpful. The combination of COVID-19 clinical data and genome sequence information is providing a potential route to such mechanisms. Here we took a candidate gene approach to UK Biobank data based on the suggested roles of endothelium and membrane proteins in COVID-19. We focussed on the PIEZO1 gene, which encodes a non-selective cation channel that mediates endothelial responses to blood flow. The analysis suggests 3 missense PIEZO1 single nucleotide polymorphisms (SNPs) associated with COVID-19 fatality independently of risk factors. All of them affect amino acids in the proximal N-terminus of PIEZO1, which is an unexplored region of the protein. By using molecular modelling we predict location of all 3 amino acids to a common outward-facing structure of unknown functional significance at the tips of the PIEZO1 propeller blades. Through genome sequence analysis we show that these SNPs vary in prevalence with ethnicity and that the most significant SNP (rs7184427) varies between 65 to 90% even though the reference amino acid is evolutionarily conserved. The data suggest PIEZO1 as a contributor to COVID-19 fatality and factor in ethnic susceptibility