1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.![]()
Collapse
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
| | | | | |
Collapse
|
3
|
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.![]()
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| | | | | |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Morris KL, Rodger A, Hicks MR, Debulpaep M, Schymkowitz J, Rousseau F, Serpell LC. Exploring the sequence-structure relationship for amyloid peptides. Biochem J 2013; 450:275-83. [PMID: 23252554 PMCID: PMC3573774 DOI: 10.1042/bj20121773] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [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: 11/23/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 01/10/2023]
Abstract
Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with 'steric-zipper' features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.
Collapse
Affiliation(s)
- Kyle L Morris
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
| | | | | | | | | | | | | |
Collapse
|
7
|
Madine J, Pandya MJ, Hicks MR, Rodger A, Yates EA, Radford SE, Middleton DA. Site-Specific Identification of an Aβ Fibril-Heparin Interaction Site by Using Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
8
|
Madine J, Pandya MJ, Hicks MR, Rodger A, Yates EA, Radford SE, Middleton DA. Site-specific identification of an aβ fibril-heparin interaction site by using solid-state NMR spectroscopy. Angew Chem Int Ed Engl 2012; 51:13140-3. [PMID: 23161730 PMCID: PMC3749465 DOI: 10.1002/anie.201204459] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 10/04/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Jillian Madine
- Institute of Integrative Biology, University of Liverpool, UK
| | | | | | | | | | | | | |
Collapse
|
9
|
Orwick-Rydmark M, Lovett JE, Graziadei A, Lindholm L, Hicks MR, Watts A. Detergent-free incorporation of a seven-transmembrane receptor protein into nanosized bilayer Lipodisq particles for functional and biophysical studies. Nano Lett 2012; 12:4687-92. [PMID: 22827450 DOI: 10.1021/nl3020395] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
SMA-Lipodisq nanoparticles, with one bacteriorhodopsin (bR) per 12 nm particle on average (protein/lipid molar ratio, 1:172), were prepared without the use of detergents. Using pulsed and continuous wave nitroxide spin label electron paramagnetic resonance, the structural and dynamic integrity of bR was retained when compared with data for bR obtained in the native membrane and in detergents and then with crystal data. This indicates the potential of Lipodisq nanoparticles as a useful membrane mimetic.
Collapse
Affiliation(s)
- Marcella Orwick-Rydmark
- Department of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | | | | | | | | | | |
Collapse
|
10
|
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
| |
Collapse
|
11
|
Rittman M, Hoffmann SV, Gilroy E, Hicks MR, Finkenstadt B, Rodger A. Probing the structure of long DNA molecules in solution using synchrotron radiation linear dichroism. Phys Chem Chem Phys 2012; 14:353-66. [DOI: 10.1039/c1cp22371b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
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
| |
Collapse
|
13
|
Abstract
Circular dichroism (CD) has become an increasingly important tool in the study of biological molecules as it enables structural information to be obtained nondestructively on solution-phase samples. However, sample requirements for CD are often seen as being too high with protein backbone measurements in standard cuvettes typically requiring ∼100-300 μL of 0.1 mg/ml protein. To address this issue, we have designed a new form of CD sample holder, which reduces the sample requirements of the technique by two orders of magnitude, with a sample requirement of less than 3 μl. This sample saving has been achieved through the use of extruded quartz capillaries, the sample being held within the internal diameter of the quartz capillary through capillary action. The extruded quartz capillaries exhibit remarkably little birefringence, although still transmitting high energy UV circularly polarized light. The optics associated with capillaries were investigated. A configuration has been adopted with the light beam of the spectrophotometer being focused in front of the front face of the capillary using a biconvex lens and advantage being taken of the additional focusing effect of the capillary itself. The focusing is vital to the low wavelength performance of the cell, where we have acquired reliable data down to 180 nm using a Jasco J-815 spectrophotometer. The system performance was validated with Na[Co(EDDS)].H(2)O (EDDS = N,N-ethylenediaminedisuccinic acid), concanavalin A, lysozyme, and progesterone.
Collapse
Affiliation(s)
- Daniel E Waldron
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | | | | | | | | |
Collapse
|
14
|
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).
Collapse
|
15
|
Gilroy EL, Hicks MR, Smith DJ, Rodger A. Viscosity of aqueous DNA solutions determined using dynamic light scattering. Analyst 2011; 136:4159-63. [DOI: 10.1039/c1an15475c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
16
|
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.
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Karen E Marshall
- Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
18
|
Hamley IW, Castelletto V, Moulton CM, Rodríguez-Pérez J, Squires AM, Eralp T, Held G, Hicks MR, Rodger A. Alignment of a Model Amyloid Peptide Fragment in Bulk and at a Solid Surface. J Phys Chem B 2010; 114:8244-54. [DOI: 10.1021/jp101374e] [Citation(s) in RCA: 31] [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: 01/15/2023]
|
19
|
Chen L, Morris K, Laybourn A, Elias D, Hicks MR, Rodger A, Serpell L, Adams DJ. Self-assembly mechanism for a naphthalene-dipeptide leading to hydrogelation. Langmuir 2010; 26:5232-42. [PMID: 19921840 DOI: 10.1021/la903694a] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Suitably functionalized dipeptides have been shown to be effective hydrogelators. The design of the hydrogelators and the mechanism by which hydrogelation occurs are both currently not well understood. Here, we have utilized the hydrolysis of glucono-delta-lactone to gluconic acid as a means of adjusting the pH in a naphthalene-alanylvaline solution allowing the specific targeting of the final pH. In addition, this method allows the assembly process to be characterized. We show that assembly begins as charge is removed from the C-terminus of the dipeptide. The removal of charge allows lateral assembly of the molecules leading to pi-pi stacking (shown by CD) and beta-sheet formation (as shown by IR and X-ray fiber diffraction). This leads to the formation of fibrous structures. Electron microscopy reveals that thin fibers form initially, with low persistence length. Lateral association then occurs to give bundles of fibers with higher persistence length. This results in the initially weak hydrogel becoming stronger with time. The final mechanical properties of the hydrogels are very similar irrespective of the amount of GdL added; rather, the time taken to achieving the final gel is determined by the GdL concentration. However, differences are observed between the networks under strain, implying that the kinetics of assembly do impart different final materials' properties. Overall, this study provides detailed understanding of the assembly process that leads to hydrogelation.
Collapse
Affiliation(s)
- Lin Chen
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | | | | | | | | | | | | | | |
Collapse
|
20
|
|
21
|
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
| |
Collapse
|
22
|
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.
Collapse
Affiliation(s)
- Matthew R Hicks
- Department of Chemistry, University of Warwick, Coventry, UK CV4 7AL.
| | | | | | | | | | | |
Collapse
|
23
|
Ennaceur SM, Hicks MR, Pridmore CJ, Dafforn TR, Rodger A, Sanderson JM. Peptide adsorption to lipid bilayers: slow processes revealed by linear dichroism spectroscopy. Biophys J 2009; 96:1399-407. [PMID: 19217857 DOI: 10.1016/j.bpj.2008.10.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 10/28/2008] [Indexed: 12/16/2022] Open
Abstract
The adsorption and insertion kinetics for the association of two 34-residue cyclic peptides with phosphocholine membranes have been studied using circular and linear dichroism approaches. The two peptides studied are identical with the exception of two residues, which are both tyrosine in one of the peptides and tryptophan in the other. Both peptides adopt random coil conformations in solution in the absence of membranes and do not aggregate at concentrations below 20 microM. After addition to liposome dispersions, circular dichroism spectroscopy indicated that both peptides undergo an extremely rapid transformation to a beta-conformation that remains unchanged throughout the remainder of the experiment. Linear dichroism (LD) spectroscopy was used to study the kinetics of membrane adsorption and insertion. The data were analyzed by nonlinear least squares approaches, leading to identification of a number of bound states and their corresponding LD spectra. Two pseudo-first order processes could be identified that were common to both peptides. The first occurred with a time constant of the order of 1 min and led to a bound state characterized by weak LD signals, with significant bands corresponding to the transitions of aromatic side chains. The second process occurred with an unusually long time constant of between 75 and 100 min, forming a state with considerably stronger positive LD absorbance in the far-ultraviolet region of the spectrum. For the tyrosine-substituted peptide, a third slow process with a long time constant (76 min) could also be delineated and was attributed to rearrangements of the peptide within the membrane.
Collapse
Affiliation(s)
- Sue M Ennaceur
- Department of Chemistry, University Science Laboratories, Durham, DH1 3LE, United Kingdom
| | | | | | | | | | | |
Collapse
|
24
|
McDonnell U, Hicks MR, Hannon MJ, Rodger A. DNA binding and bending by dinuclear complexes comprising ruthenium polypyridyl centres linked by a bis(pyridylimine) ligand. J Inorg Biochem 2008; 102:2052-9. [DOI: 10.1016/j.jinorgbio.2008.06.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2008] [Revised: 06/03/2008] [Accepted: 06/03/2008] [Indexed: 11/16/2022]
|
25
|
Hicks MR, Rullay AK, Pedrido R, Crout DH, Pinheiro TJT. Efficient Synthesis of Methanesulphonate-Derived Lipid Chains for Attachment of Proteins to Lipid Membranes. SYNTHETIC COMMUN 2008. [DOI: 10.1080/00397910802213794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Matthew R. Hicks
- a Department of Biological Sciences , University of Warwick , Coventry, UK
- b Department of Chemistry , University of Warwick , Coventry, UK
| | - Atvinder K. Rullay
- a Department of Biological Sciences , University of Warwick , Coventry, UK
| | - Rosa Pedrido
- c Department of Inorganic Chemistry, Faculty of Chemistry , University of Santiago de Compostela, Santiago de Compostela , Galicia, Spain
| | - David H. Crout
- a Department of Biological Sciences , University of Warwick , Coventry, UK
| | | |
Collapse
|
26
|
Damianoglou A, Crust EJ, Hicks MR, Howson SE, Knight AE, Ravi J, Scott P, Rodger A. A new reference material for UV-visible circular dichroism spectroscopy. Chirality 2008; 20:1029-38. [DOI: 10.1002/chir.20566] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
27
|
Conner M, Hicks MR, Dafforn T, Knowles TJ, Ludwig C, Staddon S, Overduin M, Günther UL, Thome J, Wheatley M, Poyner DR, Conner AC. Functional and biophysical analysis of the C-terminus of the CGRP-receptor; a family B GPCR. Biochemistry 2008; 47:8434-44. [PMID: 18636754 DOI: 10.1021/bi8004126] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-protein coupled receptors (GPCRs) typically have a functionally important C-terminus which, in the largest subfamily (family A), includes a membrane-parallel eighth helix. Mutations of this region are associated with several diseases. There are few C-terminal studies on the family B GPCRs and no data supporting the existence of a similar eighth helix in this second major subfamily, which has little or no sequence homology to family A GPCRs. Here we show that the C-terminus of a family B GPCR (CLR) has a disparate region from N400 to C436 required for CGRP-mediated internalization, and a proximal region of twelve residues (from G388 to W399), in a similar position to the family A eighth helix, required for receptor localization at the cell surface. A combination of circular and linear dichroism, fluorescence and modified waterLOGSY NMR spectroscopy (SALMON) demonstrated that a peptide mimetic of this domain readily forms a membrane-parallel helix anchored to the liposome by an interfacial tryptophan residue. The study reveals two key functions held within the C-terminus of a family B GPCR and presents support for an eighth helical region with striking topological similarity to the nonhomologous family A receptor. This helix structure appears to be found in most other family B GPCRs.
Collapse
|
28
|
McDonnell U, Kerchoffs JMCA, Castineiras RPM, Hicks MR, Hotze ACG, Hannon MJ, Rodger A. Synthesis and cytotoxicity of dinuclear complexes containing ruthenium(ii) bipyridyl units linked by a bis(pyridylimine) ligand. Dalton Trans 2008:667-75. [DOI: 10.1039/b711080d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
29
|
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.
Collapse
Affiliation(s)
- Matthew R Hicks
- Department of Chemistry, University of Warwick, Coventry, UK.
| | | | | | | | | |
Collapse
|
30
|
Hicks MR, Gill AC, Bath IK, Rullay AK, Sylvester ID, Crout DH, Pinheiro TJT. Synthesis and structural characterization of a mimetic membrane-anchored prion protein. FEBS J 2006; 273:1285-99. [PMID: 16519692 DOI: 10.1111/j.1742-4658.2006.05152.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [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: 11/28/2022]
Abstract
During pathogenesis of transmissible spongiform encephalopathies (TSEs) an abnormal form (PrP(Sc)) of the host encoded prion protein (PrP(C)) accumulates in insoluble fibrils and plaques. The two forms of PrP appear to have identical covalent structures, but differ in secondary and tertiary structure. Both PrP(C) and PrP(Sc) have glycosylphospatidylinositol (GPI) anchors through which the protein is tethered to cell membranes. Membrane attachment has been suggested to play a role in the conversion of PrP(C) to PrP(Sc), but the majority of in vitro studies of the function, structure, folding and stability of PrP use recombinant protein lacking the GPI anchor. In order to study the effects of membranes on the structure of PrP, we synthesized a GPI anchor mimetic (GPIm), which we have covalently coupled to a genetically engineered cysteine residue at the C-terminus of recombinant PrP. The lipid anchor places the protein at the same distance from the membrane as does the naturally occurring GPI anchor. We demonstrate that PrP coupled to GPIm (PrP-GPIm) inserts into model lipid membranes and that structural information can be obtained from this membrane-anchored PrP. We show that the structure of PrP-GPIm reconstituted in phosphatidylcholine and raft membranes resembles that of PrP, without a GPI anchor, in solution. The results provide experimental evidence in support of previous suggestions that NMR structures of soluble, anchor-free forms of PrP represent the structure of cellular, membrane-anchored PrP. The availability of a lipid-anchored construct of PrP provides a unique model to investigate the effects of different lipid environments on the structure and conversion mechanisms of PrP.
Collapse
Affiliation(s)
- Matthew R Hicks
- Department of Biological Sciences, University of Warwick, Coventry, UK
| | | | | | | | | | | | | |
Collapse
|
31
|
Hicks MR, Al-Mehairi SS, Sinclair AJ. The zipper region of Epstein-Barr virus bZIP transcription factor Zta is necessary but not sufficient to direct DNA binding. J Virol 2003; 77:8173-7. [PMID: 12829857 PMCID: PMC161931 DOI: 10.1128/jvi.77.14.8173-8177.2003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The viral bZIP transcription factor Zta (BZLF1, EB1, ZEBRA) mediates the switch between the latent and lytic cycles of Epstein-Barr virus (EBV). In part, its activity requires the formation of homodimers and interaction with specific DNA sequence elements (ZREs). Zta has an atypical zipper motif that has a lower stability than do typical bZIP proteins. Here we show that a synthetic peptide directed against the zipper can disrupt the DNA-binding function of Zta. This highlights the relevance of this region for the function of Zta and demonstrates that the zipper region is a potential target for therapeutic agents. We also unmask the relevance of a region adjacent to the zipper (CT region), which is required to direct the interaction of Zta with DNA and to transactivate ZRE-dependent promoters in vivo.
Collapse
Affiliation(s)
- Matthew R Hicks
- School of Biological Sciences, University of Sussex, Brighton, East Sussex BN1 9QG, United Kingdom
| | | | | |
Collapse
|
32
|
Abstract
Crick envisaged the alpha-helical coiled coil to result from systematic bending of an alpha-helix such that every seventh residue was structurally equivalent, and he derived equations for the coordinates of the backbone atoms. Crick's predictions were vindicated experimentally and coiled-coil sequences were shown to have hydrophobic residues alternately spaced 3 and 4 residues apart. Nonetheless, in some coiled coils such canonical heptad repeats are interrupted by inserts of 3 or 4 residues generating decad and hendecad motifs. The supercoiling of the coiled coils varies with the sequence pattern, being left- or right-handed in purely heptad-based or hendecad-based motifs, respectively. To model coiled coils with a mixture of motifs, we describe how Crick's equations can be modified for cases where the pitch is not constant. Using the analogy of the bending of a beam, we took the tilt angle to change linearly with distance along the major helix and the pitch of a motif to be affected by neighboring motifs depending on the rigidity of the alpha-helical strands. We tested our approach by fitting the two-, three-, and four-stranded noncanonical coiled coils of GrpE, hemagglutinin, and tetrabrachion. The backbone atoms of the model and crystal structures agreed with root mean square deviations of <1.1 A.
Collapse
Affiliation(s)
- Gerald Offer
- Muscle Contraction Group, Department of Physiology, Medical School, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom.
| | | | | |
Collapse
|
33
|
Abstract
Coiled-coil motifs foster a wide variety of protein-protein interactions. Canonical coiled coils are based on 7-residue repeats, which guide the folding and assembly of amphipathic alpha-helices. In many cases such repeats remain unbroken for tens to hundreds of residues. However, the sequences of an increasing number of putative and characterised coiled coils digress from this pattern. We probed the consequences of nonheptad inserts using a designed leucine-zipper system. The parent peptide, SKIP0, which had four contiguous heptads, was confirmed as a parallel homodimer by circular dichroism spectroscopy and analytical ultracentrifugation. Seven daughter peptides were constructed in which 1 to 7 alanine residues were inserted between the central heptads of SKIP0. Like SKIP0, SKIP7 formed a stable helical dimer, but the other peptides were highly destabilised, with the order of dimer stability SKIP4 >> SKIP5 > SKIP6 > SKIP3 > SKIP2 > SKIP1. These results are consistent with an extended theory of coiled-coil assembly in which coiled-coil-compatible motifs are based on 3- and 4-residue spacings and most notably heptad (7-residue) and hendecad (11-residue) repeats. Thus, they help explain why in natural sequences, inserts after canonical heptad repeats most commonly comprise 4 residues. Possible biological roles for nonheptad inserts are discussed.
Collapse
Affiliation(s)
- Matthew R Hicks
- Centre for Biomolecular Design and Drug Development, School of Biological Sciences, University of Sussex, Falmer, BN1 9QG, United Kingdom
| | | | | |
Collapse
|
34
|
Hicks MR, Balesaria S, Medina-Palazon C, Pandya MJ, Woolfson DN, Sinclair AJ. Biophysical analysis of natural variants of the multimerization region of Epstein-Barr virus lytic-switch protein BZLF1. J Virol 2001; 75:5381-4. [PMID: 11333921 PMCID: PMC114945 DOI: 10.1128/jvi.75.11.5381-5384.2001] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BZLF1 plays a key role in the induction of Epstein-Barr virus (EBV) replication. On the basis of limited sequence homology and mutagenesis experiments, BZLF1 has been described as a member of the bZip family of transcription factors, but this prospect has not been rigorously tested to date. Here, we present biophysical analysis of the multimerization domain of BZLF1, from three natural variants of EBV, and demonstrate for the first time that the region between amino acids 196 and 227 is sufficient to direct folding as a coiled-coil dimer in vitro.
Collapse
Affiliation(s)
- M R Hicks
- School of Biological Sciences, School of Biological Sciences, University of Sussex, Brighton, East Sussex BN1 9QG, United Kingdom
| | | | | | | | | | | |
Collapse
|
35
|
Abstract
BACKGROUND The seven-residue heptad repeat is the accepted hallmark of coiled coils. In extended filamentous proteins, however, contiguous patterns of heptads are often disrupted by 'skips' and 'stammers'. The structural consequences and roles of these digressions are not understood. RESULTS In a cytoskeleton protein from Giardia lamblia, heptads flank eleven-residue units (hendecads) to give a 7-11-7 motif that dominates the sequence. Synthetic peptides made to the consensus sequence of this motif fold in solution to fully helical, parallel dimers. Both the sequence pattern and these experimental data are consistent with the coiled-coil model. We note that breaks in other extended coiled coils can also be reconciled by hendecad insertions. CONCLUSIONS The heptad paradigm for the coiled coil must be expanded to include hendecads. As different combinations of heptads and hendecads will give different overall sequence motifs, we propose that these provide a mechanism to promote cognate protein pairings during the folding of extended coiled coils in the cell.
Collapse
Affiliation(s)
- M R Hicks
- Centre for Biomolecular Design and Drug Development, School of Biological Sciences, University of Sussex, Falmer, UK
| | | | | | | |
Collapse
|
36
|
Hicks MR, Johansson CB, Heinze AM, Halscott JF. Teacher and parent checklist ratings with learning-disabled, hyperactive, and emotionally disturbed children. J Pediatr Psychol 1981; 6:43-60. [PMID: 7252714 DOI: 10.1093/jpepsy/6.1.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
|