1
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Little HA, Ali A, Carter JG, Hicks MR, Dafforn TR, Tucker JHR. A plug-and-play aptamer diagnostic platform based on linear dichroism spectroscopy. Front Chem 2023; 11:1040873. [PMID: 37228864 PMCID: PMC10203435 DOI: 10.3389/fchem.2023.1040873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
A plug-and-play sandwich assay platform for the aptamer-based detection of molecular targets using linear dichroism (LD) spectroscopy as a read-out method has been demonstrated. A 21-mer DNA strand comprising the plug-and-play linker was bioconjugated onto the backbone of the filamentous bacteriophage M13, which gives a strong LD signal due to its ready alignment in linear flow. Extended DNA strands containing aptamer sequences that bind the protein thrombin, TBA and HD22, were then bound to the plug-and-play linker strand via complementary base pairing to generate aptamer-functionalised M13 bacteriophages. The secondary structure of the extended aptameric sequences required to bind to thrombin was checked using circular dichroism spectroscopy, with the binding confirmed using fluorescence anisotropy measurements. LD studies revealed that this sandwich sensor design is very effective at detecting thrombin down to pM levels, indicating the potential of this plug-and-play assay system as a new label-free homogenous detection system based on aptamer recognition.
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Affiliation(s)
- Haydn A. Little
- School of Chemistry, University of Birmingham, Birmingham, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Aysha Ali
- School of Chemistry, University of Birmingham, Birmingham, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Jake G. Carter
- School of Chemistry, University of Birmingham, Birmingham, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Timothy R. Dafforn
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - James H. R. Tucker
- School of Chemistry, University of Birmingham, Birmingham, United Kingdom
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2
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Martin A, Jemmett PN, Howitt T, Wood MH, Burley AW, Cox LR, Dafforn TR, Welbourn RJL, Campana M, Skoda MW, Thompson JJ, Hussain H, Rawle JL, Carlà F, Nicklin CL, Arnold T, Horswell SL. Effect of Anionic Lipids on Mammalian Plasma Cell Membrane Properties. Langmuir 2023; 39:2676-2691. [PMID: 36757323 PMCID: PMC9948536 DOI: 10.1021/acs.langmuir.2c03161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The effect of lipid composition on models of the inner leaflet of mammalian cell membranes has been investigated. Grazing incidence X-ray diffraction and X-ray and neutron reflectivity have been used to characterize lipid packing and solvation, while electrochemical and infrared spectroscopic methods have been employed to probe phase behavior in an applied electric field. Introducing a small quantity of the anionic lipid dimyristoylphosphatidylserine (DMPS) into bilayers of zwitterionic dimyristoylphosphatidylethanolamine (DMPE) results in a significant change in the bilayer response to an applied field: the tilt of the hydrocarbon chains increases before returning to the original tilt angle on detachment of the bilayer. Equimolar mixtures, with slightly closer chain packing, exhibit a similar but weaker response. The latter also tend to incorporate more solvent during this electrochemical phase transition, at levels similar to those of pure DMPS. Reflectivity measurements reveal greater solvation of lipid layers for DMPS > 30 mol %, matching the greater propensity for DMPS-rich bilayers to incorporate water. Taken together, the data indicate that the range of 10-35 mol % DMPS provides optimum bilayer properties (in flexibility and function as a barrier), which may explain why the DMPS content of cell membranes tends to be found within this range.
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Affiliation(s)
- Alexandra
L. Martin
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Philip N. Jemmett
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Thomas Howitt
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Mary H. Wood
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Andrew W. Burley
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Liam R. Cox
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Timothy R. Dafforn
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Rebecca J. L. Welbourn
- ISIS
Pulsed Neutron and Muon Source, Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
| | - Mario Campana
- ISIS
Pulsed Neutron and Muon Source, Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
| | - Maximilian W.
A. Skoda
- ISIS
Pulsed Neutron and Muon Source, Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
| | - Joseph J. Thompson
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Hadeel Hussain
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Jonathan L. Rawle
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Francesco Carlà
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Christopher L. Nicklin
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Thomas Arnold
- ISIS
Pulsed Neutron and Muon Source, Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
- European
Spallation Source ERIC PO Box 176, SE-221 00Lund, Sweden
- Department
of Chemistry, University of Bath, Claverton Down, BathBA2 7AY, U.K.
| | - Sarah L. Horswell
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
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3
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Jemmett P, Milan DC, Nichols RJ, Howitt T, Martin AL, Arnold T, Rawle JL, Nicklin CL, Dafforn TR, Cox LR, Horswell SL. Influence of the Lipid Backbone on Electrochemical Phase Behavior. Langmuir 2022; 38:14290-14301. [PMID: 36354380 PMCID: PMC9686133 DOI: 10.1021/acs.langmuir.2c02370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Sphingolipids are an important class of lipids found in mammalian cell membranes with important structural and signaling roles. They differ from another major group of lipids, the glycerophospholipids, in the connection of their hydrocarbon chains to their headgroups. In this study, a combination of electrochemical and structural methods has been used to elucidate the effect of this difference on sphingolipid behavior in an applied electric field. N-Palmitoyl sphingomyelin forms bilayers of similar coverage and thickness to its close analogue di-palmitoyl phosphatidylcholine. Grazing incidence diffraction data show slightly closer packing and a smaller chain tilt angle from the surface normal. Electrochemical IR results at low charge density show that the difference in tilt angle is retained on deposition to form bilayers. The bilayers respond differently to increasing electric field strength: chain tilt angles increase for both molecules, but sphingomyelin chains remain tilted as field strength is further increased. This behavior is correlated with disruption of the hydrogen-bonding network of small groups of sphingomyelin molecules, which may have significance for the behavior of molecules in lipid rafts in the presence of strong fields induced by ion gradients or asymmetric distribution of charged lipids.
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Affiliation(s)
- Philip
N. Jemmett
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - David C. Milan
- Department
of Chemistry, University of Liverpool, Crown Street, LiverpoolL69 7ZD, UK
| | - Richard J. Nichols
- Department
of Chemistry, University of Liverpool, Crown Street, LiverpoolL69 7ZD, UK
| | - Thomas Howitt
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - Alexandra L. Martin
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - Thomas Arnold
- Diamond
Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OxfordshireOX11
0DE, UK
- European
Spallation Source ERICPO Box 176, LundSE-221
00, Sweden
- ISIS
Pulsed Neutron and Muon Source, Science and Technology Facilities
Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, UK
- Department
of Chemistry, University of Bath, Claverton Down, BathBA2 7AY, UK
| | - Jonathan L. Rawle
- Diamond
Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OxfordshireOX11
0DE, UK
| | - Christopher L. Nicklin
- Diamond
Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OxfordshireOX11
0DE, UK
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - Liam R. Cox
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - Sarah L. Horswell
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
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4
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Carter JG, Pfukwa R, Riley L, Tucker JHR, Rodger A, Dafforn TR, Klumperman B. Linear Dichroism Activity of Chiral Poly( p-Aryltriazole) Foldamers. ACS Omega 2021; 6:33231-33237. [PMID: 34901675 PMCID: PMC8656205 DOI: 10.1021/acsomega.1c06139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 05/04/2023]
Abstract
Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(para-aryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.
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Affiliation(s)
- Jake G. Carter
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Rueben Pfukwa
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
| | - Liam Riley
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Alison Rodger
- Department
of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Bert Klumperman
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
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5
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Hawkins OP, Jahromi CPT, Gulamhussein AA, Nestorow S, Bahra T, Shelton C, Owusu-Mensah QK, Mohiddin N, O'Rourke H, Ajmal M, Byrnes K, Khan M, Nahar NN, Lim A, Harris C, Healy H, Hasan SW, Ahmed A, Evans L, Vaitsopoulou A, Akram A, Williams C, Binding J, Thandi RK, Joby A, Guest A, Tariq MZ, Rasool F, Cavanagh L, Kang S, Asparuhov B, Jestin A, Dafforn TR, Simms J, Bill RM, Goddard AD, Rothnie AJ. Membrane protein extraction and purification using partially-esterified SMA polymers. Biochim Biophys Acta Biomembr 2021; 1863:183758. [PMID: 34480878 PMCID: PMC8484863 DOI: 10.1016/j.bbamem.2021.183758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/16/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022]
Abstract
Styrene maleic acid (SMA) polymers have proven to be very successful for the extraction of membrane proteins, forming SMA lipid particles (SMALPs), which maintain a lipid bilayer around the membrane protein. SMALP-encapsulated membrane proteins can be used for functional and structural studies. The SMALP approach allows retention of important protein-annular lipid interactions, exerts lateral pressure, and offers greater stability than traditional detergent solubilisation. However, SMA polymer does have some limitations, including a sensitivity to divalent cations and low pH, an absorbance spectrum that overlaps with many proteins, and possible restrictions on protein conformational change. Various modified polymers have been developed to try to overcome these challenges, but no clear solution has been found. A series of partially-esterified variants of SMA (SMA 2625, SMA 1440 and SMA 17352) has previously been shown to be highly effective for solubilisation of plant and cyanobacterial thylakoid membranes. It was hypothesised that the partial esterification of maleic acid groups would increase tolerance to divalent cations. Therefore, these partially-esterified polymers were tested for the solubilisation of lipids and membrane proteins, and their tolerance to magnesium ions. It was found that all partially esterified polymers were capable of solubilising and purifying a range of membrane proteins, but the yield of protein was lower with SMA 1440, and the degree of purity was lower for both SMA 1440 and SMA 17352. SMA 2625 performed comparably to SMA 2000. SMA 1440 also showed an increased sensitivity to divalent cations. Thus, it appears the interactions between SMA and divalent cations are more complex than proposed and require further investigation.
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Affiliation(s)
- Olivia P Hawkins
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | | | - Aiman A Gulamhussein
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephanie Nestorow
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Taranpreet Bahra
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Christian Shelton
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Quincy K Owusu-Mensah
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Naadiya Mohiddin
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Hannah O'Rourke
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Mariam Ajmal
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Kara Byrnes
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Madiha Khan
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Nila N Nahar
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Arcella Lim
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Cassandra Harris
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Hannah Healy
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Syeda W Hasan
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Asma Ahmed
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Lora Evans
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Afroditi Vaitsopoulou
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aneel Akram
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Chris Williams
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Johanna Binding
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Rumandeep K Thandi
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aswathy Joby
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Ashley Guest
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Mohammad Z Tariq
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Farah Rasool
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Luke Cavanagh
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Simran Kang
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Biser Asparuhov
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Aleksandr Jestin
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - John Simms
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alan D Goddard
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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6
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Vafaei S, Allabush F, Tabaei SR, Male L, Dafforn TR, Tucker JHR, Mendes PM. Förster Resonance Energy Transfer Nanoplatform Based on Recognition-Induced Fusion/Fission of DNA Mixed Micelles for Nucleic Acid Sensing. ACS Nano 2021; 15:8517-8524. [PMID: 33961404 PMCID: PMC8158853 DOI: 10.1021/acsnano.1c00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/29/2021] [Indexed: 05/29/2023]
Abstract
The dynamic nature of micellar nanostructures is employed to form a self-assembled Förster resonance energy transfer (FRET) nanoplatform for enhanced sensing of DNA. The platform consists of lipid oligonucleotide FRET probes incorporated into micellar scaffolds, where single recognition events result in fusion and fission of DNA mixed micelles, triggering the fluorescence response of multiple rather than a single FRET pair. In comparison to conventional FRET substrates where a single donor interacts with a single acceptor, the micellar multiplex FRET system showed ∼20- and ∼3-fold enhancements in the limit of detection and FRET efficiency, respectively. This supramolecular signal amplification approach could potentially be used to improve FRET-based diagnostic assays of nucleic acid and non-DNA based targets.
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Affiliation(s)
- Setareh Vafaei
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Francia Allabush
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Seyed R. Tabaei
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Louise Male
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Paula M. Mendes
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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7
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Ball LE, Riley LJ, Hadasha W, Pfukwa R, Smith CJI, Dafforn TR, Klumperman B. Influence of DIBMA Polymer Length on Lipid Nanodisc Formation and Membrane Protein Extraction. Biomacromolecules 2020; 22:763-772. [PMID: 33373193 DOI: 10.1021/acs.biomac.0c01538] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polymer-based lipid nanoparticles like styrene-maleic acid lipid particles have revolutionized the study of membrane proteins. More recently, alternative polymers such as poly(diisobutylene-alt-maleic acid) (DIBMA) have been used in this field. DIBMA is commonly synthesized via conventional radical copolymerization. In order to study the influence of its chain length on lipid nanodisc formation and membrane protein extraction, we synthesized DIBMA with molar masses varying from 1.2-12 kDa via RAFT-mediated polymerization. For molar masses in the range of 3-7 kDa, the rate of lipid nanodisc formation was the highest and similar to those of poly(styrene-co-maleic acid) (SMA) and commercially available DIBMA. ZipA solubilization efficiency was significantly higher than for commercially available DIBMA and similar to SMA (circa 75%). Furthermore, RAFT-made DIBMA with a molar mass of 1.2-3.9 kDa showed a much cleaner separation on SDS-PAGE, without the smearing that is typically seen for SMA and commercially available DIBMA.
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Affiliation(s)
- Lauren E Ball
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Liam J Riley
- School of Life Sciences, The University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, United Kingdom.,School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Waled Hadasha
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Rueben Pfukwa
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Corinne J I Smith
- School of Life Sciences, The University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, United Kingdom
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Bert Klumperman
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
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8
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Passaretti P, Khan I, Dafforn TR, Goldberg Oppenheimer P. Improvements in the production of purified M13 bacteriophage bio-nanoparticle. Sci Rep 2020; 10:18538. [PMID: 33122639 PMCID: PMC7596064 DOI: 10.1038/s41598-020-75205-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/13/2020] [Indexed: 11/17/2022] Open
Abstract
M13 bacteriophage is a well-established versatile nano-building block, which can be employed to produce novel self-assembled functional materials and devices. Sufficient production and scalability of the M13, often require a large quantity of the virus and thus, improved propagation methods characterised by high capacity and degree of purity are essential. Currently, the 'gold-standard' is represented by infecting Escherichia coli cultures, followed by precipitation with polyethylene glycol (PEG). However, this is considerably flawed by the accumulation of contaminant PEG inside the freshly produced stocks, potentially hampering the reactivity of the individual M13 filaments. Our study demonstrates the effectiveness of implementing an isoelectric precipitation procedure to reduce the residual PEG along with FT-IR spectroscopy as a rapid, convenient and effective analytic validation method to detect the presence of this contaminant in freshly prepared M13 stocks.
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Affiliation(s)
- Paolo Passaretti
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Inam Khan
- School of Metallurgy and Materials, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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9
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Passaretti P, Sun Y, Dafforn TR, Oppenheimer PG. Determination and characterisation of the surface charge properties of the bacteriophage M13 to assist bio-nanoengineering. RSC Adv 2020; 10:25385-25392. [PMID: 35517472 PMCID: PMC9055230 DOI: 10.1039/d0ra04086j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
To truly understand the mechanisms behind the supramolecular self-assembly of nanocomponents, the characterisation of their surface properties is crucial. M13 emerged as a practical nanocomponent for bio-nanoassemblies of functional materials and devices, and its popularity is increasing as time goes by. The investigation performed in this study provides important information about the surface charge and the surface area of M13 determined through the comparison of structural data and the measurement of ζ-potential at pH ranging between 2 and 11. The developed methodologies along with the experimental findings can be subsequently exploited as a novel and convenient prediction tool of the total charge of modified versions of M13. This, in turn, will facilitate the design of the self-assembly strategies which would combine the virus building block with other micro and nano components via intermolecular interactions.
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Affiliation(s)
- Paolo Passaretti
- Institute of Cancer and Genomic Science, University of Birmingham Birmingham B15 2TT UK
| | - Yiwei Sun
- School of Engineering and Materials Science, Queen Mary University of London London E1 4NS UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham Birmingham B15 2TT UK
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10
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Ali A, Little HA, Carter JG, Douglas C, Hicks MR, Kenyon DM, Lacomme C, Logan RT, Dafforn TR, Tucker JHR. Combining bacteriophage engineering and linear dichroism spectroscopy to produce a DNA hybridisation assay. RSC Chem Biol 2020; 1:449-454. [PMID: 34458772 PMCID: PMC8341927 DOI: 10.1039/d0cb00135j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/12/2020] [Indexed: 11/10/2022] Open
Abstract
Nucleic acid detection is an important part of our bio-detection arsenal, with the COVID-19 pandemic clearly demonstrating the importance to healthcare of rapid and efficient detection of specific pathogenic sequences. As part of the drive to establish new DNA detection methodologies and signal read-outs, here we show how linear dichroism (LD) spectroscopy can be used to produce a rapid and modular detection system for detecting quantities of DNA from both bacterial and viral pathogens. The LD sensing method exploits changes in fluid alignment of bionanoparticles (bacteriophage M13) engineered with DNA stands covalently attached to their surfaces, with the read-out signal induced by the formation of complementary duplexes between DNA targets and two M13 bionanoparticles. This new sandwich assay can detect pathogenic material down to picomolar levels in under 1 minute without amplification, as demonstrated by the successful sensing of DNA sequences from a plant virus (Potato virus Y) and an ampicillin resistance gene, ampR. A novel DNA sensing method based on LD spectroscopy and using bionanoparticle scaffolds is described, as demonstrated by the rapid detection of DNA strands associated with bacterial and viral pathogens.![]()
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Affiliation(s)
- Aysha Ali
- School of Chemistry
- University of Birmingham
- Birmingham B15 2TT
- UK
- School of Biosciences
| | - Haydn A. Little
- School of Chemistry
- University of Birmingham
- Birmingham B15 2TT
- UK
| | - Jake G. Carter
- School of Chemistry
- University of Birmingham
- Birmingham B15 2TT
- UK
| | | | | | | | | | - Richard T. Logan
- School of Biosciences
- University of Birmingham
- Birmingham B15 2TT
- UK
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11
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Lee SC, Collins R, Lin YP, Jamshad M, Broughton C, Harris SA, Hanson BS, Tognoloni C, Parslow RA, Terry AE, Rodger A, Smith CJ, Edler KJ, Ford R, Roper DI, Dafforn TR. Nano-encapsulated Escherichia coli Divisome Anchor ZipA, and in Complex with FtsZ. Sci Rep 2019; 9:18712. [PMID: 31822696 PMCID: PMC6904479 DOI: 10.1038/s41598-019-54999-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 11/10/2019] [Indexed: 12/21/2022] Open
Abstract
The E. coli membrane protein ZipA, binds to the tubulin homologue FtsZ, in the early stage of cell division. We isolated ZipA in a Styrene Maleic Acid lipid particle (SMALP) preserving its position and integrity with native E. coli membrane lipids. Direct binding of ZipA to FtsZ is demonstrated, including FtsZ fibre bundles decorated with ZipA. Using Cryo-Electron Microscopy, small-angle X-ray and neutron scattering, we determine the encapsulated-ZipA structure in isolation, and in complex with FtsZ to a resolution of 1.6 nm. Three regions can be identified from the structure which correspond to, SMALP encapsulated membrane and ZipA transmembrane helix, a separate short compact tether, and ZipA globular head which binds FtsZ. The complex extends 12 nm from the membrane in a compact structure, supported by mesoscale modelling techniques, measuring the movement and stiffness of the regions within ZipA provides molecular scale analysis and visualisation of the early divisome.
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Affiliation(s)
- Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Richard Collins
- Faculty of Life Sciences, A4032 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yu-Pin Lin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mohammed Jamshad
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Claire Broughton
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Sarah A Harris
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Benjamin S Hanson
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Cecilia Tognoloni
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Rosemary A Parslow
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ann E Terry
- MAX IV Laboratory Lund University, P.O. Box 118, SE-221 00, Lund, Sweden
| | - Alison Rodger
- Department of Molecular Sciences, Macquarie University, Macquarie, NSW, 2109, Australia
| | - Corinne J Smith
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Karen J Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Robert Ford
- Faculty of Life Sciences, A4032 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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12
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Passaretti P, Sun Y, Khan I, Chan K, Sabo R, White H, Dafforn TR, Oppenheimer PG. Multifunctional graphene oxide-bacteriophage based porous three-dimensional micro-nanocomposites. Nanoscale 2019; 11:13318-13329. [PMID: 31271408 DOI: 10.1039/c9nr03670a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Graphene, since its successful exfoliation and characterisation has been continuously drawing extensive research interests due to its potential for a broad range of applications ranging from energy, microelectronics, through polymer fillers and sensors to environmental and biomedical devices. Exploitation of its unique chemical and physical properties for the manufacturing of functional materials, requires careful structural control and scaling-up into three-dimensional morphologies. Here, a facile method is established to create and control the bottom-up self-assembly of graphene oxide nano-sheets via unprecedented integration with a highly versatile bio-ingredient, the filamentous bacteriophage M13, into hierarchical, three-dimensional, porous sponges of GraPhage13. This study explores the interplay of the GraPhage13 structure formation and studies the mechanisms that give rise to the controllable self-assembly. The straightforward fabrication of robust hierarchical micro-nano-architectures further lays a platform for applications in energy storage and conversion, catalysis and sensing.
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Affiliation(s)
- Paolo Passaretti
- School of Chemical Engineering, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Yiwei Sun
- School of Physics and Astronomy, Queen Mary University of London, London, E1 4NS, UK
| | - Inam Khan
- School of Metallurgy and Materials, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kieran Chan
- School of Chemical Engineering, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Rania Sabo
- School of Chemical Engineering, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Henry White
- BAE-Systems-Air Sector, Buckingham House, FPC 267, Filton, Bristol, BS34 7QW, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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13
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Ali A, Bullen GA, Cross B, Dafforn TR, Little HA, Manchester J, Peacock AFA, Tucker JHR. Light-controlled thrombin catalysis and clot formation using a photoswitchable G-quadruplex DNA aptamer. Chem Commun (Camb) 2019; 55:5627-5630. [PMID: 31025680 DOI: 10.1039/c9cc01540j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The reversible photocontrol of an enzyme governing blood coagulation is demonstrated. The thrombin binding aptamer (TBA), was rendered photochromic by modification with two anthracene groups. Light-triggered anthracene photodimerisation distorts its structure, inhibiting binding of the enzyme thrombin, which in turn triggers catalysis and the resulting clotting process.
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Affiliation(s)
- Aysha Ali
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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14
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Gulamhussein AA, Meah D, Soja DD, Fenner S, Saidani Z, Akram A, Lallie S, Mathews A, Painter C, Liddar MK, Mohammed Z, Chiu LK, Sumar SS, Healy H, Hussain N, Patel JH, Hall SC, Dafforn TR, Rothnie AJ. Examining the stability of membrane proteins within SMALPs. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Teo ACK, Lee SC, Pollock NL, Stroud Z, Hall S, Thakker A, Pitt AR, Dafforn TR, Spickett CM, Roper DI. Analysis of SMALP co-extracted phospholipids shows distinct membrane environments for three classes of bacterial membrane protein. Sci Rep 2019; 9:1813. [PMID: 30755655 PMCID: PMC6372662 DOI: 10.1038/s41598-018-37962-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/05/2018] [Indexed: 11/24/2022] Open
Abstract
Biological characterisation of membrane proteins lags behind that of soluble proteins. This reflects issues with the traditional use of detergents for extraction, as the surrounding lipids are generally lost, with adverse structural and functional consequences. In contrast, styrene maleic acid (SMA) copolymers offer a detergent-free method for biological membrane solubilisation to produce SMA-lipid particles (SMALPs) containing membrane proteins together with their surrounding lipid environment. We report the development of a reverse-phase LC-MS/MS method for bacterial phospholipids and the first comparison of the profiles of SMALP co-extracted phospholipids from three exemplar bacterial membrane proteins with different topographies: FtsA (associated membrane protein), ZipA (single transmembrane helix), and PgpB (integral membrane protein). The data showed that while SMA treatment per se did not preferentially extract specific phospholipids from the membrane, SMALP-extracted ZipA showed an enrichment in phosphatidylethanolamines and depletion in cardiolipins compared to the bulk membrane lipid. Comparison of the phospholipid profiles of the 3 SMALP-extracted proteins revealed distinct lipid compositions for each protein: ZipA and PgpB were similar, but in FtsA samples longer chain phosphatidylglycerols and phosphatidylethanolamines were more abundant. This method offers novel information on the phospholipid interactions of these membrane proteins.
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Affiliation(s)
- Alvin C K Teo
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry, CV4 7AL, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Naomi L Pollock
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Zoe Stroud
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stephen Hall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alpesh Thakker
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - David I Roper
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry, CV4 7AL, UK.
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16
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Kopf AH, Koorengevel MC, van Walree CA, Dafforn TR, Killian JA. A simple and convenient method for the hydrolysis of styrene-maleic anhydride copolymers to styrene-maleic acid copolymers. Chem Phys Lipids 2019; 218:85-90. [DOI: 10.1016/j.chemphyslip.2018.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 01/03/2023]
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17
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Tridgett M, Lozano L, Passaretti P, Desai NR, Proctor TJ, Little HA, Logan RT, Arkill KP, Oppenheimer PG, Dafforn TR. Dye Aggregate-Mediated Self-Assembly of Bacteriophage Bioconjugates. Bioconjug Chem 2018; 29:3705-3714. [PMID: 30347978 DOI: 10.1021/acs.bioconjchem.8b00617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
One of the central themes of biomolecular engineering is the challenge of exploiting the properties of biological materials. Part of this challenge has been uncovering and harnessing properties of biological components that only emerge following their ordered self-assembly. One biomolecular building block that has received significant interest in the past decade is the M13 bacteriophage. There have been a number of recent attempts to trigger the ordered assembly of M13 bacteriophage into multivirion structures, relying on the innate tendency of M13 to form liquid crystals at high concentrations. These, in general, yield planar two-dimensional materials. Presented here is the production of multivirion assemblies of M13 bacteriophage via the chemical modification of its surface by the covalent attachment of the xanthene-based dye tetramethylrhodamine (TMR) isothiocyanate (TRITC). We show that TMR induces the formation of three-dimensional aster-like assemblies of M13 by providing "adhesive" action between bacteriophage particles through the formation of H-aggregates (face-to-face stacking of dye molecules). We also show that the H-aggregation of TMR is greatly enhanced by covalent attachment to M13 and is enhanced further still upon the ordered self-assembly of M13, leading to the suggestion that M13 could be used to promote the self-assembly of dyes that form J-aggregates, a desirable arrangement of fluorescent dye, which has interesting optical properties and potential applications in the fields of medicine and light harvesting technology.
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Affiliation(s)
| | | | | | | | - Toby J Proctor
- Research Department of Haematology , UCL Medical School, Royal Free Campus , Rowland Hill Street , London , NW3 2PF , United Kingdom
| | | | | | - Kenton P Arkill
- School of Medicine , University of Nottingham , Nottingham , NG7 2UH , United Kingdom
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18
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Tridgett M, Moore-Kelly C, Duprey JLHA, Iturbe LO, Tsang CW, Little HA, Sandhu SK, Hicks MR, Dafforn TR, Rodger A. Linear dichroism of visible-region chromophores using M13 bacteriophage as an alignment scaffold. RSC Adv 2018; 8:29535-29543. [PMID: 30713683 PMCID: PMC6333254 DOI: 10.1039/c8ra05475d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/12/2018] [Indexed: 11/22/2022] Open
Abstract
It is a challenge within the field of biomimetics to recreate the properties of light-harvesting antennae found in plants and photosynthetic bacteria. Attempts to recreate these biological structures typically rely on the alignment of fluorescent moieties via attachment to an inert linear scaffold, e.g. DNA, RNA or amyloid fibrils, to enable Förster resonance energy transfer (FRET) between attached chromophores. While there has been some success in this approach, refinement of the alignment of the chromophores is often limited, which may limit the efficiency of energy transfer achieved. Here we demonstrate how linear dichroism spectroscopy may be used to ascertain the overall alignment of chromophores bound to the M13 bacteriophage, a model linear scaffold, and demonstrate how this may be used to distinguish between lack of FRET efficiency due to chromophore separation, and chromophore misalignment. This approach will allow the refinement of artificial light-harvesting antennae in a directed fashion. Here we characterise four dyes and assess the complementarity of linear dichroism and FRET in biomimetic light-harvesting antennae optimisation.![]()
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Affiliation(s)
- Matthew Tridgett
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Charles Moore-Kelly
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Jean-Louis H A Duprey
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Lorea Orueta Iturbe
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Chi W Tsang
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Haydn A Little
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Sandeep K Sandhu
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Matthew R Hicks
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Alison Rodger
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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19
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Tridgett M, Lloyd JR, Kennefick J, Moore-Kelly C, Dafforn TR. Mutation of M13 Bacteriophage Major Coat Protein for Increased Conjugation to Exogenous Compounds. Bioconjug Chem 2018; 29:1872-1875. [PMID: 29800521 DOI: 10.1021/acs.bioconjchem.8b00307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Over the past ten years there has been increasing interest in the conjugation of exogenous compounds to the surface of the M13 bacteriophage. M13 offers a convenient scaffold for the development of nanoassemblies with useful functions, such as highly specific drug delivery and pathogen detection. However, the progress of these technologies has been hindered by the limited efficiency of conjugation to the bacteriophage. Here we generate a mutant version of M13 with an additional lysine residue expressed on the outer surface of the M13 major coat protein, pVIII. We show that this mutation is accommodated by the bacteriophage and that up to an additional 520 exogenous groups can be attached to the bacteriophage surface via amine-directed conjugation. These results could aid the development of high payload drug delivery nanoassemblies and pathogen detection systems with increased sensitivity.
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Affiliation(s)
- Matthew Tridgett
- School of Biosciences , University of Birmingham , Edgbaston, Birmingham , West Midlands , B15 2TT , United Kingdom
| | - James R Lloyd
- School of Biosciences , University of Birmingham , Edgbaston, Birmingham , West Midlands , B15 2TT , United Kingdom
| | - Jack Kennefick
- School of Biosciences , University of Birmingham , Edgbaston, Birmingham , West Midlands , B15 2TT , United Kingdom
| | - Charles Moore-Kelly
- School of Biosciences , University of Birmingham , Edgbaston, Birmingham , West Midlands , B15 2TT , United Kingdom
| | - Timothy R Dafforn
- School of Biosciences , University of Birmingham , Edgbaston, Birmingham , West Midlands , B15 2TT , United Kingdom
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20
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Parmar M, Rawson S, Scarff CA, Goldman A, Dafforn TR, Muench SP, Postis VLG. Using a SMALP platform to determine a sub-nm single particle cryo-EM membrane protein structure. Biochim Biophys Acta Biomembr 2018; 1860:378-383. [PMID: 28993151 PMCID: PMC5780298 DOI: 10.1016/j.bbamem.2017.10.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 01/10/2023]
Abstract
The field of membrane protein structural biology has been revolutionized over the last few years with a number of high profile structures being solved using cryo-EM including Piezo, Ryanodine receptor, TRPV1 and the Glutamate receptor. Further developments in the EM field hold the promise of even greater progress in terms of greater resolution, which for membrane proteins is still typically within the 4-7Å range. One advantage of a cryo-EM approach is the ability to study membrane proteins in more "native" like environments for example proteoliposomes, amphipols and nanodiscs. Recently, styrene maleic acid co-polymers (SMA) have been used to extract membrane proteins surrounded by native lipids (SMALPs) maintaining a more natural environment. We report here the structure of the Escherichia coli multidrug efflux transporter AcrB in a SMALP scaffold to sub-nm resolution, with the resulting map being consistent with high resolution crystal structures and other EM derived maps. However, both the C-terminal helix (TM12) and TM7 are poorly defined in the map. These helices are at the exterior of the helical bundle and form the greater interaction with the native lipids and SMA polymer and may represent a more dynamic region of the protein. This work shows the promise of using an SMA approach for single particle cryo-EM studies to provide sub-nm structures.
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Affiliation(s)
- Mayuriben Parmar
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Charlotte A Scarff
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Adrian Goldman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK; Department of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.
| | - Vincent L G Postis
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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21
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Wemyss AM, Chmel NP, Lobo DP, Sutherland JA, Dafforn TR, Rodger A. Fluorescence detected linear dichroism spectroscopy: A selective and sensitive probe for fluorophores in flow-oriented systems. Chirality 2018; 30:227-237. [PMID: 29314266 DOI: 10.1002/chir.22795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/22/2017] [Accepted: 10/27/2017] [Indexed: 11/06/2022]
Abstract
Fluorescence detection typically enhances sensitivity and selectivity for fluorescent analytes. The potential for combining fluorescence detection with flow orientation of the sample in the normal configuration of linear dichroism experiments is explored in this work by measuring the fluorescence emitted from flow-orientated DNA-bound ligands and M13 bacteriophage. Data for ethidium bromide, Hoechst 33258, and 4,6-diamidino-2-phenyindole are presented. The theoretical basis of the technique is also presented for instruments running in both the fixed direct-current mode, which is the normal operation mode of circular dichroism spectropolarimeters, and also in fixed high-tension voltage mode. The role of the stray light reaching the detector that results in a spectral shape in fixed direct current mode that resembles the shape of a linear dichroism spectrum, rather than the expected reduced linear dichroism, is also explored.
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Affiliation(s)
- Alan M Wemyss
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - Nikola P Chmel
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - Daniela P Lobo
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - John A Sutherland
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia, USA
| | | | - Alison Rodger
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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22
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Laursen T, Borch J, Knudsen C, Bavishi K, Torta F, Martens HJ, Silvestro D, Hatzakis NS, Wenk MR, Dafforn TR, Olsen CE, Motawia MS, Hamberger B, Møller BL, Bassard JE. Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum. Science 2016; 354:890-893. [PMID: 27856908 DOI: 10.1126/science.aag2347] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2023]
Abstract
Metabolic highways may be orchestrated by the assembly of sequential enzymes into protein complexes, or metabolons, to facilitate efficient channeling of intermediates and to prevent undesired metabolic cross-talk while maintaining metabolic flexibility. Here we report the isolation of the dynamic metabolon that catalyzes the formation of the cyanogenic glucoside dhurrin, a defense compound produced in sorghum plants. The metabolon was reconstituted in liposomes, which demonstrated the importance of membrane surface charge and the presence of the glucosyltransferase for metabolic channeling. We used in planta fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy to study functional and structural characteristics of the metabolon. Understanding the regulation of biosynthetic metabolons offers opportunities to optimize synthetic biology approaches for efficient production of high-value products in heterologous hosts.
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Affiliation(s)
- Tomas Laursen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Jonas Borch
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Center For Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Camilla Knudsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Helle Juel Martens
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Daniele Silvestro
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Nikos S Hatzakis
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- Department of Chemistry, Nano-Science Center, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Department of Biological Sciences, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Business, Energy and Industrial Strategy, Her Majesty's Government, UK
| | - Carl Erik Olsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Björn Hamberger
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Carlsberg Research Laboratory, DK-1799 Copenhagen V, Denmark
| | - Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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23
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Lee SC, Knowles TJ, Postis VLG, Jamshad M, Parslow RA, Lin YP, Goldman A, Sridhar P, Overduin M, Muench SP, Dafforn TR. A method for detergent-free isolation of membrane proteins in their local lipid environment. Nat Protoc 2016; 11:1149-62. [PMID: 27254461 DOI: 10.1038/nprot.2016.070] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the great importance of membrane proteins, structural and functional studies of these proteins present major challenges. A significant hurdle is the extraction of the functional protein from its natural lipid membrane. Traditionally achieved with detergents, purification procedures can be costly and time consuming. A critical flaw with detergent approaches is the removal of the protein from the native lipid environment required to maintain functionally stable protein. This protocol describes the preparation of styrene maleic acid (SMA) co-polymer to extract membrane proteins from prokaryotic and eukaryotic expression systems. Successful isolation of membrane proteins into SMA lipid particles (SMALPs) allows the proteins to remain with native lipid, surrounded by SMA. We detail procedures for obtaining 25 g of SMA (4 d); explain the preparation of protein-containing SMALPs using membranes isolated from Escherichia coli (2 d) and control protein-free SMALPS using E. coli polar lipid extract (1-2 h); investigate SMALP protein purity by SDS-PAGE analysis and estimate protein concentration (4 h); and detail biophysical methods such as circular dichroism (CD) spectroscopy and sedimentation velocity analytical ultracentrifugation (svAUC) to undertake initial structural studies to characterize SMALPs (∼2 d). Together, these methods provide a practical tool kit for those wanting to use SMALPs to study membrane proteins.
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Affiliation(s)
- Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Tim J Knowles
- School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Present address: Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Vincent L G Postis
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds, UK
| | | | | | - Yu-Pin Lin
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Adrian Goldman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Department of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland
| | - Pooja Sridhar
- School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Present address: Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Michael Overduin
- School of Biosciences, University of Birmingham, Birmingham, UK.,Department of Biochemistry, Faculty of Medicine &Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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24
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Lee SC, Khalid S, Pollock NL, Knowles TJ, Edler K, Rothnie AJ, R T Thomas O, Dafforn TR. Encapsulated membrane proteins: A simplified system for molecular simulation. Biochim Biophys Acta 2016; 1858:2549-2557. [PMID: 26946242 DOI: 10.1016/j.bbamem.2016.02.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/19/2022]
Abstract
Over the past 50years there has been considerable progress in our understanding of biomolecular interactions at an atomic level. This in turn has allowed molecular simulation methods employing full atomistic modelling at ever larger scales to develop. However, some challenging areas still remain where there is either a lack of atomic resolution structures or where the simulation system is inherently complex. An area where both challenges are present is that of membranes containing membrane proteins. In this review we analyse a new practical approach to membrane protein study that offers a potential new route to high resolution structures and the possibility to simplify simulations. These new approaches collectively recognise that preservation of the interaction between the membrane protein and the lipid bilayer is often essential to maintain structure and function. The new methods preserve these interactions by producing nano-scale disc shaped particles that include bilayer and the chosen protein. Currently two approaches lead in this area: the MSP system that relies on peptides to stabilise the discs, and SMALPs where an amphipathic styrene maleic acid copolymer is used. Both methods greatly enable protein production and hence have the potential to accelerate atomic resolution structure determination as well as providing a simplified format for simulations of membrane protein dynamics. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Naomi L Pollock
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tim J Knowles
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Karen Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Alice J Rothnie
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Owen R T Thomas
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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25
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Carr-Smith J, Pacheco-Gómez R, Little HA, Hicks MR, Sandhu S, Steinke N, Smith DJ, Rodger A, Goodchild SA, Lukaszewski RA, Tucker JHR, Dafforn TR. Polymerase Chain Reaction on a Viral Nanoparticle. ACS Synth Biol 2015; 4:1316-25. [PMID: 26046486 DOI: 10.1021/acssynbio.5b00034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The field of synthetic biology includes studies that aim to develop new materials and devices from biomolecules. In recent years, much work has been carried out using a range of biomolecular chassis including α-helical coiled coils, β-sheet amyloids and even viral particles. In this work, we show how hybrid bionanoparticles can be produced from a viral M13 bacteriophage scaffold through conjugation with DNA primers that can template a polymerase chain reaction (PCR). This unprecedented example of a PCR on a virus particle has been studied by flow aligned linear dichroism spectroscopy, which gives information on the structure of the product as well as a new protototype methodology for DNA detection. We propose that this demonstration of PCR on the surface of a bionanoparticle is a useful addition to ways in which hybrid assemblies may be constructed using synthetic biology.
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Affiliation(s)
| | | | | | | | | | | | | | - Alison Rodger
- Department
of Chemistry, University of Warwick, Coventry, Warwickshire CV4 7AL, United Kingdom
| | - Sarah A. Goodchild
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Roman A. Lukaszewski
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
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26
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Lobo DP, Wemyss AM, Smith DJ, Straube A, Betteridge KB, Salmon AHJ, Foster RR, Elhegni HE, Satchell SC, Little HA, Pacheco-Gómez R, Simmons MJ, Hicks MR, Bates DO, Rodger A, Dafforn TR, Arkill KP. Direct detection and measurement of wall shear stress using a filamentous bio-nanoparticle. Nano Res 2015; 8:3307-3315. [PMID: 27570611 PMCID: PMC4996322 DOI: 10.1007/s12274-015-0831-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 05/24/2023]
Abstract
The wall shear stress (WSS) that a moving fluid exerts on a surface affects many processes including those relating to vascular function. WSS plays an important role in normal physiology (e.g. angiogenesis) and affects the microvasculature's primary function of molecular transport. Points of fluctuating WSS show abnormalities in a number of diseases; however, there is no established technique for measuring WSS directly in physiological systems. All current methods rely on estimates obtained from measured velocity gradients in bulk flow data. In this work, we report a nanosensor that can directly measure WSS in microfluidic chambers with sub-micron spatial resolution by using a specific type of virus, the bacteriophage M13, which has been fluorescently labeled and anchored to a surface. It is demonstrated that the nanosensor can be calibrated and adapted for biological tissue, revealing WSS in micro-domains of cells that cannot be calculated accurately from bulk flow measurements. This method lends itself to a platform applicable to many applications in biology and microfluidics.
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Affiliation(s)
- Daniela P Lobo
- Department of Chemistry and Warwick Analytical Science Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Alan M Wemyss
- Department of Chemistry and Warwick Analytical Science Centre, University of Warwick, Coventry CV4 7AL, UK; MOAC Doctoral Training Centre, University of Warwick, Coventry CV4 7AL, UK
| | - David J Smith
- Mathematics, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Anne Straube
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Kai B Betteridge
- Physiology and Pharmacology, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Andrew H J Salmon
- Physiology and Pharmacology, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Rebecca R Foster
- Clinical Sciences, Whitson Street, University of Bristol, Bristol BS1 3NY, UK
| | - Hesham E Elhegni
- Clinical Sciences, Whitson Street, University of Bristol, Bristol BS1 3NY, UK
| | - Simon C Satchell
- Clinical Sciences, Whitson Street, University of Bristol, Bristol BS1 3NY, UK
| | - Haydn A Little
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Raúl Pacheco-Gómez
- Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Mark J Simmons
- Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Matthew R Hicks
- Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - David O Bates
- School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham NG2 7UH, UK
| | - Alison Rodger
- Department of Chemistry and Warwick Analytical Science Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy R Dafforn
- Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Kenton P Arkill
- Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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27
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Sinden NJ, Baker MJ, Smith DJ, Kreft JU, Dafforn TR, Stockley RA. α-1-antitrypsin variants and the proteinase/antiproteinase imbalance in chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2015; 308:L179-90. [PMID: 25416382 DOI: 10.1152/ajplung.00179.2014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The excessive activities of the serine proteinases neutrophil elastase and proteinase 3 are associated with tissue damage in chronic obstructive pulmonary disease. Reduced concentrations and/or inhibitory efficiency of the main circulating serine proteinase inhibitor α-1-antitrypsin result from point mutations in its gene. In addition, α-2-macroglobulin competes with α-1-antitrypsin for proteinases, and the α-2-macroglobulin-sequestered enzyme can retain its catalytic activity. We have studied how serine proteinases partition between these inhibitors and the effects of α-1-antitrypsin mutations on this partitioning. Subsequently, we have developed a three-dimensional reaction-diffusion model to describe events occurring in the lung interstitium when serine proteinases diffuse from the neutrophil azurophil granule following degranulation and subsequently bind to either α-1-antitrypsin or α-2-macroglobulin. We found that the proteinases remained uninhibited on the order of 0.1 s after release and diffused on the order of 10 μm into the tissue before becoming sequestered. We have shown that proteinases sequestered to α-2-macroglobulin retain their proteolytic activity and that neutrophil elastase complexes with α-2-macroglobulin are able to degrade elastin. Although neutrophil elastase is implicated in the pathophysiology of emphysema, our results highlight a potentially important role for proteinase 3 because of its greater concentration in azurophil granules, its reduced association rate constant with all α-1-antitrypsin variants studied here, its greater diffusion distance, time spent uninhibited following degranulation, and its greater propensity to partition to α-2-macroglobulin where it retains proteolytic activity.
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28
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Dörr JM, Koorengevel MC, Schäfer M, Prokofyev AV, Scheidelaar S, van der Cruijsen EAW, Dafforn TR, Baldus M, Killian JA. Detergent-free isolation, characterization, and functional reconstitution of a tetrameric K+ channel: the power of native nanodiscs. Proc Natl Acad Sci U S A 2014; 111:18607-12. [PMID: 25512535 PMCID: PMC4284610 DOI: 10.1073/pnas.1416205112] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A major obstacle in the study of membrane proteins is their solubilization in a stable and active conformation when using detergents. Here, we explored a detergent-free approach to isolating the tetrameric potassium channel KcsA directly from the membrane of Escherichia coli, using a styrene-maleic acid copolymer. This polymer self-inserts into membranes and is capable of extracting membrane patches in the form of nanosize discoidal proteolipid particles or "native nanodiscs." Using circular dichroism and tryptophan fluorescence spectroscopy, we show that the conformation of KcsA in native nanodiscs is very similar to that in detergent micelles, but that the thermal stability of the protein is higher in the nanodiscs. Furthermore, as a promising new application, we show that quantitative analysis of the co-isolated lipids in purified KcsA-containing nanodiscs allows determination of preferential lipid-protein interactions. Thin-layer chromatography experiments revealed an enrichment of the anionic lipids cardiolipin and phosphatidylglycerol, indicating their close proximity to the channel in biological membranes and supporting their functional relevance. Finally, we demonstrate that KcsA can be reconstituted into planar lipid bilayers directly from native nanodiscs, which enables functional characterization of the channel by electrophysiology without first depriving the protein of its native environment. Together, these findings highlight the potential of the use of native nanodiscs as a tool in the study of ion channels, and of membrane proteins in general.
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Affiliation(s)
- Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Marre Schäfer
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Alexander V Prokofyev
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - Stefan Scheidelaar
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Elwin A W van der Cruijsen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - Timothy R Dafforn
- School of Bio Sciences, University of Birmingham, Edgbaston Birmingham B15 2TT, United Kingdom
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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29
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Zhu Y, Jameson E, Parslow RA, Lidbury I, Fu T, Dafforn TR, Schäfer H, Chen Y. Identification and characterization of trimethylamine N-oxide (TMAO) demethylase and TMAO permease in Methylocella silvestris BL2. Environ Microbiol 2014; 16:3318-30. [PMID: 25088783 DOI: 10.1111/1462-2920.12585] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/24/2014] [Indexed: 11/28/2022]
Abstract
Methylocella silvestris, an alphaproteobacterium isolated from a forest soil, can grow on trimethylamine N-oxide (TMAO) as a sole nitrogen source; however, the molecular and biochemical mechanisms underpinning its growth remain unknown. Marker-exchange mutagenesis enabled the identification of several genes involved in TMAO metabolism, including Msil_3606, a permease of the amino acids-polyamine (APC) superfamily, and Msil_3603, consisting of an N-terminal domain of unknown function (DUF1989) and a C-terminal tetrahydrofolate-binding domain. Null mutants of Msil_3603 and Msil_3606 can no longer grow on TMAO. Purified Msil_3603 from recombinant Escherichia coli can convert TMAO to dimethylamine and formaldehyde (1 TMAO → 1 dimethylamine + 1 formaldehyde), confirming that it encodes a bona fide TMAO demethylase (Tdm). Tdm of M. silvestris and eukaryotic Tdms have no sequence homology and contrasting characteristics. Recombinant Tdm of M. silvestris appears to be hexameric, has a high affinity for TMAO (Km = 3.3 mM; Vmax = 21.7 nmol min(-1) mg(-1) ) and only catalyses demethylation of TMAO and a structural homologue, dimethyldodecylamine N-oxide. Our study has contributed to the understanding of the genetic and biochemical mechanisms for TMAO degradation in M. silvestris.
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Affiliation(s)
- Yijun Zhu
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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30
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Paulin S, Jamshad M, Dafforn TR, Garcia-Lara J, Foster SJ, Galley NF, Roper DI, Rosado H, Taylor PW. Surfactant-free purification of membrane protein complexes from bacteria: application to the staphylococcal penicillin-binding protein complex PBP2/PBP2a. Nanotechnology 2014; 25:285101. [PMID: 24972373 DOI: 10.1088/0957-4484/25/28/285101] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Surfactant-mediated removal of proteins from biomembranes invariably results in partial or complete loss of function and disassembly of multi-protein complexes. We determined the capacity of styrene-co-maleic acid (SMA) co-polymer to remove components of the cell division machinery from the membrane of drug-resistant staphylococcal cells. SMA-lipid nanoparticles solubilized FtsZ-PBP2-PBP2a complexes from intact cells, demonstrating the close physical proximity of these proteins within the lipid bilayer. Exposure of bacteria to (-)-epicatechin gallate, a polyphenolic agent that abolishes β-lactam resistance in staphylococci, disrupted the association between PBP2 and PBP2a. Thus, SMA purification provides a means to remove native integral membrane protein assemblages with minimal physical disruption and shows promise as a tool for the interrogation of molecular aspects of bacterial membrane protein structure and function.
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Affiliation(s)
- Sarah Paulin
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
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31
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Berwick MR, Lewis DJ, Jones AW, Parslow RA, Dafforn TR, Cooper HJ, Wilkie J, Pikramenou Z, Britton MM, Peacock AFA. De novo design of Ln(III) coiled coils for imaging applications. J Am Chem Soc 2014; 136:1166-9. [PMID: 24405157 PMCID: PMC3950886 DOI: 10.1021/ja408741h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
A new
peptide sequence (MB1) has been designed which, in the presence
of a trivalent lanthanide ion, has been programmed to self-assemble
to form a three stranded metallo-coiled coil, Ln(III)(MB1)3. The binding site has been incorporated into the hydrophobic core
using natural amino acids, restricting water access to the lanthanide.
The resulting terbium coiled coil displays luminescent properties
consistent with a lack of first coordination sphere water molecules.
Despite this the gadolinium coiled coil, the first to be reported,
displays promising magnetic resonance contrast capabilities.
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Affiliation(s)
- Matthew R Berwick
- School of Chemistry and ‡School of Biosciences, University of Birmingham , Edgbaston, B15 2TT, United Kingdom
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32
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Razmkhah K, Little H, Sandhu S, Dafforn TR, Rodger A. Optical properties of xanthene based fluorescent dyes studied by stretched-film linear dichroism. RSC Adv 2014. [DOI: 10.1039/c4ra06126h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Xanthene dyes are commonly used to label proteins in order to probe their location and activity using fluorescence spectroscopy and microscopy.
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Affiliation(s)
- Kasra Razmkhah
- Department of Chemistry
- University of Warwick
- Coventry, UK
| | - Haydn Little
- School of Chemistry
- University of Birmingham
- Birmingham, UK
| | - Sandeep Sandhu
- School of Biosciences
- University of Birmingham
- Birmingham, UK
| | | | - Alison Rodger
- Department of Chemistry
- University of Warwick
- Coventry, UK
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33
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Bonander N, Jamshad M, Oberthür D, Clare M, Barwell J, Hu K, Farquhar MJ, Stamataki Z, Harris HJ, Dierks K, Dafforn TR, Betzel C, McKeating JA, Bill RM. Production, purification and characterization of recombinant, full-length human claudin-1. PLoS One 2013; 8:e64517. [PMID: 23704991 PMCID: PMC3660353 DOI: 10.1371/journal.pone.0064517] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 04/16/2013] [Indexed: 01/20/2023] Open
Abstract
The transmembrane domain proteins of the claudin superfamily are the major structural components of cellular tight junctions. One family member, claudin-1, also associates with tetraspanin CD81 as part of a receptor complex that is essential for hepatitis C virus (HCV) infection of the liver. To understand the molecular basis of claudin-1/CD81 association we previously produced and purified milligram quantities of functional, full-length CD81, which binds a soluble form of HCV E2 glycoprotein (sE2). Here we report the production, purification and characterization of claudin-1. Both yeast membrane-bound and detergent-extracted, purified claudin-1 were antigenic and recognized by specific antibodies. Analytical ultracentrifugation demonstrated that extraction with n-octyl-β-d-glucopyranoside yielded monodispersed, dimeric pools of claudin-1 while extraction with profoldin-8 or n-decylphosphocholine yielded a dynamic mixture of claudin-1 oligomers. Neither form bound sE2 in line with literature expectations, while further functional analysis was hampered by the finding that incorporation of claudin-1 into proteoliposomes rendered them intractable to study. Dynamic light scattering demonstrated that claudin-1 oligomers associate with CD81 in vitro in a defined molar ratio of 1∶2 and that complex formation was enhanced by the presence of cholesteryl hemisuccinate. Attempts to assay the complex biologically were limited by our finding that claudin-1 affects the properties of proteoliposomes. We conclude that recombinant, correctly-folded, full-length claudin-1 can be produced in yeast membranes, that it can be extracted in different oligomeric forms that do not bind sE2 and that a dynamic preparation can form a specific complex with CD81 in vitro in the absence of any other cellular components. These findings pave the way for the structural characterization of claudin-1 alone and in complex with CD81.
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Affiliation(s)
- Nicklas Bonander
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, United Kingdom
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Abdul-Wahab MF, Homma T, Wright M, Olerenshaw D, Dafforn TR, Nagata K, Miller AD. The pH sensitivity of murine heat shock protein 47 (HSP47) binding to collagen is affected by mutations in the breach histidine cluster. J Biol Chem 2012; 288:4452-61. [PMID: 23212911 DOI: 10.1074/jbc.m112.409029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Heat shock protein 47 (HSP47) is a single-substrate molecular chaperone crucial for collagen biosynthesis. Although its function is well established, the molecular mechanisms that govern binding to procollagen peptides and triple helices in the endoplasmic reticulum (followed by controlled release in the Golgi) are unclear. HSP47 binds procollagen at a neutral pH but releases at a pH similar to the pK(a) of the imidazole side chain of histidine residues. It thus seems likely that these residues are involved in this pH-dependent mechanism. Murine HSP47 has 14 histidine residues grouped into three clusters, known as the breach, gate, and shutter. Here, we report the use of histidine mutagenesis to demonstrate the relative contribution of these three clusters to HSP47 structure and the "pH switch." Many of the tested mutants are silent; however, breach mutants H197A and H198A show binding but no apparent pH switch and are unable to control release. Another breach mutant, H191A, shows perturbed collagen release characteristics, consistent with observed perturbations in pH-driven trans-conformational changes. Thus, His-198, His-197 and His-191 are important (if not central) to HSP47 mechanism of binding/release to collagen. This is consistent with the breach cluster residues being well conserved across the HSP47 family.
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Affiliation(s)
- Mohd Firdaus Abdul-Wahab
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
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35
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Hicks MR, Rodger A, Lin YP, Jones NC, Hoffmann SV, Dafforn TR. Rapid Injection Linear Dichroism for Studying the Kinetics of Biological Processes. Anal Chem 2012; 84:6561-6. [DOI: 10.1021/ac300842h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Matthew R. Hicks
- Department of Chemistry and
Warwick Centre for Analytical Science, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Alison Rodger
- Department of Chemistry and
Warwick Centre for Analytical Science, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Yu-pin Lin
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United
Kingdom
| | - Nykola C. Jones
- Institute for Storage
Ring Facilities
(ISA), Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- Institute for Storage
Ring Facilities
(ISA), Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Timothy R. Dafforn
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United
Kingdom
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Pacheco-Gómez R, Kraemer J, Stokoe S, England HJ, Penn CW, Stanley E, Rodger A, Ward J, Hicks MR, Dafforn TR. Detection of Pathogenic Bacteria Using a Homogeneous Immunoassay Based on Shear Alignment of Virus Particles and Linear Dichroism. Anal Chem 2011; 84:91-7. [PMID: 22017566 DOI: 10.1021/ac201544h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Raúl Pacheco-Gómez
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
| | - Julia Kraemer
- TU Dresden, Institut für Lebensmittel- und Bioverfahrenstechnik (Institute of Food Technology and Bioprocess Engineering) 01062 Dresden
| | - Susan Stokoe
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
| | - Hannah J. England
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
| | - Charles W. Penn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
| | - Emma Stanley
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, U.K
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, Warwickshire, CV4 7AL, U.K
| | - John Ward
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, U.K
| | - Matthew R. Hicks
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
- Department of Chemistry, University of Warwick, Coventry, Warwickshire, CV4 7AL, U.K
| | - Timothy R. Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
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Kosmoliaptsis V, Dafforn TR, Chaudhry AN, Halsall DJ, Bradley JA, Taylor CJ. High-resolution, three-dimensional modeling of human leukocyte antigen class I structure and surface electrostatic potential reveals the molecular basis for alloantibody binding epitopes. Hum Immunol 2011; 72:1049-59. [PMID: 21840357 DOI: 10.1016/j.humimm.2011.07.303] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 06/25/2011] [Accepted: 07/05/2011] [Indexed: 10/17/2022]
Abstract
The potential of human leukocyte antigens (HLA) to stimulate humoral alloimmunity depends on the orientation, accessibility and physiochemical properties of polymorphic amino acids. We have generated high-resolution structural and physiochemical models of all common HLA class I alleles and analyzed the impact of amino acid polymorphisms on surface electrostatic potential. Atomic resolution three-dimensional structural models of HLA class I molecules were generated using the MODELLER computer algorithm. The molecular surface electrostatic potential was calculated using the DelPhi program. To confirm that electrostatic surface topography reflects known HLA B cell epitopes, we examined Bw4 and Bw6 and ascertained the impact of amino acid polymorphisms on their tertiary and physiochemical composition. The HLA protein structures generated performed well when subjected to stereochemical and energy-based testing for structural integrity. The electrostatic pattern and conformation of Bw4 and Bw6 epitopes are maintained among HLA molecules even when expressed in a different structural context. Importantly, variation in epitope amino acid composition does not always translate into a different electrostatic motif, providing an explanation for serologic cross-reactivity. Mutations of critical amino acids that abrogate antibody binding also induce distinct changes in epitope electrostatic properties. In conclusion, high-resolution structural modeling provides a physiochemical explanation for serologic patterns of antibody binding and provides novel insights into HLA immunogenicity.
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Affiliation(s)
- Vasilis Kosmoliaptsis
- Tissue Typing Laboratory, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, England.
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38
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Pacheco-Gómez R, Roper DI, Dafforn TR, Rodger A. The pH dependence of polymerization and bundling by the essential bacterial cytoskeletal protein FtsZ. PLoS One 2011; 6:e19369. [PMID: 21738567 PMCID: PMC3125165 DOI: 10.1371/journal.pone.0019369] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 04/02/2011] [Indexed: 11/19/2022] Open
Abstract
There is a growing body of evidence that bacterial cell division is an intricate coordinated process of comparable complexity to that seen in eukaryotic cells. The dynamic assembly of Escherichia coli FtsZ in the presence of GTP is fundamental to its activity. FtsZ polymerization is a very attractive target for novel antibiotics given its fundamental and universal function. In this study our aim was to understand further the GTP-dependent FtsZ polymerization mechanism and our main focus is on the pH dependence of its behaviour. A key feature of this work is the use of linear dichroism (LD) to follow the polymerization of FtsZ monomers into polymeric structures. LD is the differential absorption of light polarized parallel and perpendicular to an orientation direction (in this case that provided by shear flow). It thus readily distinguishes between FtsZ polymers and monomers. It also distinguishes FtsZ polymers and less well-defined aggregates, which light scattering methodologies do not. The polymerization of FtsZ over a range of pHs was studied by right-angled light scattering to probe mass of FtsZ structures, LD to probe real-time formation of linear polymeric fibres, a specially developed phosphate release assay to relate guanosine triphosphate (GTP) hydrolysis to polymer formation, and electron microscopy (EM) imaging of reaction products as a function of time and pH. We have found that lowering the pH from neutral to 6.5 does not change the nature of the FtsZ polymers in solution—it simply facilitates the polymerization so the fibres present are longer and more abundant. Conversely, lowering the pH to 6.0 has much the same effect as introducing divalent cations or the FtsZ-associated protein YgfE (a putative ZapA orthologue in E. coli)—it stablizes associations of protofilaments.
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Affiliation(s)
- Raúl Pacheco-Gómez
- Molecular Organization and Assembly in Cells Doctoral Training Centre, University of Warwick, Coventry, United Kingdom
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Timothy R. Dafforn
- Department of Biosciences, University of Birmingham, Edgebaston, Birmingham, United Kingdom
| | - Alison Rodger
- Molecular Organization and Assembly in Cells Doctoral Training Centre, University of Warwick, Coventry, United Kingdom
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
- * E-mail:
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Damianoglou A, Rodger A, Pridmore C, Dafforn TR, Mosely JA, Sanderson JM, Hicks MR. The synergistic action of melittin and phospholipase A2 with lipid membranes: development of linear dichroism for membrane-insertion kinetics. Protein Pept Lett 2011; 17:1351-62. [PMID: 20673225 DOI: 10.2174/0929866511009011351] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Accepted: 06/08/2010] [Indexed: 11/22/2022]
Abstract
Here we present data on the kinetics of insertion of melittin, a peptide from bee venom, into lipid membranes of different composition. Another component of bee venom is the enzyme phospholipase A2 (PLA₂). We have examined the interaction of melittin and PLA₂ with liposomes both separately and combined and demonstrate that they work synergistically to disrupt the membranes. A dramatic difference in the action of melittin and PLA₂ is observed when the composition of the membrane is altered. Temperature also has a large effect on the kinetics of insertion and membrane disruption. We use a combination of techniques to measure liposome size (dynamic light scattering), peptide secondary structure (circular dichroism spectroscopy), peptide orientation relative to the membrane (linear dichroism spectroscopy) and enzymatic digestion of the lipids (mass spectrometry).
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40
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Bromley EHC, Channon KJ, King PJS, Mahmoud ZN, Banwell EF, Butler MF, Crump MP, Dafforn TR, Hicks MR, Hirst JD, Rodger A, Woolfson DN. Assembly pathway of a designed alpha-helical protein fiber. Biophys J 2010; 98:1668-76. [PMID: 20409488 DOI: 10.1016/j.bpj.2009.12.4309] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 12/18/2009] [Accepted: 12/21/2009] [Indexed: 12/22/2022] Open
Abstract
Interest in the design of peptide-based fibrous materials is growing because it opens possibilities to explore fundamental aspects of peptide self-assembly and to exploit the resulting structures--for example, as scaffolds for tissue engineering. Here we investigate the assembly pathway of self-assembling fibers, a rationally designed alpha-helical coiled-coil system comprising two peptides that assemble on mixing. The dimensions spanned by the peptides and final structures (nanometers to micrometers), and the timescale over which folding and assembly occur (seconds to hours), necessitate a multi-technique approach employing spectroscopy, analytical ultracentrifugation, electron and light microscopy, and protein design to produce a physical model. We show that fibers form via a nucleation and growth mechanism. The two peptides combine rapidly (in less than seconds) to form sticky ended, partly helical heterodimers. A lag phase follows, on the order of tens of minutes, and is concentration-dependent. The critical nucleus comprises six to eight partially folded dimers. Growth is then linear in dimers, and subsequent fiber growth occurs in hours through both elongation and thickening. At later times (several hours), fibers grow predominantly through elongation. This kinetic, biomolecular description of the folding-and-assembly process allows the self-assembling fiber system to be manipulated and controlled, which we demonstrate through seeding experiments to obtain different distributions of fiber lengths. This study and the resulting mechanism we propose provide a potential route to achieving temporal control of functional fibers with future applications in biotechnology and nanoscale science and technology.
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41
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Marshall KE, Hicks MR, Williams TL, Hoffmann SV, Rodger A, Dafforn TR, Serpell LC. Characterizing the assembly of the Sup35 yeast prion fragment, GNNQQNY: structural changes accompany a fiber-to-crystal switch. Biophys J 2010; 98:330-8. [PMID: 20338855 DOI: 10.1016/j.bpj.2009.10.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 10/13/2009] [Accepted: 10/15/2009] [Indexed: 01/18/2023] Open
Abstract
Amyloid-like fibrils can be formed by many different proteins and peptides. The structural characteristics of these fibers are very similar to those of amyloid fibrils that are deposited in a number of protein misfolding diseases, including Alzheimer's disease and the transmissible spongiform encephalopathies. The elucidation of two crystal structures from an amyloid-like fibril-forming fragment of the yeast prion, Sup35, with sequence GNNQQNY, has contributed to knowledge regarding side-chain packing of amyloid-forming peptides. Both structures share a cross-beta steric zipper arrangement but vary in the packing of the peptide, particularly in terms of the tyrosine residue. We investigated the fibrillar and crystalline structure and assembly of the GNNQQNY peptide using x-ray fiber diffraction, electron microscopy, intrinsic and quenched tyrosine fluorescence, and linear dichroism. Electron micrographs reveal that at concentrations between 0.5 and 10 mg/mL, fibers form initially, followed by crystals. Fluorescence studies suggest that the environment of the tyrosine residue changes as crystals form. This is corroborated by linear dichroism experiments that indicate a change in the orientation of the tyrosine residue over time, which suggests that a structural rearrangement occurs as the crystals form. Experimental x-ray diffraction patterns from fibers and crystals also suggest that these species are structurally distinct. A comparison of experimental and calculated diffraction patterns contributes to an understanding of the different arrangements accessed by the peptide.
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Affiliation(s)
- Karen E Marshall
- Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, United Kingdom
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42
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Lawson AJ, Walker EA, White SA, Dafforn TR, Stewart PM, Ride JP. Mutations of key hydrophobic surface residues of 11 beta-hydroxysteroid dehydrogenase type 1 increase solubility and monodispersity in a bacterial expression system. Protein Sci 2009; 18:1552-63. [PMID: 19507261 DOI: 10.1002/pro.150] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
11 beta-Hydroxysteroid dehydrogenase type 1 (11 beta-HSD1) is a key enzyme in the conversion of cortisone to the functional glucocorticoid hormone cortisol. This activation has been implicated in several human disorders, notably the metabolic syndrome where 11 beta-HSD1 has been identified as a novel target for potential therapeutic drugs. Recent crystal structures have revealed the presence of a pronounced hydrophobic surface patch lying on two helices at the C-terminus. The physiological significance of this region has been attributed to facilitating substrate access by allowing interactions with the endoplasmic reticulum membrane. Here, we report that single mutations that alter the hydrophobicity of this patch (I275E, L266E, F278E, and L279E in the human enzyme and I275E, Y266E, F278E, and L279E in the guinea pig enzyme) result in greatly increased yields of soluble protein on expression in E. coli. Kinetic analyses of both reductase and dehydrogenase reactions indicate that the F278E mutant has unaltered K(m) values for steroids and an unaltered or increased k(cat). Analytical ultracentrifugation shows that this mutation also decreases aggregation of both the human and guinea pig enzymes, resulting in greater monodispersity. One of the mutants (guinea pig F278E) has proven easy to crystallize and has been shown to have a virtually identical structure to that previously reported for the wild-type enzyme. The human F278E enzyme is shown to be a suitable background for analyzing the effects of naturally occurring mutations (R137C, K187N) on enzyme activity and stability. Hence, the F278E mutants should be useful for many future biochemical and biophysical studies of the enzyme.
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Affiliation(s)
- Alexander J Lawson
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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43
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Bulheller BM, Rodger A, Hicks MR, Dafforn TR, Serpell LC, Marshall KE, Bromley EHC, King PJS, Channon KJ, Woolfson DN, Hirst JD. Flow Linear Dichroism of Some Prototypical Proteins. J Am Chem Soc 2009; 131:13305-14. [DOI: 10.1021/ja902662e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin M. Bulheller
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Alison Rodger
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Matthew R. Hicks
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Timothy R. Dafforn
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Louise C. Serpell
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Karen E. Marshall
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Elizabeth H. C. Bromley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Patrick J. S. King
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Kevin J. Channon
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
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Hicks MR, Dafforn TR, Damianoglou A, Wormell P, Rodger A, Hoffmann SV. Synchrotron radiation linear dichroism spectroscopy of the antibiotic peptide gramicidin in lipid membranes. Analyst 2009; 134:1623-8. [PMID: 20448930 DOI: 10.1039/b902523e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed synchrotron radiation linear dichroism (SRLD) to measure the insertion of peptides into lipid bilayers, significantly improving both signal-to-noise and wavelength range over existing methods. Our wavelength cut-off is currently determined by the quality of quartz in the cell, rather than the light source, with signal quality still high at the cut-off. We demonstrate the use of a lipid probe to measure the orientation of the lipid bilayers under flow and describe the way in which this can be used to further interpret SRLD data. The antibiotic peptide gramicidin is shown to exhibit drastically different kinetic and equilibrium behaviour when interacting with lipid membranes with different properties. The charge on the membrane is of interest because of differences in charge between human and bacterial membranes. For this reason we increased the negative charge on the membrane by changing the lipid composition. Increasing negative charge in the gel phase stabilises the liposomes but changes the kinetics of peptide folding. In a gel phase with no negatively charged lipids, gramicidin does not fold well and gives a small signal that indicates a change in orientation of the tryptophan side chains over time. In the fluid phase with no negatively charged lipids, there is initially >10-fold greater peptide signal relative to the gel phase indicating a highly folded and ordered gramicidin backbone. This is followed by liposome disruption. In the gel phase with negatively charged lipids the liposomes are resistant to disruption by gramicidin and exhibit different folding kinetics depending on membrane composition. In the fluid phase with negatively charged lipids there is little signal from either the peptide or the lipid probe indicating that the liposomes have been disrupted by the gramicidin in the time it takes to make the first measurement.
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Affiliation(s)
- Matthew R Hicks
- Department of Chemistry, University of Warwick, Coventry, UK CV4 7AL.
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45
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Oates J, Hicks M, Dafforn TR, DiMaio D, Dixon AM. In vitro dimerization of the bovine papillomavirus E5 protein transmembrane domain. Biochemistry 2008; 47:8985-92. [PMID: 18672907 DOI: 10.1021/bi8006252] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The E5 protein from bovine papillomavirus is a type II membrane protein and the product of the smallest known oncogene. E5 causes cell transformation by binding and activating the platelet-derived growth factor beta receptor (PDGFbetaR). In order to productively interact with the receptor, it is thought that E5 binds as a dimer. However, wild-type E5 and various mutants have also been shown to form trimers, tetramers, and even higher order oligomers. The residues in E5 that drive and stabilize a dimeric state are also still in question. At present, two different models for the E5 dimer exist in the literature, one symmetric and one asymmetric. There is universal agreement, however, that the transmembrane (TM) domain plays a vital role in stabilizing the functional oligomer; indeed, mutation of various TM domain residues can abolish E5 function. In order to better resolve the role of the E5 TM domain in function, we have undertaken the first quantitative in vitro characterization of the E5 TM domain in detergent micelles and liposomes. Circular and linear dichroism analyses verify that the TM domain adopts a stable alpha-helical structure and is able to partition efficiently across lipid bilayers. SDS-PAGE and analytical ultracentrifugation demonstrate for the first time that the TM domain of E5 forms a strong dimer with a standard state free energy of dissociation of 5.0 kcal mol (-1). We have used our new results to interpret existing models of E5 dimer formation and provide a direct link between TM helix interactions and E5 function.
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Affiliation(s)
- Joanne Oates
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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46
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Brissett NC, Pitcher RS, Juarez R, Picher AJ, Green AJ, Dafforn TR, Fox GC, Blanco L, Doherty AJ. Structure of a NHEJ polymerase-mediated DNA synaptic complex. Science 2007; 318:456-9. [PMID: 17947582 DOI: 10.1126/science.1145112] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Nonhomologous end joining (NHEJ) is a critical DNA double-strand break (DSB) repair pathway required to maintain genome stability. Many prokaryotes possess a minimalist NHEJ apparatus required to repair DSBs during stationary phase, composed of two conserved core proteins, Ku and ligase D (LigD). The crystal structure of Mycobacterium tuberculosis polymerase domain of LigD mediating the synapsis of two noncomplementary DNA ends revealed a variety of interactions, including microhomology base pairing, mismatched and flipped-out bases, and 3' termini forming hairpin-like ends. Biochemical and biophysical studies confirmed that polymerase-induced end synapsis also occurs in solution. We propose that this DNA synaptic structure reflects an intermediate bridging stage of the NHEJ process, before end processing and ligation, with both the polymerase and the DNA sequence playing pivotal roles in determining the sequential order of synapsis and remodeling before end joining.
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Affiliation(s)
- Nigel C Brissett
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
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Small E, Marrington R, Rodger A, Scott DJ, Sloan K, Roper D, Dafforn TR, Addinall SG. FtsZ polymer-bundling by the Escherichia coli ZapA orthologue, YgfE, involves a conformational change in bound GTP. J Mol Biol 2007; 369:210-21. [PMID: 17428494 DOI: 10.1016/j.jmb.2007.03.025] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 03/07/2007] [Accepted: 03/09/2007] [Indexed: 10/23/2022]
Abstract
Cell division is a fundamental process for both eukaryotic and prokaryotic cells. In bacteria, cell division is driven by a dynamic, ring-shaped, cytoskeletal element (the Z-ring) made up of polymers of the tubulin-like protein FtsZ. It is thought that lateral associations between FtsZ polymers are important for function of the Z-ring in vivo, and that these interactions are regulated by accessory cell division proteins such as ZipA, EzrA and ZapA. We demonstrate that the putative Escherichia coli ZapA orthologue, YgfE, exists in a dimer/tetramer equilibrium in solution, binds to FtsZ polymers, strongly promotes FtsZ polymer bundling and is a potent inhibitor of the FtsZ GTPase activity. We use linear dichroism, a technique that allows structure analysis of molecules within linear polymers, to reveal a specific conformational change in GTP bound to FtsZ polymers, upon bundling by YgfE. We show that the consequences of FtsZ polymer bundling by YgfE and divalent cations are very similar in terms of GTPase activity, bundle morphology and GTP orientation and therefore propose that this conformational change in bound GTP reveals a general mechanism of FtsZ bundling.
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Affiliation(s)
- Elaine Small
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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Abstract
Structures of protein complexes offer some of the most interesting insights into biological processes. In this article, the methods required to show that the complex observed is the physiological one are investigated. Protein in crystal form is at an extremely high concentration and yet retains the complex secondary structure that defines an active protein. The protein crystal itself is made up of a repeating lattice of protein–protein and protein–solvent interactions. The problem that confronts any crystallographer is to identify those interactions that represent physiological interactions and those that do not. This review explores the tools that are available to provide such information using the original crystal liquor as a sample. The review is aimed at postgraduate and postdoctoral researchers who may well be coming up against this problem for the first time. Techniques are discussed that will provide information on the stoichiometry of complexes as well as low-resolution information on complex structure. Together, these data will help to identify the physiological complex.
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Affiliation(s)
- Timothy R Dafforn
- Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, England.
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Robertson AS, Belorgey D, Gubb D, Dafforn TR, Lomas DA. Inhibitory Activity of the Drosophila melanogaster Serpin Necrotic Is Dependent on Lysine Residues in the D-helix. J Biol Chem 2006; 281:26437-43. [PMID: 16835244 DOI: 10.1074/jbc.m606085200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Necrotic is a member of the serine protease inhibitor or serpin superfamily. It is a potent inhibitor of elastase and chymotrypsin type proteases and is responsible for regulating the anti-fungal response in Drosophila melanogaster. Necrotic contains three basic lysine residues within the D-helix that are homologous to those found in the heparin-binding domain of antithrombin and heparin co-factor II. We show here that substitution of all three lysine residues for glutamines caused cellular necrosis and premature death in Drosophila in keeping with a loss of function phenotype. The lysine to glutamine substitutions had no effect on the overall structure of recombinant Necrotic protein but abolished the formation of stable complexes with target proteases. Individual substitutions with either glutamine or alanine demonstrated that lysine 68 was the most critical residue for inhibitory activity. Despite the homology to other serpins, Necrotic did not bind, nor was it activated by sulfated glycans. These data demonstrate a critical role for basic residues within the D-helix (and lysine 68 in particular) in the inhibitory mechanism of the serpin Necrotic.
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Affiliation(s)
- Andrew S Robertson
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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Abstract
The use of linear dichroism (LD) spectroscopy for biological applications has been brought to the forefront recently by our development of thermostated microvolume Couette cells. We present a method for following the digestion of DNA by restriction endonucleases in real time without the use of any extrinsic dyes or labels. This is accomplished using linear dichroism spectroscopy (the differential absorbance of light polarized parallel and perpendicular to the sample orientation axis). The differential absorbance signal depends on the degree of alignment of the molecules. In this case the DNA is aligned by Couette flow (flowing the solution in the annular gap between two concentric cylinders), and we monitor the increase in alignment upon linearization of a circular DNA molecule. In addition, we observe a decrease in alignment upon further digestion and subsequent shortening of the DNA. Ten enzymes were investigated: seven enzymes with a single cut site (EcoRI, KpnI, NdeI, NotI, NruI, SmaI, XbaI), two enzymes with two cut sites (BstZ17I, EagI), and one enzyme with no cut site (ClaI). LD, as implemented in this new assay, is broadly applicable across a wide range of DNA-modifying enzymes and compounds and, as such, is a useful addition to the toolbox of biological characterization.
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Affiliation(s)
- Matthew R Hicks
- Department of Chemistry, University of Warwick, Coventry, UK.
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