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Article ; Online: Interleaflet organization of membrane nanodomains: What can(not) be resolved by FRET?

Chmelová, Barbora / Davidović, David / Šachl, Radek

2022 Volume 122, Issue 11, Page(s) 2053–2067

Abstract: Plasma membranes as well as their simplified model systems show an inherent nanoscale heterogeneity. As a result of strong interleaflet interactions, these nanoheterogeneities (called here lipid nanodomains) can be found in perfect registration (i.e., ... ...

Abstract	Plasma membranes as well as their simplified model systems show an inherent nanoscale heterogeneity. As a result of strong interleaflet interactions, these nanoheterogeneities (called here lipid nanodomains) can be found in perfect registration (i.e., nanodomains in the inner leaflet are registered with the nanodomains in the outer leaflet). Alternatively, they might be interleaflet independent, antiregistered, or located asymmetrically in one bilayer leaflet only. To distinguish these scenarios from each other appears to be an experimental challenge. In this work, we analyzed the potential of Förster resonance energy transfer to characterize interleaflet organization of nanodomains. We generated in silico time-resolved fluorescence decays for a large set of virtual as well as real donor/acceptor pairs distributed over the bilayer containing registered, independent, antiregistered, or asymmetrically distributed nanodomains. In this way, we were able to identify conditions that gave satisfactory or unsatisfactory resolution. Overall, Förster resonance energy transfer appears as a robust method that, when using donor/acceptor pairs with good characteristics, yields otherwise difficult-to-reach characteristics of membrane lipid nanodomains.
MeSH term(s)	Fluorescence Resonance Energy Transfer/methods ; Cell Membrane/metabolism ; Membranes/metabolism ; Membrane Lipids ; Models, Biological ; Lipid Bilayers/metabolism
Chemical Substances	Membrane Lipids ; Lipid Bilayers
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.11.014
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Article: Regulation of Cell Death by Mitochondrial Transport Systems of Calcium and Bcl-2 Proteins.

Naumova, Natalia / Šachl, Radek

Membranes

2020 Volume 10, Issue 10

Abstract: Mitochondria represent the fundamental system for cellular energy metabolism, by not only supplying energy in the form of ATP, but also by affecting physiology and cell death via the regulation of calcium homeostasis and the activity of Bcl-2 proteins. A ...

Abstract	Mitochondria represent the fundamental system for cellular energy metabolism, by not only supplying energy in the form of ATP, but also by affecting physiology and cell death via the regulation of calcium homeostasis and the activity of Bcl-2 proteins. A lot of research has recently been devoted to understanding the interplay between Bcl-2 proteins, the regulation of these interactions within the cell, and how these interactions lead to the changes in calcium homeostasis. However, the role of Bcl-2 proteins in the mediation of mitochondrial calcium homeostasis, and therefore the induction of cell death pathways, remain underestimated and are still not well understood. In this review, we first summarize our knowledge about calcium transport systems in mitochondria, which, when miss-regulated, can induce necrosis. We continue by reviewing and analyzing the functions of Bcl-2 proteins in apoptosis. Finally, we link these two regulatory mechanisms together, exploring the interactions between the mitochondrial Ca
Language	English
Publishing date	2020-10-21
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2614641-1
ISSN	2077-0375
ISSN	2077-0375
DOI	10.3390/membranes10100299
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Article: Interleaflet Coupling of Lipid Nanodomains - Insights From

Sarmento, Maria J / Hof, Martin / Šachl, Radek

Frontiers in cell and developmental biology

2020 Volume 8, Page(s) 284

Abstract: The plasma membrane is a complex system, consisting of two layers of lipids and proteins compartmentalized into small structures called nanodomains. Despite the asymmetric composition of both leaflets, coupling between the layers is surprisingly strong. ... ...

Abstract	The plasma membrane is a complex system, consisting of two layers of lipids and proteins compartmentalized into small structures called nanodomains. Despite the asymmetric composition of both leaflets, coupling between the layers is surprisingly strong. This can be evidenced, for example, by recent experimental studies performed on phospholipid giant unilamellar vesicles showing that nanodomains formed in the outer layer are perfectly registered with those in the inner leaflet. Similarly, microscopic phase separation in one leaflet can induce phase separation in the opposing leaflet that would otherwise be homogeneous. In this review, we summarize the current theoretical and experimental knowledge that led to the current view that domains are - irrespective of their size - commonly registered across the bilayer. Mechanisms inducing registration of nanodomains suggested by theory and calculations are discussed. Furthermore, domain coupling is evidenced by experimental studies based on the sparse number of methods that can resolve registered from independent nanodomains. Finally, implications that those findings using model membrane studies might have for cellular membranes are discussed.
Language	English
Publishing date	2020-04-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2020.00284
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Article ; Online: Determining the Functional Oligomeric State of Membrane-Associated Protein Oligomers Forming Membrane Pores on Giant Lipid Vesicles.

Singh, Vandana / Macharová, Sabína / Riegerová, Petra / Steringer, Julia P / Müller, Hans-Michael / Lolicato, Fabio / Nickel, Walter / Hof, Martin / Šachl, Radek

Analytical chemistry

2023 Volume 95, Issue 23, Page(s) 8807–8815

Abstract: Several peripheral membrane proteins are known to form membrane pores through multimerization. In many cases, in biochemical reconstitution experiments, a complex distribution of oligomeric states has been observed that may, in part, be irrelevant to ... ...

Abstract	Several peripheral membrane proteins are known to form membrane pores through multimerization. In many cases, in biochemical reconstitution experiments, a complex distribution of oligomeric states has been observed that may, in part, be irrelevant to their physiological functions. This phenomenon makes it difficult to identify the functional oligomeric states of membrane lipid interacting proteins, for example, during the formation of transient membrane pores. Using fibroblast growth factor 2 (FGF2) as an example, we present a methodology applicable to giant lipid vesicles by which functional oligomers can be distinguished from nonspecifically aggregated proteins without functionality. Two distinct populations of fibroblast growth factor 2 were identified with (i) dimers to hexamers and (ii) a broad population of higher oligomeric states of membrane-associated FGF2 oligomers significantly distorting the original unfiltered histogram of all detectable oligomeric species of FGF2. The presented statistical approach is relevant for various techniques for characterizing membrane-dependent protein oligomerization.
MeSH term(s)	Cell Membrane/metabolism ; Membrane Proteins/metabolism ; Fibroblast Growth Factor 2/metabolism ; Membranes ; Lipids ; Protein Multimerization
Chemical Substances	Membrane Proteins ; Fibroblast Growth Factor 2 (103107-01-3) ; Lipids
Language	English
Publishing date	2023-05-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c05692
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Article ; Online: Determining the Functional Oligomeric State of Membrane-Associated Protein Oligomers Forming Membrane Pores on Giant Lipid Vesicles

Singh, Vandana / Macharová, Sabína / Riegerová, Petra / Steringer, Julia P. / Müller, Hans-Michael / Lolicato, Fabio / Nickel, Walter / Hof, M. / Šachl, Radek

Analytical Chemistry. 2023 May 06, v. 95, no. 23 p.8807-8815

2023

Abstract	Several peripheral membrane proteins are known to form membrane pores through multimerization. In many cases, in biochemical reconstitution experiments, a complex distribution of oligomeric states has been observed that may, in part, be irrelevant to their physiological functions. This phenomenon makes it difficult to identify the functional oligomeric states of membrane lipid interacting proteins, for example, during the formation of transient membrane pores. Using fibroblast growth factor 2 (FGF2) as an example, we present a methodology applicable to giant lipid vesicles by which functional oligomers can be distinguished from nonspecifically aggregated proteins without functionality. Two distinct populations of fibroblast growth factor 2 were identified with (i) dimers to hexamers and (ii) a broad population of higher oligomeric states of membrane-associated FGF2 oligomers significantly distorting the original unfiltered histogram of all detectable oligomeric species of FGF2. The presented statistical approach is relevant for various techniques for characterizing membrane-dependent protein oligomerization.
Keywords	analytical chemistry ; fibroblast growth factor 2 ; lipids ; membrane proteins ; oligomerization ; protein subunits ; statistical analysis
Language	English
Dates of publication	2023-0506
Size	p. 8807-8815.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c05692
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Article ; Online: Organization of gangliosides into membrane nanodomains.

Sarmento, Maria J / Ricardo, Joana C / Amaro, Mariana / Šachl, Radek

FEBS letters

2020 Volume 594, Issue 22, Page(s) 3668–3697

Abstract: Gangliosides are glycosphingolipids consisting of a ceramide base and a bulky sugar chain that contains one or more sialic acids. This unique structure endows gangliosides with a strong tendency to self-aggregate in solution, as well as in cellular ... ...

Abstract	Gangliosides are glycosphingolipids consisting of a ceramide base and a bulky sugar chain that contains one or more sialic acids. This unique structure endows gangliosides with a strong tendency to self-aggregate in solution, as well as in cellular membranes, where they can form nanoscopic assemblies called ganglioside nanodomains. As gangliosides are important biological molecules involved in a number of physiological processes, characterization of their lateral organization in membranes is essential. This review aims at providing comprehensive information about the nanoscale organization of gangliosides in various synthetic models. To this end, the impact of the hydrophobic backbone and the headgroup on the segregation of gangliosides into nanodomains are discussed in detail, as well as the way in which the properties of nanodomains are affected by ligand binding. Small size makes the characterization of ganglioside nanodomains challenging, and we thus highlight the biophysical methods that have advanced this research, such as Monte Carlo Förster resonance energy transfer, atomic force microscopy and approaches based on molecular diffusion.
MeSH term(s)	Carbohydrate Sequence ; Cell Membrane/chemistry ; Fluorescence Resonance Energy Transfer ; Gangliosides/chemistry ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Lipid Bilayers/chemistry ; Microscopy, Atomic Force
Chemical Substances	Gangliosides ; Ligands ; Lipid Bilayers
Language	English
Publishing date	2020-07-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.13871
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Article ; Online: Disulfide bridge-dependent dimerization triggers FGF2 membrane translocation into the extracellular space.

Lolicato, Fabio / Steringer, Julia P / Saleppico, Roberto / Beyer, Daniel / Fernandez-Sobaberas, Jaime / Unger, Sebastian / Klein, Steffen / Riegerová, Petra / Wegehingel, Sabine / Müller, Hans-Michael / Schmitt, Xiao J / Kaptan, Shreyas / Freund, Christian / Hof, Martin / Šachl, Radek / Chlanda, Petr / Vattulainen, Ilpo / Nickel, Walter

eLife

2024 Volume 12

Abstract: Fibroblast growth factor 2 (FGF2) exits cells by direct translocation across the plasma membrane, a type I pathway of unconventional protein secretion. This process is initiated by phosphatidylinositol-4,5-bisphosphate (PI(4,5) ... ...

Abstract	Fibroblast growth factor 2 (FGF2) exits cells by direct translocation across the plasma membrane, a type I pathway of unconventional protein secretion. This process is initiated by phosphatidylinositol-4,5-bisphosphate (PI(4,5)P
MeSH term(s)	Extracellular Space ; Dimerization ; Fibroblast Growth Factor 2 ; Sodium-Potassium-Exchanging ATPase ; Disulfides
Chemical Substances	Fibroblast Growth Factor 2 (103107-01-3) ; Sodium-Potassium-Exchanging ATPase (EC 7.2.2.13) ; Disulfides
Language	English
Publishing date	2024-01-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.88579
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Article: Organization of gangliosides into membrane nanodomains

Sarmento, Maria J. / Ricardo, Joana C. / Amaro, Mariana / Šachl, Radek

FEBS letters. 2020 Nov., v. 594, no. 22

2020

Abstract: Gangliosides are glycosphingolipids consisting of a ceramide base and a bulky sugar chain that contains one or more sialic acids. This unique structure endows gangliosides with a strong tendency to self‐aggregate in solution, as well as in cellular ... ...

Abstract	Gangliosides are glycosphingolipids consisting of a ceramide base and a bulky sugar chain that contains one or more sialic acids. This unique structure endows gangliosides with a strong tendency to self‐aggregate in solution, as well as in cellular membranes, where they can form nanoscopic assemblies called ganglioside nanodomains. As gangliosides are important biological molecules involved in a number of physiological processes, characterization of their lateral organization in membranes is essential. This review aims at providing comprehensive information about the nanoscale organization of gangliosides in various synthetic models. To this end, the impact of the hydrophobic backbone and the headgroup on the segregation of gangliosides into nanodomains are discussed in detail, as well as the way in which the properties of nanodomains are affected by ligand binding. Small size makes the characterization of ganglioside nanodomains challenging, and we thus highlight the biophysical methods that have advanced this research, such as Monte Carlo Förster resonance energy transfer, atomic force microscopy and approaches based on molecular diffusion.
Keywords	atomic force microscopy ; ceramides ; energy transfer ; gangliosides ; hydrophobicity ; ligands
Language	English
Dates of publication	2020-11
Size	p. 3668-3697.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.13871
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Article ; Online: Which Moiety Drives Gangliosides to Form Nanodomains?

Davidović, David / Kukulka, Mercedes / Sarmento, Maria J / Mikhalyov, Ilya / Gretskaya, Natalia / Chmelová, Barbora / Ricardo, Joana C / Hof, Martin / Cwiklik, Lukasz / Šachl, Radek

The journal of physical chemistry letters

2023 Volume 14, Issue 25, Page(s) 5791–5797

Abstract: Gangliosides are important glycosphingolipids involved in a multitude of physiological functions. From a physicochemical standpoint, this is related to their ability to self-organize into nanoscopic domains, even at molar concentrations of one per 1000 ... ...

Abstract	Gangliosides are important glycosphingolipids involved in a multitude of physiological functions. From a physicochemical standpoint, this is related to their ability to self-organize into nanoscopic domains, even at molar concentrations of one per 1000 lipid molecules. Despite recent experimental and theoretical efforts suggesting that a hydrogen bonding network is crucial for nanodomain stability, the specific ganglioside moiety decisive for the development of these nanodomains has not yet been identified. Here, we combine an experimental technique achieving nanometer resolution (Förster resonance energy transfer analyzed by Monte Carlo simulations) with atomistic molecular dynamic simulations to demonstrate that the sialic acid (Sia) residue(s) at the oligosaccharide headgroup dominates the hydrogen bonding network between gangliosides, driving the formation of nanodomains even in the absence of cholesterol or sphingomyelin. Consequently, the clustering pattern of asialoGM
MeSH term(s)	Gangliosides/chemistry ; Sphingomyelins ; Glycosphingolipids ; G(M1) Ganglioside ; Molecular Dynamics Simulation
Chemical Substances	Gangliosides ; Sphingomyelins ; Glycosphingolipids ; G(M1) Ganglioside (37758-47-7)
Language	English
Publishing date	2023-06-16
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.3c00761
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Article: Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments

Owen, Michael C / Karner, Andreas / Šachl, Radek / Preiner, Johannes / Amaro, Mariana / Vácha, Robert

Journal of physical chemistry. 2019 Aug. 09, v. 123, no. 35

2019

Abstract: The great physiological relevance of glycolipids is being increasingly recognized, and glycolipid interactions have been shown to be central to cell–cell recognition, neuronal plasticity, protein–ligand recognition, and other important processes. However, ...

Abstract	The great physiological relevance of glycolipids is being increasingly recognized, and glycolipid interactions have been shown to be central to cell–cell recognition, neuronal plasticity, protein–ligand recognition, and other important processes. However, detailed molecular-level understanding of these processes remains to be fully resolved. Molecular dynamics simulations could reveal the details of the glycolipid interactions, but the results may be influenced by the choice of the employed force field. Here, we have compared the behavior and properties of GM1, a common, biologically important glycolipid, using the CHARMM36, OPLS, GROMOS, and Amber99-GLYCAM06 (in bilayers comprising SLIPIDS and LIPID14 lipids) force fields in bilayers comprising 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids and compared the results to atomic force microscopy and fluorescence resonance energy transfer experiments. We found discrepancies within the GM1 behavior displayed between the investigated force fields. Based on a direct comparison with complementary experimental results derived from fluorescence and AFM measurements, we recommend using the Amber99-GLYCAM force field in bilayers comprising LIPID14 or SLIPIDS lipids followed by CHARMM36 and OPLS force fields in simulations. The GROMOS force field is not recommended for reproducing the properties of the GM1 head group.
Keywords	atomic force microscopy ; energy transfer ; fluorescence ; glycolipids ; molecular dynamics ; neuroplasticity ; simulation models
Language	English
Dates of publication	2019-0809
Size	p. 7504-7517.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.9b05095
Database	NAL-Catalogue (AGRICOLA)

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