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Bashkirov PV, Kuzmin PI, Chekashkina K, Arrasate P, Vera Lillo J, Shnyrova AV, Frolov VA. Reconstitution and real-time quantification of membrane remodeling by single proteins and protein complexes. Nat Protoc 2020; 15:2443-2469. [PMID: 32591769 PMCID: PMC10839814 DOI: 10.1038/s41596-020-0337-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/14/2020] [Indexed: 02/08/2023]
Abstract
Cellular membrane processes, from signal transduction to membrane fusion and fission, depend on acute membrane deformations produced by small and short-lived protein complexes working in conditions far from equilibrium. Real-time monitoring and quantitative assessment of such deformations are challenging; hence, mechanistic analyses of the protein action are commonly based on ensemble averaging, which masks important mechanistic details of the action. In this protocol, we describe how to reconstruct and quantify membrane remodeling by individual proteins and small protein complexes in vitro, using an ultra-short (80- to 400-nm) lipid nanotube (usNT) template. We use the luminal conductance of the usNT as the real-time reporter of the protein interaction(s) with the usNT. We explain how to make and calibrate the usNT template to achieve subnanometer precision in the geometrical assessment of the molecular footprints on the nanotube membrane. We next demonstrate how membrane deformations driven by purified proteins implicated in cellular membrane remodeling can be analyzed at a single-molecule level. The preparation of one usNT takes ~1 h, and the shortest procedure yielding the basic geometrical parameters of a small protein complex takes 10 h.
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Affiliation(s)
- Pavel V Bashkirov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia.
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudnyy, Russia.
| | - Peter I Kuzmin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ksenia Chekashkina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Pedro Arrasate
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Javier Vera Lillo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Anna V Shnyrova
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Vadim A Frolov
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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Stanley C, Rau DC. Evidence for water structuring forces between surfaces. Curr Opin Colloid Interface Sci 2011; 16:551-556. [PMID: 22125414 DOI: 10.1016/j.cocis.2011.04.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Structured water on apposing surfaces can generate significant energies due to reorganization and displacement of water as the surfaces encounter each other. Force measurements on a multitude of biological structures using the osmotic stress technique have elucidated commonalities that point toward an underlying hydration force. In this review, the forces of two contrasting systems are considered in detail: highly charged DNA and nonpolar, uncharged hydroxypropyl cellulose. Conditions for both net repulsion and attraction, along with the measured exclusion of chemically different solutes from these macromolecular surfaces, are explored and demonstrate common features consistent with a hydration force origin. Specifically, the observed interaction forces can be reduced to the effects of perturbing structured surface water.
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Affiliation(s)
- Christopher Stanley
- Neutron Scattering Science Division, Oak Ridge National Laboratory, PO Box 2008 MSC 6473, Oak Ridge, TN 37831
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Bonnet-Gonnet C, Leikin S, Chi S, Rau DC, Parsegian VA. Measurement of Forces between Hydroxypropylcellulose Polymers: Temperature Favored Assembly and Salt Exclusion. J Phys Chem B 2001. [DOI: 10.1021/jp002531f] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cecile Bonnet-Gonnet
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-0924
| | - Sergey Leikin
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-0924
| | - Sulene Chi
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-0924
| | - Donald C. Rau
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-0924
| | - V. Adrian Parsegian
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-0924
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Chapter 4 Hydration, Curvature, and Bending Elasticity of Phospholipid Monolayers. CURRENT TOPICS IN MEMBRANES 1997. [DOI: 10.1016/s0070-2161(08)60208-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Patrick HN, Warr GG. Counterion Binding and Regulation of Interactions between Charged Bilayers. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp961157+] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Leikin S, Rau DC, Parsegian VA. Direct measurement of forces between self-assembled proteins: temperature-dependent exponential forces between collagen triple helices. Proc Natl Acad Sci U S A 1994; 91:276-80. [PMID: 8278378 PMCID: PMC42930 DOI: 10.1073/pnas.91.1.276] [Citation(s) in RCA: 124] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We report direct measurements of force vs. separation between self-assembled proteins. These forces are observed between collagen triple helices in native and reconstituted fibers. They are a combination of a short-range repulsion, which varies exponentially over at least five decay lengths, and an inferred, longer-ranged attraction responsible for spontaneous assembly. From 5 degrees C to 35 degrees C the relative contribution of the attraction to the net force increases with temperature. These forces are strikingly similar to the "hydration" forces measured between several other linear macromolecules (DNA, polysaccharides) and between lipid bilayer membranes. The decay length of the repulsive force agrees well with a theoretical estimate based on axial periodicity of the triple helix, suggesting another connection between molecular architecture and protein-protein interaction.
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Affiliation(s)
- S Leikin
- Laboratory of Structural Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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