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Bespalova M, Öz R, Westerlund F, Krishnan M. Single-Molecule Trapping and Measurement in a Nanostructured Lipid Bilayer System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13923-13934. [PMID: 36326814 PMCID: PMC9671048 DOI: 10.1021/acs.langmuir.2c02203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The repulsive electrostatic force between a biomolecule and a like-charged surface can be geometrically tailored to create spatial traps for charged molecules in solution. Using a parallel-plate system composed of silicon dioxide surfaces, we recently demonstrated single-molecule trapping and high precision molecular charge measurements in a nanostructured free energy landscape. Here we show that surfaces coated with charged lipid bilayers provide a system with tunable surface properties for molecular electrometry experiments. Working with molecular species whose effective charge and geometry are well-defined, we demonstrate the ability to quantitatively probe the electrical charge density of a supported lipid bilayer. Our findings indicate that the fraction of charged lipids in nanoslit lipid bilayers can be significantly different from that in the precursor lipid mixtures used to generate them. We also explore the temporal stability of bilayer properties in nanofluidic systems. Beyond their relevance in molecular measurement, such experimental systems offer the opportunity to examine lipid bilayer formation and wetting dynamics on nanostructured surfaces.
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Affiliation(s)
- Maria Bespalova
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
| | - Robin Öz
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Fredrik Westerlund
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Madhavi Krishnan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
- The
Kavli Institute for Nanoscience Discovery, Sherrington Road, OxfordOX1 3QU, United Kingdom
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2
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Kloes G, Bennett TJD, Chapet-Batlle A, Behjatian A, Turberfield AJ, Krishnan M. Far-Field Electrostatic Signatures of Macromolecular 3D Conformation. NANO LETTERS 2022; 22:7834-7840. [PMID: 36125326 PMCID: PMC9562458 DOI: 10.1021/acs.nanolett.2c02485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In solution as in vacuum, the electrostatic field distribution in the vicinity of a charged object carries information on its three-dimensional geometry. We report on an experimental study exploring the effect of molecular shape on long-range electrostatic interactions in solution. Working with DNA nanostructures carrying approximately equal amounts of total charge but each in a different three-dimensional conformation, we demonstrate that the geometry of the distribution of charge in a molecule has substantial impact on its electrical interactions. For instance, a tetrahedral structure, which is the most compact distribution of charge we tested, can create a far-field effect that is effectively identical to that of a rod-shaped molecule carrying half the amount of total structural charge. Our experiments demonstrate that escape-time electrometry (ETe) furnishes a rapid and facile method to screen and identify 3D conformations of charged biomolecules or molecular complexes in solution.
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Affiliation(s)
- Gunnar Kloes
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Timothy J. D. Bennett
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Alma Chapet-Batlle
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Ali Behjatian
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Andrew J. Turberfield
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
- The Kavli
Institute for Nanoscience Discovery, Sherrington Road, Oxford OX1 3QU, United Kingdom
| | - Madhavi Krishnan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
- The Kavli
Institute for Nanoscience Discovery, Sherrington Road, Oxford OX1 3QU, United Kingdom
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3
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Bespalova M, Behjatian A, Karedla N, Walker-Gibbons R, Krishnan M. Opto-Electrostatic Determination of Nucleic Acid Double-Helix Dimensions and the Structure of the Molecule–Solvent Interface. Macromolecules 2022; 55:6200-6210. [PMID: 35910310 PMCID: PMC9330769 DOI: 10.1021/acs.macromol.2c00657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A DNA molecule is
highly electrically charged in solution. The
electrical potential at the molecular surface is known to vary strongly
with the local geometry of the double helix and plays a pivotal role
in DNA–protein interactions. Further out from the molecular
surface, the electrical field propagating into the surrounding electrolyte
bears fingerprints of the three-dimensional arrangement of the charged
atoms in the molecule. However, precise extraction of the structural
information encoded in the electrostatic “far field”
has remained experimentally challenging. Here, we report an optical
microscopy-based approach that detects the field distribution surrounding
a charged molecule in solution, revealing geometric features such
as the radius and the average rise per basepair of the double helix
with up to sub-Angstrom precision, comparable with traditional molecular
structure determination techniques like X-ray crystallography and
nuclear magnetic resonance. Moreover, measurement of the helical radius
furnishes an unprecedented view of both hydration and the arrangement
of cations at the molecule–solvent interface. We demonstrate
that a probe in the electrostatic far field delivers structural and
chemical information on macromolecules, opening up a new dimension
in the study of charged molecules and interfaces in solution.
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Affiliation(s)
- Maria Bespalova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Narain Karedla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Rowan Walker-Gibbons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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4
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Behjatian A, Krishnan M. Electrostatic free energies carry structural information on nucleic acid molecules in solution. J Chem Phys 2022; 156:134201. [DOI: 10.1063/5.0080008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Over the last several decades, a range of experimental techniques from x-ray crystallography and atomic force microscopy to nuclear magnetic resonance and small angle x-ray scattering have probed nucleic acid structure and conformation with high resolution both in the condensed state and in solution. We present a computational study that examines the prospect of using electrostatic free energy measurements to detect 3D conformational properties of nucleic acid molecules in solution. As an example, we consider the conformational difference between A- and B-form double helices whose structures differ in the values of two key parameters—the helical radius and rise per basepair. Mapping the double helix onto a smooth charged cylinder reveals that electrostatic free energies for molecular helices can, indeed, be described by two parameters: the axial charge spacing and the radius of a corresponding equivalent cylinder. We show that electrostatic free energies are also sensitive to the local structure of the molecular interface with the surrounding electrolyte. A free energy measurement accuracy of 1%, achievable using the escape time electrometry (ET e) technique, could be expected to offer a measurement precision on the radius of the double helix of approximately 1 Å. Electrostatic free energy measurements may, therefore, not only provide information on the structure and conformation of biomolecules but could also shed light on the interfacial hydration layer and the size and arrangement of counterions at the molecular interface in solution.
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Affiliation(s)
- Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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5
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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6
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Polson JM, Rehel DA. Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement. SOFT MATTER 2021; 17:5792-5805. [PMID: 34028486 DOI: 10.1039/d1sm00308a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as flexible bead-spring chains, and the box has a square cross-section of side length L and a height that is small enough to compress the polymers in that dimension. For sufficiently large L, the system behaviour approaches that of an isolated polymer in a slit. However, the combined effects of crowding and confinement on the polymer organization, conformation and equilibrium dynamics become significant when where is the transverse radius of gyration for a slit geometry. In this regime, the centre-of-mass probability distribution in the transverse plane exhibits a depletion zone near the centre of the cavity (except at very small L) and a 4-fold symmetry with quasi-discrete positions. Reduction in polymer size with decreasing L arises principally from confinement rather than inter-polymer crowding. By contrast, polymer diffusion and internal motion are strongly affected by inter-polymer crowding. The two polymers tend to occupy opposite positions relative to the box centre, about which they diffuse relatively freely. Qualitatively, this static and dynamical behaviour differs significantly from that previously observed for confinement of two polymers to a narrow channel. The simulation results for a suitably chosen box width are qualitatively consistent with results from a recent experimental study of two λ-DNA chains confined to a nanofluidic cavity.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada.
| | - Desiree A Rehel
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada.
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Avni Y, Komura S, Andelman D. Brownian motion of a charged colloid in restricted confinement. Phys Rev E 2021; 103:042607. [PMID: 34005855 DOI: 10.1103/physreve.103.042607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/23/2021] [Indexed: 11/07/2022]
Abstract
We study the Brownian motion of a charged colloid, confined between two charged walls, for small separation between the colloid and the walls. The system is embedded in an ionic solution. The combined effect of electrostatic repulsion and reduced diffusion due to hydrodynamic forces results in a specific motion in the direction perpendicular to the confining walls. The apparent diffusion coefficient at short times as well as the diffusion characteristic time are shown to follow a sigmoid curve as a function of a dimensionless parameter. This parameter depends on the electrostatic properties and can be controlled by tuning the solution ionic strength. At low ionic strength, the colloid moves faster and is localized, while at high ionic strength it moves slower and explores a wider region between the walls, resulting in a larger diffusion characteristic time.
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Affiliation(s)
- Yael Avni
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.,Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Shigeyuki Komura
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - David Andelman
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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8
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Bespalova MI, Mahanta S, Krishnan M. Single-molecule trapping and measurement in solution. Curr Opin Chem Biol 2019; 51:113-121. [DOI: 10.1016/j.cbpa.2019.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
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9
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Ruggeri F, Krishnan M. Entropic Trapping of a Singly Charged Molecule in Solution. NANO LETTERS 2018; 18:3773-3779. [PMID: 29688720 DOI: 10.1021/acs.nanolett.8b01011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate the ability to confine a single molecule in solution by spatial modulation of its local configurational entropy. Previously we established electrostatic trapping of a charged macromolecule by geometric tailoring of a repulsive electrical interaction potential in a parallel plate system. However, since the lifetime of the trapped state depends exponentially on the electrical charge of the molecule, the electrostatic interaction alone is often insufficient in magnitude to stably confine molecules carrying a net charge of magnitude ≤5 e. Here we show that the configurational entropy of a thermally fluctuating molecule in a geometrically modulated system can be exploited to spatially confine weakly charged molecules in solution. Measurement of the configurational entropy contribution reveals good agreement with theoretical expectations. This additional translational contribution to the total free energy facilitates direct optical imaging and measurement of the effective charge of molecules on the size scale of ∼1 nm and a charge as low as 1 e, physical properties comparable with those of a monovalent ion in solution.
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Affiliation(s)
- Francesca Ruggeri
- Department of Chemistry , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
| | - Madhavi Krishnan
- Department of Chemistry , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
- Department of Physics , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
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