scholarly journals A cationic lipid site at the outward transmembrane face of a pentameric ligand-gated ion channel

2021 ◽  
Author(s):  
Akshay Sridhar ◽  
Sarah C.R. Lummis ◽  
Diletta Pasini ◽  
Aujan Mehregan ◽  
Marijke Brams ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Cationic Lipid ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Structural Basis ◽  
Lipid Interactions ◽  
Canonical Amino Acid ◽  
Preferential Binding ◽  
Electrochemical Signal ◽  
Dynamics Simulations

AbstractPentameric ligand-gated ion channels (pLGICs) are crucial mediators of electrochemical signal transduction from bacteria to humans. Lipids play an important role in regulating pLGIC function, yet the structural basis for specific pLGIC-lipid interactions remains poorly understood. The bacterial channel ELIC recapitulates several properties of eukaryotic pLGICs, including activation by the neurotransmitter GABA and sensitivity to lipids, offering a simplified model system for structure-function studies. In this study, functional effects of non-canonical amino acid substitution of W206 at the top of the M1-helix, combined with detergent interactions observed in recent X-ray structures, are consistent with this region being the location of a lipid binding site on the outward face of the ELIC transmembrane domain. Coarse-grained and atomistic molecular dynamics simulations revealed preferential binding of lipids containing a positive charge, particularly involving interactions with residue W206 consistent with cation-π binding. Polar contacts from the principal subunit, particularly M3 residue Q264, further supported lipid binding via headgroup ester linkages. Aromatic residues were identified at analogous sites in a handful of eukaryotic family members, including the human GABAA receptor subunit ɛ, suggesting conservation of relevant interactions in other evolutionary branches. Further mutagenesis experiments indicated that mutations at this site in ɛ-containing GABAA receptors can change the apparent affinity of the agonist response to GABA, consistent with a potential role of this site in channel gating. In conclusion, this work is a detailed case study in type-specific lipid interactions at an evolutionarily distinctive pLGIC site, with implications for lipid modulation and lipophilic drug design.

scholarly journals State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane

2021 ◽  
Vol 17 (2) ◽  
pp. e1007856
Author(s):  
Marc A. Dämgen ◽  
Philip C. Biggin
Keyword(s):  
Rational Design ◽  
Transmembrane Domain ◽  
Conformational Dynamics ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Neuronal Membrane ◽  
Dependent Manner ◽  
Lipid Interactions ◽  
Interaction Sites ◽  
State Dependent

Pentameric ligand-gated ion channels (pLGICs) are receptor proteins that are sensitive to their membrane environment, but the mechanism for how lipids modulate function under physiological conditions in a state dependent manner is not known. The glycine receptor is a pLGIC whose structure has been resolved in different functional states. Using a realistic model of a neuronal membrane coupled with coarse-grained molecular dynamics simulations, we demonstrate that some key lipid-protein interactions are dependent on the receptor state, suggesting that lipids may regulate the receptor’s conformational dynamics. Comparison with existing structural data confirms known lipid binding sites, but we also predict further protein-lipid interactions including a site at the communication interface between the extracellular and transmembrane domain. Moreover, in the active state, cholesterol can bind to the binding site of the positive allosteric modulator ivermectin. These protein-lipid interaction sites could in future be exploited for the rational design of lipid-like allosteric drugs.

scholarly journals Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors

2018 ◽  
Vol 115 (35) ◽  
pp. E8172-E8180 ◽  
Author(s):  
Camille I. Pataki ◽  
João Rodrigues ◽  
Lichao Zhang ◽  
Junyang Qian ◽  
Bradley Efron ◽  
...  
Keyword(s):  
Lipid Droplets ◽  
Coarse Grained ◽  
Structural Basis ◽  
Endoplasmic Reticulum Membrane ◽  
Membrane Surfaces ◽  
Common Motif ◽  
Cysteine Scanning Mutagenesis ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Integral Proteins

Despite not spanning phospholipid bilayers, monotopic integral proteins (MIPs) play critical roles in organizing biochemical reactions on membrane surfaces. Defining the structural basis by which these proteins are anchored to membranes has been hampered by the paucity of unambiguously identified MIPs and a lack of computational tools that accurately distinguish monolayer-integrating motifs from bilayer-spanning transmembrane domains (TMDs). We used quantitative proteomics and statistical modeling to identify 87 high-confidence candidate MIPs in lipid droplets, including 21 proteins with predicted TMDs that cannot be accommodated in these monolayer-enveloped organelles. Systematic cysteine-scanning mutagenesis showed the predicted TMD of one candidate MIP, DHRS3, to be a partially buried amphipathic α-helix in both lipid droplet monolayers and the cytoplasmic leaflet of endoplasmic reticulum membrane bilayers. Coarse-grained molecular dynamics simulations support these observations, suggesting that this helix is most stable at the solvent–membrane interface. The simulations also predicted similar interfacial amphipathic helices when applied to seven additional MIPs from our dataset. Our findings suggest that interfacial helices may be a common motif by which MIPs are integrated into membranes, and provide high-throughput methods to identify and study MIPs.

Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations

2014 ◽  
Vol 42 (5) ◽  
pp. 1418-1424 ◽  
Author(s):  
Antreas C. Kalli ◽  
Mark S. P. Sansom
Keyword(s):  
Lipid Bilayers ◽  
Molecular Mechanisms ◽  
Phospholipid Composition ◽  
Md Simulations ◽  
Multiscale Simulation ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Peripheral Proteins ◽  
Dynamics Simulations ◽  
Phosphatidylinositol Phosphates

Many cellular signalling and related events are triggered by the association of peripheral proteins with anionic lipids in the cell membrane (e.g. phosphatidylinositol phosphates or PIPs). This association frequently occurs via lipid-binding modules, e.g. pleckstrin homology (PH), C2 and four-point-one, ezrin, radixin, moesin (FERM) domains, present in peripheral and cytosolic proteins. Multiscale simulation approaches that combine coarse-grained and atomistic MD simulations may now be applied with confidence to investigate the molecular mechanisms of the association of peripheral proteins with model bilayers. Comparisons with experimental data indicate that such simulations can predict specific peripheral protein–lipid interactions. We discuss the application of multiscale MD simulation and related approaches to investigate the association of peripheral proteins which contain PH, C2 or FERM-binding modules with lipid bilayers of differing phospholipid composition, including bilayers containing multiple PIP molecules.

scholarly journals Inverse design of cholesterol attracting transmembrane helices reveals a paradoxical role of hydrophobic length

2021 ◽  
Author(s):  
Jeroen Methorst ◽  
Niek van Hilten ◽  
Herre Jelger Risselada
Keyword(s):  
Molecular Dynamics ◽  
Lipid Membranes ◽  
Transmembrane Domain ◽  
Optimal Solution ◽  
Molecular Shape ◽  
Global Optimum ◽  
Coarse Grained ◽  
Hydrophobic Core ◽  
Recognition Motifs ◽  
Dynamics Simulations

The occurrence of linear cholesterol-recognition motifs in alpha-helical transmembrane domains has long been debated. Here, we demonstrate the ability of a genetic algorithm guided by coarse-grained molecular dynamics simulations---a method coined evolutionary molecular dynamics (evo-MD)---to directly resolve the sequence which maximally attracts/sorts cholesterol within a single-pass alpha-helical transmembrane domain (TMDs). We illustrate that the evolutionary landscape of cholesterol attraction in membrane proteins is characterized by a sharp, well-defined global optimum. Surprisingly, this optimal solution features an unusual short hydrophobic block, consisting of typically only eight short chain hydrophobic amino acids, surrounded by three successive lysines. Owing to the membrane thickening effect of cholesterol, cholesterol-enriched ordered phases favor TMDs characterized by a long rather than a short hydrophobic length. However, this short hydrophobic pattern evidently offers a pronounced net advantage for the binding of free cholesterol in both coarse-grained and atomistic simulations. Attraction is mediated by the unique ability of cholesterol to snorkel within the hydrophobic core of the membrane and thereby shield deeply located lysines from the unfavorable hydrophobic surrounding. Since this mechanism of attraction is of a thermodynamic nature and is not based on molecular shape specificity, a large diversity of sub-optimal cholesterol attracting sequences can exist. The puzzling sequence variability of proposed linear cholesterol-recognition motifs is thus consistent with sub-optimal, unspecific binding of cholesterol. Importantly, since evo-MD uniquely enables the targeted design of recognition motifs for distinct fluid lipid membranes, we foresee wide applications for evo-MD in the biological and biomedical fields.

scholarly journals Cotranslational folding stimulates programmed ribosomal frameshifting in the alphavirus structural polyprotein

2020 ◽  
Vol 295 (20) ◽  
pp. 6798-6808 ◽  
Author(s):  
Haley R. Harrington ◽  
Matthew H. Zimmer ◽  
Laura M. Chamness ◽  
Veronica Nash ◽  
Wesley D. Penn ◽  
...  
Keyword(s):  
Sindbis Virus ◽  
Polypeptide Chain ◽  
Transmembrane Domain ◽  
Coarse Grained ◽  
Computational Techniques ◽  
Ribosomal Frameshifting ◽  
Nascent Polypeptide ◽  
Cotranslational Folding ◽  
Biochemical Mechanisms ◽  
Dynamics Simulations

Viruses maximize their genetic coding capacity through a variety of biochemical mechanisms, including programmed ribosomal frameshifting (PRF), which facilitates the production of multiple proteins from a single mRNA transcript. PRF is typically stimulated by structural elements within the mRNA that generate mechanical tension between the transcript and ribosome. However, in this work, we show that the forces generated by the cotranslational folding of the nascent polypeptide chain can also enhance PRF. Using an array of biochemical, cellular, and computational techniques, we first demonstrate that the Sindbis virus structural polyprotein forms two competing topological isomers during its biosynthesis at the ribosome-translocon complex. We then show that the formation of one of these topological isomers is linked to PRF. Coarse-grained molecular dynamics simulations reveal that the translocon-mediated membrane integration of a transmembrane domain upstream from the ribosomal slip site generates a force on the nascent polypeptide chain that scales with observed frameshifting. Together, our results indicate that cotranslational folding of this viral protein generates a tension that stimulates PRF. To our knowledge, this constitutes the first example in which the conformational state of the nascent polypeptide chain has been linked to PRF. These findings raise the possibility that, in addition to RNA-mediated translational recoding, a variety of cotranslational folding or binding events may also stimulate PRF.

scholarly journals Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2 (PC2)

2019 ◽  
Author(s):  
Qinrui Wang ◽  
George Hedger ◽  
Prafulla Aryal ◽  
Mariana Grieben ◽  
Chady Nasrallah ◽  
...  
Keyword(s):  
Binding Site ◽  
Trp Channels ◽  
Md Simulations ◽  
Lipid Binding ◽  
Cryoelectron Microscopy ◽  
Trpv1 Channel ◽  
Lipid Interactions ◽  
Dynamics Simulations ◽  
Phosphatidylinositol Phosphates ◽  
Lipid Binding Site

AbstractPolycystin-2 (PC2) is a member of the TRPP subfamily of TRP channels and is present in ciliary membranes of the kidney. PC2 can be either homo-tetrameric, or heterotetrameric with PC1. PC2 shares a common transmembrane fold with other TRP channels, in addition to having a novel extracellular domain. Several TRP channels have been suggested to be regulated by lipids, including phosphatidylinositol phosphates (PIPs). We have combined molecular dynamics simulations with cryoelectron microscopy to explore possible lipid interactions sites on PC2. We propose that PC2 has a PIP-binding site close to the equivalent vanilloid/lipid-binding site in the TRPV1 channel. A 3.0 Å cryoelectron microscopy map reveals a binding site for cholesterol on PC2. Cholesterol interactions with the channel at this site are further characterized by MD simulations. These results help to position PC2 within an emerging model of the complex roles of lipids in the regulation and organization of ciliary membranes.

scholarly journals Structure of the ancestral TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium

2020 ◽  
Author(s):  
Tofayel Ahmed ◽  
Collin R. Nisler ◽  
Edwin C. Fluck ◽  
Marcos Sotomayor ◽  
Vera Y. Moiseenkova-Bell
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transient Receptor Potential ◽  
Transmembrane Domain ◽  
Trp Channels ◽  
Receptor Potential ◽  
Lipid Binding ◽  
Channel Modulation ◽  
Channel Inhibition ◽  
Transient Receptor ◽  
Dynamics Simulations

ABSTRACTTransient Receptor Potential (TRP) channels have evolved in eukaryotes to control various cellular functions in response to a wide variety of chemical and physical stimuli. This large and diverse family of channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, but the molecular details of channel modulation remain elusive so far. Here, we describe the full-length cryo-electron microscopy structure of TRPY1 at 3.1 Å resolution. The structure reveals a distinctive architecture for TRPY1 among all eukaryotic TRP channels with an evolutionarily conserved and archetypical transmembrane domain, but distinct structural folds for the cytosolic N- and C-termini. We identified the inhibitory phosphatidylinositol 3-phosphate (PI(3)P) lipid binding site, which sheds light into the lipid modulation of TRPY1 in the vacuolar membrane. The structure also exhibited two Ca2+-binding sites: one in the cytosolic side, implicated in channel activation, and the other in the vacuolar lumen side, involved in channel inhibition. These findings, together with data from molecular dynamics simulations, provide structural insights into the basis of TRPY1 channel modulation by lipids and Ca2+.

scholarly journals Coarse-grained molecular dynamics simulations reveal lipid access pathways in P-glycoprotein

2018 ◽  
Vol 150 (3) ◽  
pp. 417-429 ◽  
Author(s):  
Estefania Barreto-Ojeda ◽  
Valentina Corradi ◽  
Ruo-Xu Gu ◽  
D. Peter Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Glycoprotein P ◽  
P Glycoprotein ◽  
Dynamics Simulations ◽  
Positively Charged ◽  
Coarse Grained Molecular Dynamics

P-glycoprotein (P-gp) exports a broad range of dissimilar compounds, including drugs, lipids, and lipid-like molecules. Because of its substrate promiscuity, P-gp is a key player in the development of cancer multidrug resistance. Although P-gp is one of the most studied ABC transporters, the mechanism by which its substrates access the cavity remains unclear. In this study, we perform coarse-grained molecular dynamics simulations to explore possible lipid access pathways in the inward-facing conformation of P-gp embedded in bilayers of different lipid compositions. In the inward-facing orientation, only lipids from the lower leaflet access the cavity of the transporter. We identify positively charged residues at the portals of P-gp that favor lipid entrance to the cavity, as well as lipid-binding sites at the portals and within the cavity, which is in good agreement with previous experimental studies. This work includes several examples of lipid pathways for phosphatidylcholine and phosphatidylethanolamine lipids that help elucidate the molecular mechanism of lipid binding in P-gp.

scholarly journals Direct binding of phosphatidylglycerol at specific sites modulates desensitization of a ligand-gated ion channel

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Ailing Tong ◽  
John T Petroff ◽  
Fong-Fu Hsu ◽  
Philipp AM Schmidpeter ◽  
Crina M Nimigean ◽  
...  
Keyword(s):  
Ion Channel ◽  
Transmembrane Domain ◽  
Native Mass Spectrometry ◽  
Coarse Grained ◽  
Specific Lipids ◽  
Anionic Phospholipid ◽  
Anionic Phospholipids ◽  
Functional Assays ◽  
Direct Binding ◽  
Dynamics Simulations

Pentameric ligand-gated ion channels (pLGICs) are essential determinants of synaptic transmission, and are modulated by specific lipids including anionic phospholipids. The exact modulatory effect of anionic phospholipids in pLGICs and the mechanism of this effect are not well understood. Using native mass spectrometry, coarse-grained molecular dynamics simulations and functional assays, we show that the anionic phospholipid, 1-palmitoyl-2-oleoyl phosphatidylglycerol (POPG), preferentially binds to and stabilizes the pLGIC, Erwinia ligand-gated ion channel (ELIC), and decreases ELIC desensitization. Mutations of five arginines located in the interfacial regions of the transmembrane domain (TMD) reduce POPG binding, and a subset of these mutations increase ELIC desensitization. In contrast, a mutation that decreases ELIC desensitization, increases POPG binding. The results support a mechanism by which POPG stabilizes the open state of ELIC relative to the desensitized state by direct binding at specific sites.

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