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Thakur GCN, Uday A, Jurkiewicz P. FRET-GP - A Local Measure of the Impact of Transmembrane Peptide on Lipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18390-18402. [PMID: 38048524 DOI: 10.1021/acs.langmuir.3c02505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Reconstitution of a transmembrane protein in model lipid systems allows studying its structure and dynamics in isolation from the complexity of the natural environment. This approach also provides a well-defined environment for studying the interactions of proteins with lipids. In this work, we describe the FRET-GP method, which utilizes Förster resonance energy transfer (FRET) to specifically probe the nanoenvironment of a transmembrane domain. The tryptophan residues flanking this domain act as efficient FRET donors, while Laurdan acts as acceptor. The fluorescence of this solvatochromic probe is quantified using generalized polarization (GP) to report on lipid mobility in the vicinity of the transmembrane domain. We applied FRET-GP to study the transmembrane peptide WALP incorporated in liposomes. We found that the direct excitation of Laurdan to its second singlet state strongly contributes to GP values measured in FRET conditions. Removal of this parasitic contribution was essential for proper determination of GPFRET - the local analogue of classical GP parameter. The presence of WALP significantly increased both parameters but the local effects were considerably stronger (GPFRET ≫ GP). We conclude that WALP restricts lipid movement in its vicinity, inducing lateral inhomogeneity in membrane fluidity. WALP was also found to influence lipid phase transition. Our findings demonstrated that FRET-GP simultaneously provides local and global results, thereby enhancing the depth of information obtained from the measurement. We highlight the simplicity and sensitivity of the method, but also discuss its potential and limitations in studying protein-lipid interactions.
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Affiliation(s)
- Garima C N Thakur
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Arunima Uday
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
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2
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Clayton AHA. Spectral Relaxation Imaging Microscopy II: Complex Dynamics. Int J Mol Sci 2023; 24:12271. [PMID: 37569641 PMCID: PMC10419246 DOI: 10.3390/ijms241512271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The dynamics of condensed matter can be measured by the time-dependent Stokes shift of a suitable fluorescent probe. The time-dependent spectral correlation function is typically described by one or more spectral relaxation correlation times, which, in liquid solvents, characterize the timescales of the dipolar relaxation processes around the excited-state probe. The phasor plot provides a powerful approach to represent and analyze time and frequency-domain data acquired as images, thus providing a spatial map of spectral dynamics in a complex structure such as a living cell. Measurements of the phase and modulation at two emission wavelength channels were shown to be sufficient to extract a single excited-state lifetime and a single spectral relaxation correlation time, supplying estimates of the mean rate of excited-state depopulation and the mean rate of spectral shift. In the present contribution, two more issues were addressed. First, the provision of analytic formulae allowing extraction of the initial generalized polarization and the relaxed generalized polarization, which characterize the fluorescence spectrum of the unrelaxed state and the fully relaxed state. Second, improved methods of model discrimination and model parameter extraction for more complex spectral relaxation phenomena. The analysis workflow was illustrated with examples from the literature.
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Affiliation(s)
- Andrew H A Clayton
- Cell Biophysics Laboratory, Department of Physics and Astronomy, Optical Sciences Centre, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Melbourne 3122, Australia
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3
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Modulation of Anionic Lipid Bilayers by Specific Interplay of Protons and Calcium Ions. Biomolecules 2022; 12:biom12121894. [PMID: 36551322 PMCID: PMC9775051 DOI: 10.3390/biom12121894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Biomembranes, important building blocks of living organisms, are often exposed to large local fluctuations of pH and ionic strength. To capture changes in the membrane organization under such harsh conditions, we investigated the mobility and hydration of zwitterionic and anionic lipid bilayers upon elevated H3O+ and Ca2+ content by the time-dependent fluorescence shift (TDFS) technique. While the zwitterionic bilayers remain inert to lower pH and increased calcium concentrations, anionic membranes are responsive. Specifically, both bilayers enriched in phosphatidylserine (PS) and phosphatidylglycerol (PG) become dehydrated and rigidified at pH 4.0 compared to at pH 7.0. However, their reaction to the gradual Ca2+ increase in the acidic environment differs. While the PG bilayers exhibit strong rehydration and mild loosening of the carbonyl region, restoring membrane properties to those observed at pH 7.0, the PS bilayers remain dehydrated with minor bilayer stiffening. Molecular dynamics (MD) simulations support the strong binding of H3O+ to both PS and PG. Compared to PS, PG exhibits a weaker binding of Ca2+ also at a low pH.
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Ragaller F, Andronico L, Sykora J, Kulig W, Rog T, Urem YB, Abhinav, Danylchuk DI, Hof M, Klymchenko A, Amaro M, Vattulainen I, Sezgin E. Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. Open Biol 2022; 12:220175. [PMID: 36099931 PMCID: PMC9470265 DOI: 10.1098/rsob.220175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades, several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis versus trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.
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Affiliation(s)
- Franziska Ragaller
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Luca Andronico
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Jan Sykora
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Rog
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Yagmur Balim Urem
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Abhinav
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Andrey Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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Tempra C, Scollo F, Pannuzzo M, Lolicato F, La Rosa C. A unifying framework for amyloid-mediated membrane damage: The lipid-chaperone hypothesis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140767. [PMID: 35144022 DOI: 10.1016/j.bbapap.2022.140767] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Over the past thirty years, researchers have highlighted the role played by a class of proteins or polypeptides that forms pathogenic amyloid aggregates in vivo, including i) the amyloid Aβ peptide, which is known to form senile plaques in Alzheimer's disease; ii) α-synuclein, responsible for Lewy body formation in Parkinson's disease and iii) IAPP, which is the protein component of type 2 diabetes-associated islet amyloids. These proteins, known as intrinsically disordered proteins (IDPs), are present as highly dynamic conformational ensembles. IDPs can partially (mis) fold into (dys) functional conformations and accumulate as amyloid aggregates upon interaction with other cytosolic partners such as proteins or lipid membranes. In addition, an increasing number of reports link the toxicity of amyloid proteins to their harmful effects on membrane integrity. Still, the molecular mechanism underlying the amyloidogenic proteins transfer from the aqueous environment to the hydrocarbon core of the membrane is poorly understood. This review starts with a historical overview of the toxicity models of amyloidogenic proteins to contextualize the more recent lipid-chaperone hypothesis. Then, we report the early molecular-level events in the aggregation and ion-channel pore formation of Aβ, IAPP, and α-synuclein interacting with model membranes, emphasizing the complexity of these processes due to their different spatial-temporal resolutions. Next, we underline the need for a combined experimental and computational approach, focusing on the strengths and weaknesses of the most commonly used techniques. Finally, the last two chapters highlight the crucial role of lipid-protein complexes as molecular switches among ion-channel-like formation, detergent-like, and fibril formation mechanisms and their implication in fighting amyloidogenic diseases.
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Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
| | - Federica Scollo
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Pannuzzo
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
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7
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Schachter I, Paananen RO, Fábián B, Jurkiewicz P, Javanainen M. The Two Faces of the Liquid Ordered Phase. J Phys Chem Lett 2022; 13:1307-1313. [PMID: 35104407 PMCID: PMC8842317 DOI: 10.1021/acs.jpclett.1c03712] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Coexisting liquid ordered (Lo) and liquid disordered (Ld) lipid phases in synthetic and plasma membrane-derived vesicles are commonly used to model the heterogeneity of biological membranes, including their putative ordered rafts. However, raft-associated proteins exclusively partition to the Ld and not the Lo phase in these model systems. We believe that the difference stems from the different microscopic structures of the lipid rafts at physiological temperature and the Lo phase studied at room temperature. To probe this structural diversity across temperatures, we performed atomistic molecular dynamics simulations, differential scanning calorimetry, and fluorescence spectroscopy on Lo phase membranes. Our results suggest that raft-associated proteins are excluded from the Lo phase at room temperature due to the presence of a stiff, hexagonally packed lipid structure. This structure melts upon heating, which could lead to the preferential solvation of proteins by order-preferring lipids. This structural transition is manifested as a subtle crossover in membrane properties; yet, both temperature regimes still fulfill the definition of the Lo phase. We postulate that in the compositionally complex plasma membrane and in vesicles derived therefrom, both molecular structures can be present depending on the local lipid composition. These structural differences must be taken into account when using synthetic or plasma membrane-derived vesicles as a model for cellular membrane heterogeneity below the physiological temperature.
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Affiliation(s)
- Itay Schachter
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
- Institute
of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger
Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Riku O. Paananen
- Department
of Chemistry, FI-00014 University of Helsinki, Helsinki, Finland
- Department
of Ophthalmology, FI-00014 University of
Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Balázs Fábián
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Piotr Jurkiewicz
- J.
Heyrovský Institute of Physical Chemistry of the Czech Academy
of Sciences, Dolejškova
2155/3, CZ-18223 Prague 8, Czech Republic
- E-mail:
| | - Matti Javanainen
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
- Institute
of Biotechnology, FI-00014 University of
Helsinki, Helsinki, Finland
- E-mail:
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