1
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Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
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2
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Knop JM, Mukherjee S, Jaworek MW, Kriegler S, Manisegaran M, Fetahaj Z, Ostermeier L, Oliva R, Gault S, Cockell CS, Winter R. Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View. Chem Rev 2023; 123:73-104. [PMID: 36260784 DOI: 10.1021/acs.chemrev.2c00491] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Elucidating the details of the formation, stability, interactions, and reactivity of biomolecular systems under extreme environmental conditions, including high salt concentrations in brines and high osmotic and high hydrostatic pressures, is of fundamental biological, astrobiological, and biotechnological importance. Bacteria and archaea are able to survive in the deep ocean or subsurface of Earth, where pressures of up to 1 kbar are reached. The deep subsurface of Mars may host high concentrations of ions in brines, such as perchlorates, but we know little about how these conditions and the resulting osmotic stress conditions would affect the habitability of such environments for cellular life. We discuss the combined effects of osmotic (salts, organic cosolvents) and hydrostatic pressures on the structure, stability, and reactivity of biomolecular systems, including membranes, proteins, and nucleic acids. To this end, a variety of biophysical techniques have been applied, including calorimetry, UV/vis, FTIR and fluorescence spectroscopy, and neutron and X-ray scattering, in conjunction with high pressure techniques. Knowledge of these effects is essential to our understanding of life exposed to such harsh conditions, and of the physical limits of life in general. Finally, we discuss strategies that not only help us understand the adaptive mechanisms of organisms that thrive in such harsh geological settings but could also have important ramifications in biotechnological and pharmaceutical applications.
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Affiliation(s)
- Jim-Marcel Knop
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Sanjib Mukherjee
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Michel W Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Simon Kriegler
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Magiliny Manisegaran
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Zamira Fetahaj
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Lena Ostermeier
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Rosario Oliva
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany.,Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
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3
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Kusumi A, Fujiwara TK, Tsunoyama TA, Kasai RS, Liu AA, Hirosawa KM, Kinoshita M, Matsumori N, Komura N, Ando H, Suzuki KGN. Defining raft domains in the plasma membrane. Traffic 2021; 21:106-137. [PMID: 31760668 DOI: 10.1111/tra.12718] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/03/2023]
Abstract
Many plasma membrane (PM) functions depend on the cholesterol concentration in the PM in strikingly nonlinear, cooperative ways: fully functional in the presence of physiological cholesterol levels (35~45 mol%), and nonfunctional below 25 mol% cholesterol; namely, still in the presence of high concentrations of cholesterol. This suggests the involvement of cholesterol-based complexes/domains formed cooperatively. In this review, by examining the results obtained by using fluorescent lipid analogs and avoiding the trap of circular logic, often found in the raft literature, we point out the fundamental similarities of liquid-ordered (Lo)-phase domains in giant unilamellar vesicles, Lo-phase-like domains formed at lower temperatures in giant PM vesicles, and detergent-resistant membranes: these domains are formed by cooperative interactions of cholesterol, saturated acyl chains, and unsaturated acyl chains, in the presence of >25 mol% cholesterol. The literature contains evidence, indicating that the domains formed by the same basic cooperative molecular interactions exist and play essential roles in signal transduction in the PM. Therefore, as a working definition, we propose that raft domains in the PM are liquid-like molecular complexes/domains formed by cooperative interactions of cholesterol with saturated acyl chains as well as unsaturated acyl chains, due to saturated acyl chains' weak multiple accommodating interactions with cholesterol and cholesterol's low miscibility with unsaturated acyl chains and TM proteins. Molecules move within raft domains and exchange with those in the bulk PM. We provide a logically established collection of fluorescent lipid probes that preferentially partition into raft and non-raft domains, as defined here, in the PM.
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Affiliation(s)
- Akihiro Kusumi
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Takahiro K Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Taka A Tsunoyama
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Rinshi S Kasai
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - An-An Liu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, P. R. China
| | - Koichiro M Hirosawa
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Naoko Komura
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu, Japan
| | - Hiromune Ando
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu, Japan
| | - Kenichi G N Suzuki
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu, Japan
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4
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Steinkühler J, Sezgin E, Urbančič I, Eggeling C, Dimova R. Mechanical properties of plasma membrane vesicles correlate with lipid order, viscosity and cell density. Commun Biol 2019; 2:337. [PMID: 31531398 PMCID: PMC6744421 DOI: 10.1038/s42003-019-0583-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 08/15/2019] [Indexed: 11/08/2022] Open
Abstract
Regulation of plasma membrane curvature and composition governs essential cellular processes. The material property of bending rigidity describes the energetic cost of membrane deformations and depends on the plasma membrane molecular composition. Because of compositional fluctuations and active processes, it is challenging to measure it in intact cells. Here, we study the plasma membrane using giant plasma membrane vesicles (GPMVs), which largely preserve the plasma membrane lipidome and proteome. We show that the bending rigidity of plasma membranes under varied conditions is correlated to readout from environment-sensitive dyes, which are indicative of membrane order and microviscosity. This correlation holds across different cell lines, upon cholesterol depletion or enrichment of the plasma membrane, and variations in cell density. Thus, polarity- and viscosity-sensitive probes represent a promising indicator of membrane mechanical properties. Additionally, our results allow for identifying synthetic membranes with a few well defined lipids as optimal plasma membrane mimetics.
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Affiliation(s)
- Jan Steinkühler
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS UK
| | - Iztok Urbančič
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS UK
- Condensed Matter Physics Department, “Jožef Stefan” Institute, Ljubljana, Slovenia
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS UK
- Institute of Applied Optics Friedrich‐Schiller‐University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Rumiana Dimova
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
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5
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Winter R. Interrogating the Structural Dynamics and Energetics of Biomolecular Systems with Pressure Modulation. Annu Rev Biophys 2019; 48:441-463. [DOI: 10.1146/annurev-biophys-052118-115601] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High hydrostatic pressure affects the structure, dynamics, and stability of biomolecular systems and is a key parameter in the context of the exploration of the origin and the physical limits of life. This review lays out the conceptual framework for exploring the conformational fluctuations, dynamical properties, and activity of biomolecular systems using pressure perturbation. Complementary pressure-jump relaxation studies are useful tools to study the kinetics and mechanisms of biomolecular phase transitions and structural transformations, such as membrane fusion or protein and nucleic acid folding. Finally, the advantages of using pressure to explore biomolecular assemblies and modulate enzymatic reactions are discussed.
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Affiliation(s)
- Roland Winter
- Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44227 Dortmund, Germany
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6
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Gaur D, Yogalakshmi Y, Kulanthaivel S, Agarwal T, Mukherjee D, Prince A, Tiwari A, Maiti TK, Pal K, Giri S, Saleem M, Banerjee I. Osteoblast-Derived Giant Plasma Membrane Vesicles Induce Osteogenic Differentiation of Human Mesenchymal Stem Cells. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Deepanjali Gaur
- Department of Biotechnology and Medical Engineering; National Institute of Technology Rourkela; Odisha 769008 India
| | - Yamini Yogalakshmi
- Department of Biotechnology and Medical Engineering; National Institute of Technology Rourkela; Odisha 769008 India
| | - Senthilguru Kulanthaivel
- Department of Biotechnology and Medical Engineering; National Institute of Technology Rourkela; Odisha 769008 India
| | - Tarun Agarwal
- Department of Biotechnology; Indian Institute of Technology Kharagpur; West Bengal 721302 India
| | - Devdeep Mukherjee
- Department of Biotechnology; Indian Institute of Technology Kharagpur; West Bengal 721302 India
| | - Ashutosh Prince
- Department of Life Science; National Institute of Technology Rourkela; Odisha 769008 India
| | - Anuj Tiwari
- Department of Life Science; National Institute of Technology Rourkela; Odisha 769008 India
| | - Tapas K. Maiti
- Department of Biotechnology; Indian Institute of Technology Kharagpur; West Bengal 721302 India
| | - Kunal Pal
- Department of Biotechnology and Medical Engineering; National Institute of Technology Rourkela; Odisha 769008 India
| | - Supratim Giri
- Department of Chemistry; National Institute of Technology Rourkela; Odisha 769008 India
| | - Mohammed Saleem
- Department of Life Science; National Institute of Technology Rourkela; Odisha 769008 India
| | - Indranil Banerjee
- Department of Biotechnology and Medical Engineering; National Institute of Technology Rourkela; Odisha 769008 India
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7
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Erwin N, Patra S, Dwivedi M, Weise K, Winter R. Influence of isoform-specific Ras lipidation motifs on protein partitioning and dynamics in model membrane systems of various complexity. Biol Chem 2017; 398:547-563. [PMID: 27977396 DOI: 10.1515/hsz-2016-0289] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/07/2016] [Indexed: 12/17/2022]
Abstract
The partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into various membrane systems, ranging from single-component fluid bilayers, binary fluid mixtures, heterogeneous raft model membranes up to complex native-like lipid mixtures (GPMVs) in the absence and presence of integral membrane proteins have been explored in the last decade in a combined chemical-biological and biophysical approach. These studies have revealed pronounced isoform-specific differences regarding the lateral distribution in membranes and formation of protein-rich membrane domains. In this context, we will also discuss the effects of lipid head group structure and charge density on the partitioning behavior of the lipoproteins. Moreover, the dynamic properties of N-Ras and K-Ras4B have been studied in different model membrane systems and native-like crowded milieus. Addition of crowding agents such as Ficoll and its monomeric unit, sucrose, gradually favors clustering of Ras proteins in forming small oligomers in the bulk; only at very high crowder concentrations association is disfavored.
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Affiliation(s)
- Nelli Erwin
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
| | - Satyajit Patra
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
| | - Mridula Dwivedi
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
| | - Katrin Weise
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
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8
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Erwin N, Sperlich B, Garivet G, Waldmann H, Weise K, Winter R. Lipoprotein insertion into membranes of various complexity: lipid sorting, interfacial adsorption and protein clustering. Phys Chem Chem Phys 2017; 18:8954-62. [PMID: 26960984 DOI: 10.1039/c6cp00563b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In a combined chemical-biological and biophysical approach we explored the membrane partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into membrane systems of different complexity, ranging from one-component lipid bilayers and anionic binary and ternary heterogeneous membrane systems even up to partitioning studies on protein-free and protein-containing giant plasma membrane vesicles (GPMVs). To yield a pictorial view of the localization process, imaging using confocal laser scanning and atomic force microscopy was performed. The results reveal pronounced isoform-specific differences regarding the lateral distribution and formation of protein-rich membrane domains. Line tension is one of the key parameters controlling not only the size and dynamic properties of segregated lipid domains but also the partitioning process of N-Ras that acts as a lineactant. The formation of N-Ras protein clusters is even recorded for almost vanishing hydrophobic mismatch. Conversely, for K-Ras4B, selective localization and clustering are electrostatically mediated by its polybasic farnesylated C-terminus. The formation of K-Ras4B clusters is also observed for the multi-component GPMV membrane, i.e., it seems to be a general phenomenon, largely independent of the details of the membrane composition, including the anionic charge density of lipid headgroups. Our data indicate that unspecific and entropy-driven membrane-mediated interactions play a major role in the partitioning behavior, thus relaxing the need for a multitude of fine-tuned interactions. Such a scenario seems also to be reasonable recalling the high dynamic nature of cellular membranes. Finally, we note that even relatively simple models of heterogeneous membranes are able to reproduce many of the properties of much more complex biological membranes.
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Affiliation(s)
- Nelli Erwin
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, D-44221 Dortmund, Germany.
| | - Benjamin Sperlich
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, D-44221 Dortmund, Germany.
| | - Guillaume Garivet
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany and Faculty of Chemistry and Chemical Biology, Department of Chemical Biology, TU Dortmund University, D-44221 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany and Faculty of Chemistry and Chemical Biology, Department of Chemical Biology, TU Dortmund University, D-44221 Dortmund, Germany
| | - Katrin Weise
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, D-44221 Dortmund, Germany.
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, D-44221 Dortmund, Germany.
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Houston JE, Kraft M, Scherf U, Evans RC. Sequential detection of multiple phase transitions in model biological membranes using a red-emitting conjugated polyelectrolyte. Phys Chem Chem Phys 2016; 18:12423-7. [DOI: 10.1039/c6cp01553k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Charge-mediated assembly of an anionic poly(thiophene) leads to a highly sensitive probe of membrane order.
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Affiliation(s)
- Judith E. Houston
- School of Chemistry
- University of Dublin
- Trinity College
- Dublin 2
- Ireland
| | - Mario Kraft
- Macromolecular Chemistry Group (buwmacro) and Institute for Polymer Technology
- Bergische Universität Wuppertal
- Wuppertal
- Germany
| | - Ullrich Scherf
- Macromolecular Chemistry Group (buwmacro) and Institute for Polymer Technology
- Bergische Universität Wuppertal
- Wuppertal
- Germany
| | - Rachel C. Evans
- School of Chemistry
- University of Dublin
- Trinity College
- Dublin 2
- Ireland
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