scholarly journals Unroofing site-specific α-synuclein–lipid interactions at the plasma membrane

2020 ◽  
Vol 117 (32) ◽  
pp. 18977-18983 ◽  
Author(s):  
Upneet Kaur ◽  
Jennifer C. Lee
Keyword(s):  
Protein Interactions ◽  
Lifetime Distributions ◽  
Biophysical Characterization ◽  
Biologically Relevant ◽  
Lipid Interactions ◽  
C Terminus ◽  
Liquid Ordered ◽  
Lipid Environment ◽  
Lipid Protein Interactions ◽  
Synaptic Vesicle Fusion

Parkinson’s disease is associated with α-synuclein (α-syn), a cytosolic protein enriched in presynaptic terminals. The biological function of α-syn remains elusive; however, increasing evidence suggests that the protein is involved in the regulation of synaptic vesicle fusion, signifying the importance of α-syn–lipid interactions. We show that α-syn preferentially binds to GM1-rich, liquid-ordered lipid domains on cytoplasmic membranes by using unroofed cells, which encapsulates lipid complexity and cellular topology. Moreover, proteins (Rab3a, syntaxin-1A, and VAMP2) involved in exocytosis also localize with α-syn, supporting its proposed functional role in exocytosis. To investigate how these lipid/protein interactions influence α-syn at the residue level, α-syn was derivatized with an environmentally sensitive fluorophore (7-nitrobenz-2-oxa-1,3-diazol-4-yl [NBD]) at different N- and C-terminal sites. Measurements of NBD fluorescence lifetime distributions reveal that α-syn adopts a multitude of membrane-bound conformations, which were not recapitulated in simple micelle or vesicle models, indicating an exquisite sensitivity of the protein to the complex lipid environment. Interestingly, these data also suggest the participation of the C terminus in membrane localization, which is generally overlooked and thus emphasize the need to use cellularly derived and biologically relevant membranes for biophysical characterization. Collectively, our results demonstrate that α-syn is more conformationally dynamic at the membrane interface than previously appreciated, which may be important for both its physiological and pathological functions.

scholarly journals Lipid-protein interactions are unique fingerprints for membrane proteins

2017 ◽  
Author(s):  
Valentina Corradi ◽  
Eduardo Mendez-Villuendas ◽  
Helgi I. Ingólfsson ◽  
Ruo-Xu Gu ◽  
Iwona Siuda ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Protein Interactions ◽  
Cell Membranes ◽  
Spatiotemporal Resolution ◽  
Lipid Dynamics ◽  
Lipid Species ◽  
Lipid Environment ◽  
Lipid Protein Interactions ◽  
Dynamics Simulations ◽  
Asymmetrically Distributed

ABSTRACTCell membranes contain hundreds of different proteins and lipids in an asymmetric arrangement. Understanding the lateral organization principles of these complex mixtures is essential for life and health. However, our current understanding of the detailed organization of cell membranes remains rather elusive, owing to the lack of experimental methods suitable for studying these fluctuating nanoscale assemblies of lipids and proteins with the required spatiotemporal resolution. Here, we use molecular dynamics simulations to characterize the lipid environment of ten membrane proteins. To provide a realistic lipid environment, the proteins are embedded in a model plasma membrane, where more than 60 lipid species are represented, asymmetrically distributed between leaflets. The simulations detail how each protein modulates its local lipid environment through local lipid composition, thickness, curvature and lipid dynamics. Our results provide a molecular glimpse of the complexity of lipid-protein interactions, with potentially far reaching implications for the overall organization of the cell membrane.

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

2020 ◽  
Author(s):  
Marc A. Dämgen ◽  
Philip C. Biggin
Keyword(s):  
Ion Channels ◽  
Protein Interactions ◽  
Glycine Receptor ◽  
Realistic Model ◽  
Neuronal Membrane ◽  
Lipid Interactions ◽  
State Dependent ◽  
Lipid Protein Interactions ◽  
Dynamics Simulations ◽  
A Site

AbstractPentameric 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 the 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.Author SummaryIon channels are proteins that control the flow of ions into the cell. The family of ion channels known as the pentameric ligand gated ion channels (pLGICS) open in response to the binding of a neurotransmitter, moving the channel from a resting state to an open state. The glycine receptor is a pLGIC whose structure has been resolved in different functional states. It is also known that the response of pLGICs can also be modified by different types of lipid found within the membrane itself but exactly how is unclear. Here, we used a realistic model of a neuronal membrane and performed molecular dynamics simulations to show various lipid-protein interactions that are dependent on the channel state. Our work also reveals previously unconsidered protein-lipid interactions at a key junction of the channel known to be critical for the transmission of the opening process. We also demonstrate that cholesterol interacts with the protein at a site already known to bind to another compound that modulates the channel, called ivermectin. The work should be useful for future drug design.

Distinct interfacial ordering of liquid crystal observed by protein-lipid interactions that enabled the label free sensing of cytoplasmic protein at LC-aqueous interface

The Analyst ◽  
2021 ◽  
Author(s):  
Santanu Kumar Pal ◽  
Manisha Devi ◽  
Indu Verma
Keyword(s):  
Liquid Crystal ◽  
Protein Adsorption ◽  
Aqueous Phase ◽  
Protein Interactions ◽  
Cytoplasmic Protein ◽  
Label Free ◽  
Lipid Interactions ◽  
Lipid Protein Interactions

Interfaces formed between lipid decorated liquid crystal (LC) film and aqueous phase can mimic the bimolecular membrane where interfacial occurring biological phenonmenon (e.g., lipid-protein interactions, protein adsorption) can be visually...

A review of traditional and emerging methods to characterize lipid–protein interactions in biological membranes

2015 ◽  
Vol 7 (17) ◽  
pp. 7076-7094 ◽  
Author(s):  
Chih-Yun Hsia ◽  
Mark J. Richards ◽  
Susan Daniel
Keyword(s):  
Plasma Membrane ◽  
Membrane Protein ◽  
Protein Interactions ◽  
Protein Structures ◽  
Biological Membranes ◽  
Biological Functions ◽  
Cell Plasma Membrane ◽  
Lipid Interactions ◽  
Cell Plasma ◽  
Lipid Protein Interactions

Lipid–protein interactions are essential for modulating membrane protein structures and biological functions in the cell plasma membrane. In this review we describe the salient features of classical and emerging methodologies for studying protein–lipid interactions and their limitations.

Membrane Protein–Lipid Interactions Probed Using Mass Spectrometry

2019 ◽  
Vol 88 (1) ◽  
pp. 85-111 ◽  
Author(s):  
Jani Reddy Bolla ◽  
Mark T. Agasid ◽  
Shahid Mehmood ◽  
Carol V. Robinson
Keyword(s):  
Mass Spectrometry ◽  
Membrane Protein ◽  
Lipid Bilayers ◽  
Protein Interactions ◽  
Native Mass Spectrometry ◽  
Lipid Interactions ◽  
X Ray Crystallography ◽  
Native Ms ◽  
Molecular Aspects ◽  
Lipid Protein Interactions

Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical lipid–protein interactions is developing rapidly. Advancements in both instrumentation and software, as well as in key biophysical and biochemical techniques, are accelerating the field. In this review, we provide a brief outline of structural techniques used to probe protein–lipid interactions and focus on the molecular aspects of these interactions obtained from native mass spectrometry (native MS). We highlight examples in which lipids have been shown to modulate membrane protein structure and show how native MS has emerged as a complementary technique to X-ray crystallography and cryo–electron microscopy. We conclude with a short perspective on future developments that aim to better understand protein–lipid interactions in the native environment.

scholarly journals Lipid fingerprints are similar between SLC6 transporters in the neuronal membrane

2021 ◽  
Author(s):  
Katie A. Wilson ◽  
Lily Wang ◽  
Yie Chang Lin ◽  
Megan L. O’Mara
Keyword(s):  
Protein Interactions ◽  
Neuronal Membrane ◽  
List Type ◽  
Membrane Composition ◽  
Biophysical Properties ◽  
Complex Membrane ◽  
Lipid Environment ◽  
Lipid Protein Interactions ◽  
Dynamics Simulations ◽  
Specific Lipid

ABSTRACTWe use molecular dynamics simulations to characterise the local lipid annulus, or “fingerprint”, of three SLC6 transporters (dDAT, hSERT, and GlyT2) embedded into a complex neuronal membrane. New membrane analysis tools were created to improve leaflet detection and leaflet-dependent properties. Overall, lipid fingerprints are comprised of similar lipids when grouped by headgroup or tail saturation. The enrichment and depletion of specific lipids, including sites of cholesterol contacts, varies between transporters. The subtle differences in lipid fingerprints results in varying membrane biophysical properties near the transporter. Through comparisons to previous literature, we highlight that the lipid-fingerprint in complex membranes is highly dependent on membrane composition. Furthermore, through embedding these transporters in a simplified model membrane, we show that the simplified membrane is not able to capture the biophysical properties of the complex membrane. Our results further characterise how the presence and identity of membrane proteins affects the complex interplay of lipid-protein interactions, including the local lipid environment and membrane biophysical properties.HIGHLIGHTSLipid fingerprints are comprised of similar lipid classesSites of specific lipid contacts, including CHOL, varies between transportersChanges in lipid annulus result in variable local membrane biophysical propertiesMembrane composition, including that of complex membranes, affects lipid annulusGRAPHICAL ABSTRACT

scholarly journals Application of electron spin resonance for investigating peptide-lipid interactions, and correlation with thermodynamics

2001 ◽  
Vol 29 (4) ◽  
pp. 582-589 ◽  
Author(s):  
D. Marsh
Keyword(s):  
Electron Spin Resonance ◽  
Membrane Proteins ◽  
Electron Spin ◽  
Protein Interactions ◽  
Surface Binding ◽  
Lipid Interactions ◽  
Peripheral Membrane Proteins ◽  
Spin Resonance ◽  
Surface Active ◽  
Lipid Protein Interactions

Peptide-lipid interactions can be investigated with spin-labelled lipid probes by using electron spin resonance (ESR) methods that have been developed for studying lipid-protein interactions with both integral and peripheral membrane proteins and also with surface-binding proteins that additionally penetrate the membrane. This approach has the advantage that a direct comparison can be made with the databank of ESR results from the various types of membrane protein. The appropriateness of the peptides as models for membrane proteins, or for their specific segments, can then be assessed. Further, differences in behaviour can be readily identified, as for example in the case of surface-active cytolytic or fusogenic peptides. Comparison with thermodynamic predictions for membrane insertion provides a useful adjunct to the spin-label method.

Reconstitution of rabbit sarcoplasmic reticulum calcium ATPase in a series of phosphatidylcholines containing a saturated and an unsaturated chain: suggestion of an optimal lipid environment

1993 ◽  
Vol 71 (7-8) ◽  
pp. 381-389 ◽  
Author(s):  
Paul L. J. Matthews ◽  
Eileen Bartlett ◽  
V. S. Ananthanarayanan ◽  
Kevin M. W. Keough
Keyword(s):  
Sarcoplasmic Reticulum ◽  
Protein Interactions ◽  
Activation Energies ◽  
Calcium Atpase ◽  
Enzyme Function ◽  
Calcium Dependent ◽  
Mixed Acid ◽  
Lipid Environment ◽  
Lipid Protein Interactions ◽  
Sarcoplasmic Reticulum Calcium

The calcium-dependent ATPase from sarcoplasmic reticulum of rabbit has been purified and reconstituted in dispersions containing pure phosphatidylcholines. Each phosphatidylcholine (PC) had palmitate (16:0) at the sn-1 position of glycerol and stearate (18:0), oleate (18:1), linoleate (18:2), arachidonate (20:4), or docosahexaenoate (22:6) at the sn-2 position. The activities and activation energies of the enzyme indicated that the best enzyme function occurred when 16:0–18:1 PC or 16:0–18:2 PC was the lipid in which the ATPase was embedded. Circular dichroism measurements made as a function of temperature suggested that the protein in 16:0–18:0 and 16:0–18:1 PC behaved most like sarcoplasmic reticulum or purified ATPase. The results suggest that there may be an optimal lipid environment for the ATPase which is provided by 16:0–18:1 PC and 16:0–18:2 PC, the two most common lipids of the sarcoplasmic reticulum.Key words: lipid–protein interactions, adaptation, mixed acid lipids.

scholarly journals Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2

2021 ◽  
Author(s):  
Viviana Monje-Galvan ◽  
Gregory A. Voth
Keyword(s):  
Membrane Proteins ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Integral Membrane Proteins ◽  
Protein Protein Interactions ◽  
Novel Treatments ◽  
Cellular Processes ◽  
Ongoing Work ◽  
Lipid Environment ◽  
Lipid Protein Interactions

AbstractSpecific lipid-protein interactions are key for cellular processes, and even more so for the replication of pathogens. The COVID-19 pandemic has drastically changed our lives and cause the death of nearly three million people worldwide, as of this writing. SARS-CoV-2 is the virus that causes the disease and has been at the center of scientific research over the past year. Most of the research on the virus is focused on key players during its initial attack and entry into the cellular host; namely the S protein, its glycan shield, and its interactions with the ACE2 receptors of human cells. As cases continue to raise around the globe, and new mutants are identified, there is an urgent need to understand the mechanisms of this virus during different stages of its life cycle. Here, we consider two integral membrane proteins of SARS-CoV-2 known to be important for viral assembly and infectivity. We have used microsecond-long all-atom molecular dynamics to examine the lipid-protein and protein-protein interactions of the membrane (M) and envelope (E) structural proteins of SARS-CoV-2 in a complex membrane model. We contrast the two proposed protein complexes for each of these proteins, and quantify their effect on their local lipid environment. This ongoing work also aims to provide molecular-level understanding of the mechanisms of action of this virus to possibly aid in the design of novel treatments.

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