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Article ; Online: Unravelling the structural complexity of protein-lipid interactions with neutron reflectometry.

Clifton, Luke A

2021 Volume 49, Issue 4, Page(s) 1537–1546

Abstract: Neutron reflectometry (NR) is a large-facility technique used to examine structure at interfaces. In this brief review an introduction to the utilisation of NR in the study of protein-lipid interactions is given. Cold neutron beams penetrate matter ... ...

Abstract	Neutron reflectometry (NR) is a large-facility technique used to examine structure at interfaces. In this brief review an introduction to the utilisation of NR in the study of protein-lipid interactions is given. Cold neutron beams penetrate matter deeply, have low energies, wavelengths in the Ångstrom regime and are sensitive to light elements. High differential hydrogen sensitivity (between protium and deuterium) enables solution and sample isotopic labelling to be utilised to enhance or diminish the scattering signal of individual components within complex biological structures. The combination of these effects means NR can probe buried structures such as those at the solid-liquid interface and encode molecular level structural information on interfacial protein-lipid complexes revealing the relative distribution of components as well as the overall structure. Model biological membrane sample systems can be structurally probed to examine phenomena such as antimicrobial mode of activity, as well as structural and mechanistic properties peripheral/integral proteins within membrane complexes. Here, the example of the antimicrobial protein α1-purothionin binding to a model Gram negative bacterial outer membrane is used to highlight the utilisation of this technique, detailing how changes in the protein/lipid distributions across the membrane before and after the protein interaction can be easily encoded using hydrogen isotope labelling.
Language	English
Publishing date	2021-07-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20201071
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Article ; Online: Modeling the effects of malaria on red blood cell binding at the vascular interface.

Clifton, Luke A

Biophysical journal

2021 Volume 120, Issue 16, Page(s) 3240–3241

MeSH term(s)	Erythrocytes ; Humans ; Malaria
Language	English
Publishing date	2021-07-09
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.07.004
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Zs.A 235: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 2: Show issues

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Article ; Online: Exploiting neutron scattering contrast variation in biological membrane studies.

Lakey, Jeremy H / Paracini, Nicolò / Clifton, Luke A

Biophysics reviews

2022 Volume 3, Issue 2, Page(s) 21307

Abstract: Biological membranes composed of lipids and proteins are central for the function of all cells and individual components, such as proteins, that are readily studied by a range of structural approaches, including x-ray crystallography and cryo-electron ... ...

Abstract	Biological membranes composed of lipids and proteins are central for the function of all cells and individual components, such as proteins, that are readily studied by a range of structural approaches, including x-ray crystallography and cryo-electron microscopy. However, the study of complex molecular mixtures within the biological membrane structure and dynamics requires techniques that can study nanometer thick molecular bilayers in an aqueous environment at ambient temperature and pressure. Neutron methods, including scattering and spectroscopic approaches, are useful since they can measure structure and dynamics while also being able to penetrate sample holders and cuvettes. The structural approaches, such as small angle neutron scattering and neutron reflectometry, detect scattering caused by the difference in neutron contrast (scattering length) between different molecular components such as lipids or proteins. Usually, the bigger the contrast, the clearer the structural data, and this review uses examples from our research to illustrate how contrast can be increased to allow the structures of individual membrane components to be resolved. Most often this relies upon the use of deuterium in place of hydrogen, but we also discuss the use of magnetic contrast and other elements with useful scattering length values.
Language	English
Publishing date	2022-06-14
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2688-4089
ISSN (online)	2688-4089
DOI	10.1063/5.0091372
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Article ; Online: Correction to "Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques".

Qian, Shuo / Sharma, Veerendra Kumar / Clifton, Luke A

Langmuir : the ACS journal of surfaces and colloids

2021 Volume 37, Issue 17, Page(s) 5445

Language	English
Publishing date	2021-04-22
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.1c00919
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Article ; Online: Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques.

Qian, Shuo / Sharma, Veerendra Kumar / Clifton, Luke A

Langmuir : the ACS journal of surfaces and colloids

2020 Volume 36, Issue 50, Page(s) 15189–15211

Abstract: The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and ... ...

Abstract	The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H
Language	English
Publishing date	2020-12-10
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.0c02516
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Article ; Online: Studying the surfaces of bacteria using neutron scattering: finding new openings for antibiotics.

Paracini, Nicolò / Clifton, Luke A / Lakey, Jeremy H

Biochemical Society transactions

2020 Volume 48, Issue 5, Page(s) 2139–2149

Abstract: The use of neutrons as a scattering probe to investigate biological membranes has steadily grown in the past three decades, shedding light on the structure and behaviour of this ubiquitous and fundamental biological barrier. Meanwhile, the rise of ... ...

Abstract	The use of neutrons as a scattering probe to investigate biological membranes has steadily grown in the past three decades, shedding light on the structure and behaviour of this ubiquitous and fundamental biological barrier. Meanwhile, the rise of antibiotic resistance has catalysed a renewed interest in understanding the mechanisms underlying the dynamics of antibiotics interaction with the bacterial cell envelope. It is widely recognised that the key reason behind the remarkable success of Gram-negative pathogens in developing antibiotic resistance lies in the effectiveness of their outer membrane (OM) in defending the cell from antibacterial compounds. Critical to its function, the highly asymmetric lipid distribution between the inner and outer bilayer leaflets of the OM, adds an extra level of complexity to the study of this crucial defence barrier. Here we review the opportunities offered by neutron scattering techniques, in particular reflectometry, to provide structural information on the interactions of antimicrobials with in vitro models of the OM. The differential sensitivity of neutrons towards hydrogen and deuterium makes them a unique probe to study the structure and behaviour of asymmetric membranes. Molecular-level understanding of the interactions between antimicrobials and the Gram-negative OM provides valuable insights that can aid drug development and broaden our knowledge of this critically important biological barrier.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Bacterial Outer Membrane Proteins/metabolism ; Biophysics ; Cell Membrane/drug effects ; Cell Membrane/metabolism ; Deuterium/chemistry ; Gram-Negative Bacteria/metabolism ; Hydrogen/chemistry ; Lipid Bilayers/chemistry ; Lipopolysaccharides/chemistry ; Neutrons ; Scattering, Radiation
Chemical Substances	Anti-Bacterial Agents ; Bacterial Outer Membrane Proteins ; Lipid Bilayers ; Lipopolysaccharides ; Hydrogen (7YNJ3PO35Z) ; Deuterium (AR09D82C7G)
Language	English
Publishing date	2020-10-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20200320
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Article ; Online: Fully Aqueous Self-Assembly of a Gold-Nanoparticle-Based Pathogen Sensor.

Robson, Timothy / Shah, Deepan S H / Welbourn, Rebecca J L / Phillips, Sion R / Clifton, Luke A / Lakey, Jeremy H

International journal of molecular sciences

2023 Volume 24, Issue 8

Abstract: Surface plasmon resonance (SPR) is a very sensitive measure of biomolecular interactions but is generally too expensive for routine analysis of clinical samples. Here we demonstrate the simplified formation of virus-detecting gold nanoparticle (AuNP) ... ...

Abstract	Surface plasmon resonance (SPR) is a very sensitive measure of biomolecular interactions but is generally too expensive for routine analysis of clinical samples. Here we demonstrate the simplified formation of virus-detecting gold nanoparticle (AuNP) assemblies on glass using only aqueous buffers at room temperature. The AuNP assembled on silanized glass and displayed a distinctive absorbance peak due to the localized SPR (LSPR) response of the AuNPs. Next, assembly of a protein engineering scaffold was followed using LSPR and a sensitive neutron reflectometry approach, which measured the formation and structure of the biological layer on the spherical AuNP. Finally, the assembly and function of an artificial flu sensor layer consisting of an in vitro-selected single-chain antibody (scFv)-membrane protein fusion was followed using the LSPR response of AuNPs within glass capillaries. In vitro selection avoids the need for separate animal-derived antibodies and allows for the rapid production of low-cost sensor proteins. This work demonstrates a simple approach to forming oriented arrays of protein sensors on nanostructured surfaces that uses (i) an easily assembled AuNP silane layer, (ii) self-assembly of an oriented protein layer on AuNPs, and (iii) simple highly specific artificial receptor proteins.
MeSH term(s)	Animals ; Gold/chemistry ; Metal Nanoparticles/chemistry ; Surface Plasmon Resonance ; Antibodies ; Membrane Proteins
Chemical Substances	Gold (7440-57-5) ; Antibodies ; Membrane Proteins
Language	English
Publishing date	2023-04-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24087599
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Article ; Online: Creation of distinctive Bax-lipid complexes at mitochondrial membrane surfaces drives pore formation to initiate apoptosis.

Clifton, Luke A / Wacklin-Knecht, Hanna P / Ådén, Jörgen / Mushtaq, Ameeq Ul / Sparrman, Tobias / Gröbner, Gerhard

Science advances

2023 Volume 9, Issue 22, Page(s) eadg7940

Abstract: Apotosis is an essential process tightly regulated by the Bcl-2 protein family where proapoptotic Bax triggers cell death by perforating the mitochondrial outer membrane. Although intensively studied, the molecular mechanism by which these proteins ... ...

Abstract	Apotosis is an essential process tightly regulated by the Bcl-2 protein family where proapoptotic Bax triggers cell death by perforating the mitochondrial outer membrane. Although intensively studied, the molecular mechanism by which these proteins create apoptotic pores remains elusive. Here, we show that Bax creates pores by extracting lipids from outer mitochondrial membrane mimics by formation of Bax/lipid clusters that are deposited on the membrane surface. Time-resolved neutron reflectometry and Fourier transform infrared spectroscopy revealed two kinetically distinct phases in the pore formation process, both of which were critically dependent on cardiolipin levels. The initially fast adsorption of Bax on the mitochondrial membrane surface is followed by a slower formation of pores and Bax-lipid clusters on the membrane surface. Our findings provide a robust molecular understanding of mitochondrial membrane perforation by cell-killing Bax protein and illuminate the initial phases of programmed cellular death.
MeSH term(s)	Mitochondrial Membranes/metabolism ; bcl-2-Associated X Protein/chemistry ; bcl-2-Associated X Protein/metabolism ; Apoptosis/physiology ; Cardiolipins/metabolism
Chemical Substances	bcl-2-Associated X Protein ; Cardiolipins
Language	English
Publishing date	2023-06-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adg7940
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Article ; Online: An octameric PqiC toroid stabilises the outer-membrane interaction of the PqiABC transport system.

Cooper, Benjamin F / Ratkevičiūtė, Giedrė / Clifton, Luke A / Johnston, Hannah / Holyfield, Rachel / Hardy, David J / Caulton, Simon G / Chatterton, William / Sridhar, Pooja / Wotherspoon, Peter / Hughes, Gareth W / Hall, Stephen Cl / Lovering, Andrew L / Knowles, Timothy J

EMBO reports

2024 Volume 25, Issue 1, Page(s) 82–101

Abstract: The E. coli Paraquat Inducible (Pqi) Pathway is a putative Gram-negative phospholipid transport system. The pathway comprises three components: an integral inner membrane protein (PqiA), a periplasmic spanning MCE family protein (PqiB) and an outer ... ...

Abstract	The E. coli Paraquat Inducible (Pqi) Pathway is a putative Gram-negative phospholipid transport system. The pathway comprises three components: an integral inner membrane protein (PqiA), a periplasmic spanning MCE family protein (PqiB) and an outer membrane lipoprotein (PqiC). Interactions between all complex components, including stoichiometry, remain uncharacterised; nevertheless, once assembled into their quaternary complex, the trio of Pqi proteins are anticipated to provide a continuous channel between the inner and outer membranes of diderms. Here, we present X-ray structures of both the native and a truncated, soluble construct of the PqiC lipoprotein, providing insight into its biological assembly, and utilise neutron reflectometry to characterise the nature of the PqiB-PqiC-membrane interaction. Finally, we employ phenotypic complementation assays to probe specific PqiC residues, which imply the interaction between PqiB and PqiC is less intimate than previously anticipated.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Membrane Proteins/metabolism ; Biological Transport ; Lipoproteins/metabolism
Chemical Substances	Escherichia coli Proteins ; Membrane Proteins ; Lipoproteins
Language	English
Publishing date	2024-01-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.1038/s44319-023-00014-4
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Zs.A 5433: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Large scale model lipid membrane movement induced by a cation switch.

John, Laura H / Preston, Gail M / Sansom, Mark S P / Clifton, Luke A

Journal of colloid and interface science

2021 Volume 596, Page(s) 297–311

Abstract: A biomembrane sample system where millimolar changes of cations induce reversible large scale (≥ 200 Å) changes in the membrane-to-surface distance is described. The system composes of a free-floating bilayer, formed adjacent to a self-assembled ... ...

Abstract	A biomembrane sample system where millimolar changes of cations induce reversible large scale (≥ 200 Å) changes in the membrane-to-surface distance is described. The system composes of a free-floating bilayer, formed adjacent to a self-assembled monolayer (SAM). To examine the membrane movements, differently charged floating bilayers in the presence and absence of Ca
Language	English
Publishing date	2021-03-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	241597-5
ISSN	1095-7103 ; 0021-9797
ISSN (online)	1095-7103
ISSN	0021-9797
DOI	10.1016/j.jcis.2021.03.078
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