Asymmetric opening of the homopentameric 5-HT3A serotonin receptor in lipid bilayers

AbstractPentameric ligand-gated ion channels (pLGICs) of the Cys-loop receptor family are key players in fast signal transduction throughout the nervous system. They have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. We report three structures of the Cys-loop 5-HT3A serotonin receptor (5HT3R) reconstituted into saposin-based lipid bilayer discs: a symmetric and an asymmetric apo state, and an asymmetric agonist-bound state. In comparison to previously published 5HT3R conformations in detergent, the lipid bilayer stabilises the receptor in a more tightly packed, ‘coupled’ state, involving a cluster of highly conserved residues. In consequence, the agonist-bound receptor conformation adopts a wide-open pore capable of conducting sodium ions in unbiased molecular dynamics (MD) simulations. Taken together, we provide a structural basis for the modulation of 5HT3R by the membrane environment, and a model for asymmetric activation of the receptor.

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In Silico Study of the Mechanism of Binding of the N-Terminal Region of α Synuclein to Synaptic-Like Membranes

Life ◽

10.3390/life10060098 ◽

2020 ◽

Vol 10 (6) ◽

pp. 98 ◽

Cited By ~ 2

Author(s):

Carlos Navarro-Paya ◽

Maximo Sanz-Hernandez ◽

Alfonso De Simone

Keyword(s):

Lipid Bilayers ◽

Conformational Transition ◽

Md Simulations ◽

Bound State ◽

Terminal Region ◽

Coarse Grained ◽

Biological Behavior ◽

In Silico Study ◽

Membrane Bound ◽

Presynaptic Protein

The membrane binding by α-synuclein (αS), a presynaptic protein whose aggregation is strongly linked with Parkinson’s disease, influences its biological behavior under functional and pathological conditions. This interaction requires a conformational transition from a disordered-unbound to a partially helical membrane-bound state of the protein. In the present study, we used enhanced coarse-grained MD simulations to characterize the sequence and conformational determinants of the binding to synaptic-like vesicles by the N-terminal region of αS. This region is the membrane anchor and is of crucial importance for the properties of the physiological monomeric state of αS as well as for its aberrant aggregates. These results identify the key factors that play a role in the binding of αS with synaptic lipid bilayers in both membrane-tethered and membrane-locked conformational states.

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Theoretical and computational modeling of peptide-lipid bilayer interaction studied by dynamic force spectroscopy

10.32469/10355/76254 ◽

2019 ◽

Author(s):

◽

Milica Utjesanovic

Keyword(s):

Computational Modeling ◽

Lipid Bilayer ◽

Lipid Bilayers ◽

Lipid Membranes ◽

Lipid Membrane ◽

Conformational Dynamics ◽

Quantitative Description ◽

Md Simulations ◽

Dynamic Force ◽

Detachment Rate

This thesis consists of three interrelated theoretical and computational modeling projects that investigate different aspects of peptide-lipid membrane interactions. (1) A general theoretical approach is formulated for the quantitative description of the detachment force distribution, P(F), and the corresponding force dependent detachment rate, k(F), of a peptide from a lipid bilayer, by assuming that peptide detachment from lipid membranes occurs stochastically along a few dominant diffusive pathways. Besides providing a consistent interpretation of the experimental data, the new method also predicts that k(F) exhibits catch-bond behavior (when, counter intuitively, the detachment rate decreases with increasing force). (2) The proposed multiple detachment pathways method is tested and validated for a particular peptide (SecA2-11) interacting with both zwitterionic POPC lipid and polar E. Coli membranes. Furthermore, molecular dynamics (MD) simulations are used to explored the conformational dynamics of SecA2-11 during its interaction with both POPC and anionic POPG lipid bilayers. (3) Finally, MD simulations are used to explore the conformational dynamics and energetics of the peptide melittin (MWT) and its diastereomer (MD4) interacting with POPC and POPG lipid bilayers. The obtained results provide further insight into the role of secondary structure in peptide-lipid bilayer interactions.

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Lipid flip-flop and desorption from supported lipid bilayers is independent of curvature

PLoS ONE ◽

10.1371/journal.pone.0244460 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0244460

Author(s):

Haoyuan Jing ◽

Yanbin Wang ◽

Parth Rakesh Desai ◽

Kumaran S. Ramamurthi ◽

Siddhartha Das

Keyword(s):

Lipid Bilayer ◽

Lipid Bilayers ◽

Md Simulations ◽

Packing Fraction ◽

Membrane Curvature ◽

Supported Lipid Bilayer ◽

Flip Flop ◽

Lipid Molecule ◽

Membrane Asymmetry ◽

Cell Shapes

Flip-flop of lipids of the lipid bilayer (LBL) constituting the plasma membrane (PM) plays a crucial role in a myriad of events ranging from cellular signaling and regulation of cell shapes to cell homeostasis, membrane asymmetry, phagocytosis, and cell apoptosis. While extensive research has been conducted to probe the lipid flip flop of planar lipid bilayers (LBLs), less is known regarding lipid flip-flop for highly curved, nanoscopic LBL systems despite the vast importance of membrane curvature in defining the morphology of cells and organelles and in maintaining a variety of cellular functions, enabling trafficking, and recruiting and localizing shape-responsive proteins. In this paper, we conduct molecular dynamics (MD) simulations to study the energetics, structure, and configuration of a lipid molecule undergoing flip-flop and desorption in a highly curved LBL, represented as a nanoparticle-supported lipid bilayer (NPSLBL) system. We compare our findings against those of a planar substrate supported lipid bilayer (PSSLBL). Our MD simulation results reveal that despite the vast differences in the curvature and other curvature-dictated properties (e.g., lipid packing fraction, difference in the number of lipids between inner and outer leaflets, etc.) between the NPSLBL and the PSSLBL, the energetics of lipid flip-flop and lipid desorption as well as the configuration of the lipid molecule undergoing lipid flip-flop are very similar for the NPSLBL and the PSSLBL. In other words, our results establish that the curvature of the LBL plays an insignificant role in lipid flip-flop and desorption.

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Non-vesicular transfer of membrane proteins from nanoparticles to lipid bilayers

The Journal of General Physiology ◽

10.1085/jgp.201010558 ◽

2011 ◽

Vol 137 (2) ◽

pp. 217-223 ◽

Cited By ~ 18

Author(s):

Sourabh Banerjee ◽

Crina M. Nimigean

Keyword(s):

Membrane Proteins ◽

Lipid Bilayer ◽

Lipid Bilayers ◽

Single Molecule ◽

Lipid Membranes ◽

Single Channel ◽

Black Lipid Membranes ◽

Potassium Channel Kcsa ◽

Lipid Environment ◽

Biochemical Preparation

Discoidal lipoproteins are a novel class of nanoparticles for studying membrane proteins (MPs) in a soluble, native lipid environment, using assays that have not been traditionally applied to transmembrane proteins. Here, we report the successful delivery of an ion channel from these particles, called nanoscale apolipoprotein-bound bilayers (NABBs), to a distinct, continuous lipid bilayer that will allow both ensemble assays, made possible by the soluble NABB platform, and single-molecule assays, to be performed from the same biochemical preparation. We optimized the incorporation and verified the homogeneity of NABBs containing a prototypical potassium channel, KcsA. We also evaluated the transfer of KcsA from the NABBs to lipid bilayers using single-channel electrophysiology and found that the functional properties of the channel remained intact. NABBs containing KcsA were stable, homogeneous, and able to spontaneously deliver the channel to black lipid membranes without measurably affecting the electrical properties of the bilayer. Our results are the first to demonstrate the transfer of a MP from NABBs to a different lipid bilayer without involving vesicle fusion.

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Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs

10.21203/rs.3.rs-57572/v1 ◽

2020 ◽

Author(s):

Gerhard Wagner ◽

Meng Zhang ◽

Miao Gui ◽

Zi-Fu Wang ◽

Christoph Gorgulla ◽

...

Keyword(s):

Complex Formation ◽

G Protein ◽

Lipid Bilayer ◽

Lipid Bilayers ◽

Protein Interactions ◽

Protein Complex ◽

Lipid Membrane ◽

Protein Complexes ◽

Structural Basis ◽

Downstream Signaling

Abstract G protein coupled receptors (GPCRs) are the largest superfamily of transmembrane proteins and the targets of over 30% of currently marketed pharmaceuticals. Although several structures have been solved for GPCR-G protein complexes, structural studies of the complex in a physiological lipid membrane environment are lacking. Here, we report cryo-EM structures of lipid bilayer-bound complexes of neurotensin, neurotensin receptor 1, and Gai1b1g1 protein in two conformational states, resolved to 4.1 and 4.2 Å resolution. The structures were determined in lipid bilayer without any stabilizing antibodies/nanobodies, and thus provide a native-like platform for understanding the structural basis of GPCR-G protein complex formation. Our structures reveal an extended network of protein-protein interactions at the GPCR-G protein interface compared to in detergent micelles, defining roles for the lipid membrane in modulating the structure and dynamics of complex formation, and providing a molecular explanation for the stronger interaction between GPCR and G protein in lipid bilayers. We propose a detailed allosteric mechanism for GDP release, providing new insights into the activation of G proteins for downstream signaling.

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Materials Engineering of Lipid Bilayers for Drug Carrier Performance

MRS Bulletin ◽

10.1557/s0883769400053240 ◽

1999 ◽

Vol 24 (10) ◽

pp. 32-41 ◽

Cited By ~ 15

Author(s):

David Needham

Keyword(s):

Drug Delivery ◽

Lipid Bilayer ◽

Lipid Bilayers ◽

Drug Carrier ◽

Pharmaceutical Product ◽

Structural Basis ◽

Central Position ◽

Materials Engineering ◽

Intracellular Drug Delivery ◽

The Cost

The liquid-phase lipid bilayer is a unique engineering material. Biologically, it holds a central position in cellular life, providing the structural basis for the membrane that surrounds every cell on the planet. From a materials perspective, it is essentially a 4-nm-thick, water-insoluble sheet of 2-poise oil. Artificial membranes were “discovered” 35 years ago. It was soon recognized that liposomes could have a range of potential uses, and investigators sought to exploit the obvious capsular and biocompatibility properties of the membrane in applications such as liposome drug delivery. Since 1966, some 18,000 papers on liposomes have appeared in the literature (listed on Medline, and see References 4–7 for reviews), and 260 patents have been issued describing the use of liposomes in the pharmaceutical industry. These patented applications have included the delivery of cancer drugs, intracellular drug delivery, inhalation, topical drugs, gene therapy, proteins, peptides, amino acids, vaccines, targeted liposomes, lipophilic drugs, and liposome production, separation, and analysis. A huge database therefore exists with which to establish boundary conditions for predicting under which circumstances the encapsulation of drugs in liposomes or other carriers may be expected to result in improved therapy. Despite this enormous effort, only a few formulations, principally for amphotericin (an antifungal drug) and anthra-cyclins (anticancer drugs), have been approved and marketed, heralding the promise and potential that these versatile lipid-bilayer materials present. The reasons for this limited success are many, not the least of which is that the cost of developing a new pharmaceutical product can be several hundred million dollars.

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Molecular Dynamics Simulation of the Interaction Between Benzanthrone Dye and Model Lipid Membranes

East European Journal of Physics ◽

10.26565/2312-4334-2020-3-17 ◽

2020 ◽

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Lipid Bilayer ◽

Lipid Bilayers ◽

Lipid Membranes ◽

Fluorescent Dyes ◽

Md Simulations ◽

Dynamics Simulation ◽

Membrane Composition ◽

Model Lipid Membranes

The benzanthrone fluorescent dyes are known as environmentally-sensitive reporters for exploring the physicochemical properties and structural alterations of lipid membranes. In the present work the 100-ns molecular dynamics simulation (MD) was used to characterize the bilayer location and the nature of interactions between the benzanthrone fluorescent dye ABM and the model lipid membranes composed of the zwitterionic lipid phosphatidylcholine (PC) and its mixtures with the anionic lipid phosphatidylglycerol (PG20) and sterol cholesterol (Chol30). The MD simulations were performed in the CHARMM36m force field using the GROMACS package. The ABM molecule, which was initially placed at a distance of 30 Å from the midplane of the lipid bilayer, after 10 ns of simulation was found to be completely incorporated into the membrane interior and remained within the lipid bilayer for the rest of the simulation time. The analysis of the MD simulation results showed that the lipid bilayer location of the benzanthrone dye ABM depends on the membrane composition, with the distance from bilayer center being gradually shifted from 0.78 nm in the neat PC bilayer to 0.95 nm and 1.5 nm in the PG- and Chol-containing membranes, respectively. In addition, the partitioning of the ABM into the neat PC bilayer was followed by the probe translocation from the outer membrane leaflet to the inner one. A separate series of MD simulations was aimed at examining the ABM influence on the lipid bilayer structure. It was found that ABM partitioning into the lipid bilayers of various composition has no significant effect on the orientation of the fatty acid chains and leads only to a small increase of the deuterium order parameter for the carbon atoms 5-to-8 in the sn-2 acyl chains of the neat PC membranes. In addition, the interaction of the ABM with the model lipid membranes caused the slight decrease of the surface area per lipid pointing to the slight increase of the packing density of lipid molecules in the presence of ABM. The results obtained provide a basis for deeper understanding of the membrane interactions of benzanthrone dyes and may be useful for the design of the novel fluorescent probes for membrane studies.

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Does alpha-tocopherol flip-flop help to protect membranes against oxidation?

10.1101/422006 ◽

2018 ◽

Author(s):

Phansiri Boonnoy ◽

Mikko Karttunen ◽

Jirasak Wong-ekkabut

Keyword(s):

Free Energy ◽

Free Radicals ◽

Lipid Bilayer ◽

Lipid Bilayers ◽

Md Simulations ◽

Free Energy Calculations ◽

Alpha Tocopherol ◽

Oxidized Lipids ◽

Hydroxyl Groups ◽

Flip Flop

AbstractAlpha-tocopherols (α-toc) are crucial in protecting biological membranes against oxidation by free radicals. We investigate the behavior of α-toc molecules in lipid bilayers containing oxidized lipids by molecular dynamics (MD) simulations. To verify the approach, the location and orientation of α-toc are first shown to be in agreement with previous experimental results. The simulations further show that α-toc molecules stay inside the lipid bilayer with their hydroxyl groups in contact with the bilayer surface. Interestingly, interbilayer α-toc flip-flop was observed in both oxidized and non-oxidized bilayers with significantly higher frequency in aldehyde lipid bilayer. Free energy calculations were performed and estimates of the flip-flop rates across the bilayers were determined. As the main finding, our results show that the presence of oxidized lipids leads to a significant decrease of free energy barriers and that the flip-flop rates depend on the type of oxidized lipid present. Our results suggest that α-toc molecules could potentially act as high efficacy scavengers of free radicals to protect membranes from oxidative attack and help stabilize them under oxidative stress.

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Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs

10.1101/2020.06.11.145912 ◽

2020 ◽

Cited By ~ 2

Author(s):

Meng Zhang ◽

Miao Gui ◽

Zi-Fu Wang ◽

Christoph Gorgulla ◽

James J Yu ◽

...

Keyword(s):

Complex Formation ◽

G Protein ◽

G Proteins ◽

Lipid Bilayers ◽

Protein Interactions ◽

Protein Complex ◽

Lipid Membrane ◽

Complex Structure ◽

Underlying Mechanism ◽

Structural Basis

AbstractG protein coupled receptors (GPCRs) are the largest superfamily of transmembrane proteins and the targets of over 30% of currently marketed pharmaceuticals1,2. Although several structures have been solved for GPCR-G protein complexes3–17, structural studies of the complex in a physiological lipid membrane environment are lacking. Additionally, most previous studies required additional antibodies/nanobodies and/or engineered G proteins for complex stabilization. In the absence of a native complex structure, the underlying mechanism of G protein activation leading to GDP/GTP exchange remains unclear. Here, we report cryo-EM structures of lipid bilayer-bound complexes of neurotensin, neurotensin receptor 1, and Gαi1β1γ1 protein in two conformational states, resolved to 4.1 and 4.2 Å resolution. The structures were determined without any stabilizing antibodies/nanobodies, and thus provide a native-like platform for understanding the structural basis of GPCR-G protein complex formation. Our structures reveal an extended network of protein-protein interactions at the GPCR-G protein interface compared to in detergent micelles, defining roles for the lipid membrane in modulating the structure and dynamics of complex formation, and providing a molecular explanation for the stronger interaction between GPCR and G protein in lipid bilayers. We propose a detailed allosteric mechanism for GDP release, providing new insights into the activation of G proteins for downstream signaling under near native conditions.

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Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

10.26434/chemrxiv.11365943.v1 ◽

2019 ◽

Author(s):

Dimitrios Kolokouris ◽

Iris Kalenderoglou ◽

Panagiotis Lagarias ◽

Antonios Kolocouris

Keyword(s):

Molecular Dynamic ◽

Lipid Bilayer ◽

Influenza A ◽

Md Simulations ◽

Membrane Curvature ◽

Buffer Size ◽

M2 Protein ◽

Dynamic Simulations ◽

Amphipathic Helices ◽

Drug Protein Binding

We studied by molecular dynamic (MD) simulations systems including the inwardclosed state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å2 or 20x20 Å2. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å2 lipids buffer in DMPC is needed when M2TM is used but 20x20 Å2 lipids buffer of the softer POPC; when M2AH is used all 10x10 Å2 lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å2 lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å2 lipids buffer and CHARMM36.

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