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Albano G, Taddeucci A, Pescitelli G, Di Bari L. Spatially Resolved Chiroptical Spectroscopies Emphasizing Recent Applications to Thin Films of Chiral Organic Dyes. Chemistry 2023; 29:e202301982. [PMID: 37515814 DOI: 10.1002/chem.202301982] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023]
Abstract
Instrumental techniques able to identify and structurally characterize the aggregation states in thin films of chiral organic π-conjugated materials, from the first-order supramolecular arrangement up to the microscopic and mesoscopic scale, are very helpful for clarifying structure-property relationships. Chiroptical imaging is currently gaining a central role, for its ability of mapping local supramolecular structures in thin films. The present review gives an overview of electronic circular dichroism imaging (ECDi), circularly polarized luminescence imaging (CPLi), and vibrational circular dichroism imaging (VCDi), with a focus on their applications on thin films of chiral organic dyes as case studies.
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Affiliation(s)
- Gianluigi Albano
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124, Pisa, Italy
| | - Andrea Taddeucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124, Pisa, Italy
- Diamond Light Source, Ltd., Chilton, Didcot, OX11 0DE, UK
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124, Pisa, Italy
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2
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Bardelang P, Murray EJ, Blower I, Zandomeneghi S, Goode A, Hussain R, Kumari D, Siligardi G, Inoue K, Luckett J, Doutch J, Emsley J, Chan WC, Hill P, Williams P, Bonev BB. Conformational analysis and interaction of the Staphylococcus aureus transmembrane peptidase AgrB with its AgrD propeptide substrate. Front Chem 2023; 11:1113885. [PMID: 37214482 PMCID: PMC10196373 DOI: 10.3389/fchem.2023.1113885] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Virulence gene expression in the human pathogen, S. aureus is regulated by the agr (accessory gene regulator) quorum sensing (QS) system which is conserved in diverse Gram-positive bacteria. The agr QS signal molecule is an autoinducing peptide (AIP) generated via the initial processing of the AgrD pro-peptide by the transmembrane peptidase AgrB. Since structural information for AgrB and AgrBD interactions are lacking, we used homology modelling and molecular dynamics (MD) annealing to characterise the conformations of AgrB and AgrD in model membranes and in solution. These revealed a six helical transmembrane domain (6TMD) topology for AgrB. In solution, AgrD behaves as a disordered peptide, which binds N-terminally to membranes in the absence and in the presence of AgrB. In silico, membrane complexes of AgrD and dimeric AgrB show non-equivalent AgrB monomers responsible for initial binding and for processing, respectively. By exploiting split luciferase assays in Staphylococcus aureus, we provide experimental evidence that AgrB interacts directly with itself and with AgrD. We confirmed the in vitro formation of an AgrBD complex and AIP production after Western blotting using either membranes from Escherichia coli expressing AgrB or with purified AgrB and T7-tagged AgrD. AgrB and AgrD formed stable complexes in detergent micelles revealed using synchrotron radiation CD (SRCD) and Landau analysis consistent with the enhanced thermal stability of AgrB in the presence of AgrD. Conformational alteration of AgrB following provision of AgrD was observed by small angle X-ray scattering from proteodetergent micelles. An atomistic description of AgrB and AgrD has been obtained together with confirmation of the AgrB 6TMD membrane topology and existence of AgrBD molecular complexes in vitro and in vivo.
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Affiliation(s)
- Philip Bardelang
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ewan J. Murray
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Isobel Blower
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Sara Zandomeneghi
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alice Goode
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Divya Kumari
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Giuliano Siligardi
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Katsuaki Inoue
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Jeni Luckett
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - James Doutch
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
| | - Jonas Emsley
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Weng C. Chan
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Philip Hill
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Boyan B. Bonev
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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3
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Buckley A, Warren J, Hussain R, Smith R. Synchrotron radiation circular dichroism spectroscopy reveals that gold and silver nanoparticles modify the secondary structure of a lung surfactant protein B analogue. NANOSCALE 2023; 15:4591-4603. [PMID: 36763129 DOI: 10.1039/d2nr06107d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Inhaled nanoparticles (NPs) depositing in the alveolar region of the lung interact initially with a surfactant layer and in vitro studies have demonstrated that NPs can adversely affect the biophysical function of model pulmonary surfactants (PS), of which surfactant protein B (SP-B) is a key component. Other studies have demonstrated the potential for NPs to modify the structure and function of proteins. It was therefore hypothesised that NPs may affect the biophysical function of PS by modifying the structure of SP-B. Synchrotron radiation circular dichroism (SRCD) spectroscopy was used to explore the effect of various concentrations of gold nanoparticles (AuNPs) (5, 10, 20 nm), silver nanoparticles (AgNPs) (10 nm) and silver citrate on the secondary structure of surfactant protein B analogue, SP-B1-25, in a TFE/PB dispersion. For Au and Ag NPs the SRCD spectra indicated a concentration dependent reduction in the α-helical structure of SP-B1-25 (5 nm AuNP ≈ 10 nm AgNP ≫ 10 nm AuNP > 20 nm AuNP). For AuNPs the effect was greater for the 5 nm size, which was not fully explained by consideration of surface area. The impact of the 10 nm AgNPs was greater than that of the 10 nm AuNPs and the effect of AgNPs was greater than that of silver citrate at equivalent Ag mass concentrations. For 10 nm AuNPs, SRCD spectra for dispersions in, the more physiologically relevant, DPPC showed a similar concentration dependent pattern. The results demonstrate the potential for inhaled NPs to modify SP-B1-25 structure and thus potentially adversely impact the physiological function of the lung, however, further studies are necessary to confirm this.
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Affiliation(s)
- Alison Buckley
- Toxicology Department, UK Health Security Agency, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0RQ, UK.
| | - James Warren
- Toxicology Department, UK Health Security Agency, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0RQ, UK.
| | - Rohanah Hussain
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Rachel Smith
- Toxicology Department, UK Health Security Agency, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0RQ, UK.
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Ruzza P, Honisch C, Hussain R, Siligardi G. Free Radical Generation in Far-UV Synchrotron Radiation Circular Dichroism Assays-Protein and Buffer Composition Contribution. Int J Mol Sci 2021; 22:11325. [PMID: 34768758 PMCID: PMC8583428 DOI: 10.3390/ijms222111325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022] Open
Abstract
A useful tool to analyze the ligands and/or environmental contribution to protein stability is represented by the Synchrotron Radiation Circular Dichroism UV-denaturation assay that consists in the acquisition of several consecutive repeated far-UV SRCD spectra. Recently we demonstrated that the prevailing mechanism of this denaturation involves the generation of free radicals and reactive oxygen species (ROS). In this work, we analyzed the effect of buffering agents commonly used in spectroscopic measurements, including MOPS (3-(N-morpholino) propanesulfonic acid), HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), TRIS-HCl (tris-hydroxymethil aminomethane hydrochloride), and phosphate, on the efficiency of protein denaturation caused by exposure to UV radiation. Fluorescence experiments confirmed the presence of ROS and were used to determine the rate of ROS generation. Our results indicate that the efficiency of the denaturation process is strongly influenced by the buffer composition with MOPS and HEPES acting also as scavengers and that the presence of proteins itself influenced the ROS formation rate.
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Affiliation(s)
- Paolo Ruzza
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo, 1, 35131 Padova, Italy;
| | - Claudia Honisch
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo, 1, 35131 Padova, Italy;
- Department of Chemical Sciences, University of Padua, via Marzolo, 1, 35131 Padova, Italy
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK;
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK;
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Ruzza P, Honisch C, Hussain R, Siligardi G. Free Radicals and ROS Induce Protein Denaturation by UV Photostability Assay. Int J Mol Sci 2021; 22:ijms22126512. [PMID: 34204483 PMCID: PMC8234878 DOI: 10.3390/ijms22126512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
Oxidative stress, photo-oxidation, and photosensitizers are activated by UV irradiation and are affecting the photo-stability of proteins. Understanding the mechanisms that govern protein photo-stability is essential for its control enabling enhancement or reduction. Currently, two major mechanisms for protein denaturation induced by UV irradiation are available: one generated by the local heating of water molecules bound to the proteins and the other by the formation of reactive free radicals. To discriminate which is the likely or dominant mechanism we have studied the effects of thermal and UV denaturation of aqueous protein solutions with and without DHR-123 as fluorogenic probe using circular dichroism (CD), synchrotron radiation circular dichroism (SRCD), and fluorescence spectroscopies. The results indicated that the mechanism of protein denaturation induced by VUV and far-UV irradiation were mediated by the formation of reactive free radicals (FR) and reactive oxygen species (ROS). The development at Diamond B23 beamline for SRCD of a novel protein UV photo-stability assay based on consecutive repeated CD measurements in the far-UV (180-250 nm) region has been successfully used to assess and characterize the photo-stability of protein formulations and ligand binding interactions, in particular for ligand molecules devoid of significant UV absorption.
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Affiliation(s)
- Paolo Ruzza
- Padova Unit, Institute of Biomolecular Chemistry of CNR (ICB-CNR), Via F. Marzolo, 1, 35030 Padova, Italy;
- Correspondence: (P.R.); (G.S.); Tel.: +44-(0)1235-778425 (G.S.); Fax: +39-049-827-5239 (P.R.)
| | - Claudia Honisch
- Padova Unit, Institute of Biomolecular Chemistry of CNR (ICB-CNR), Via F. Marzolo, 1, 35030 Padova, Italy;
- Department of Chemical Sciences, University of Padua, Via F. Marzolo, 1, 35030 Padova, Italy
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK;
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK;
- Correspondence: (P.R.); (G.S.); Tel.: +44-(0)1235-778425 (G.S.); Fax: +39-049-827-5239 (P.R.)
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Mapping the Chiroptical Properties of Local Domains in Thin Films of Chiral Silicon Phthalocyanines by CD Imaging. Molecules 2020; 25:molecules25246048. [PMID: 33371353 PMCID: PMC7767354 DOI: 10.3390/molecules25246048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/02/2022] Open
Abstract
The first example of uniformly chiral thin films of silicon phthalocyanines (SiPcs) are reported. The local domains of the films are mapped using circular dichroism (CD) imaging (CDi) technique available at the Diamond B23 beamline. The CDi allowed us to increase the spatial resolution up to 525× when compared with benchtop spectrometers. The results indicate formation on-surface of chiral and stable supramolecular assemblies with homogenous distribution. Chemical functionalization and solvent choice for deposition allow controllable chiroptical properties to be obtained. The method and technique reported in this work could be applied to prepare and characterize a wide variety of chiral thin films.
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Nilsson O, Lindvall M, Obici L, Ekström S, Lagerstedt JO, Del Giudice R. Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux. J Lipid Res 2020; 62:100004. [PMID: 33410751 PMCID: PMC7890215 DOI: 10.1194/jlr.ra120000920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/04/2020] [Accepted: 11/17/2020] [Indexed: 01/17/2023] Open
Abstract
Apolipoprotein A-I (ApoA-I) of high density lipoproteins (HDLs) is essential for the transportation of cholesterol between peripheral tissues and the liver. However, specific mutations in ApoA-I of HDLs are responsible for a late-onset systemic amyloidosis, the pathological accumulation of protein fibrils in tissues and organs. Carriers of these mutations do not exhibit increased cardiovascular disease risk despite displaying reduced levels of ApoA-I/HDL cholesterol. To explain this paradox, we show that the HDL particle profiles of patients carrying either L75P or L174S ApoA-I amyloidogenic variants show a higher relative abundance of the 8.4-nm versus 9.6-nm particles and that serum from patients, as well as reconstituted 8.4- and 9.6-nm HDL particles (rHDL), possess increased capacity to catalyze cholesterol efflux from macrophages. Synchrotron radiation circular dichroism and hydrogen-deuterium exchange revealed that the variants in 8.4-nm rHDL have altered secondary structure composition and display a more flexible binding to lipids than their native counterpart. The reduced HDL cholesterol levels of patients carrying ApoA-I amyloidogenic variants are thus balanced by higher proportion of small, dense HDL particles, and better cholesterol efflux due to altered, region-specific protein structure dynamics.
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Affiliation(s)
- Oktawia Nilsson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Mikaela Lindvall
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Laura Obici
- Amyloidosis Research & Treatment Centre, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Simon Ekström
- BioMS - Swedish National Infrastructure for Biological Mass Spectrometry, Lund University, Lund, Sweden
| | - Jens O Lagerstedt
- Department of Experimental Medical Science, Lund University, Lund, Sweden; Lund Institute of Advanced Neutron and X-ray Science (LINXS), Lund, Sweden.
| | - Rita Del Giudice
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
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8
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Diamond B23 CD Imaging of Thin Films of Chiral Materials or Achiral Polymers Coated with Chiral Molecules. Symmetry (Basel) 2020. [DOI: 10.3390/sym12111847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The novel vertical sample chamber, developed at the B23 beamline for synchrotron radiation circular dichroism (SRCD), has enabled the Diamond User community to conduct different types of experiments from high throughput CD of protein and DNA folding using 96-well multiplates to CD imaging at high spatial resolution. Here, we present the application of CD imaging to large areas of achiral polymer PVA films doped with D-dopa to assess the chiral homogeneity of the film preparation with potential antimicrobial property. Synopsis: CDi application of Diamond B23 SRCD beamline.
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9
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Albano G, Pescitelli G, Di Bari L. Chiroptical Properties in Thin Films of π-Conjugated Systems. Chem Rev 2020; 120:10145-10243. [PMID: 32892619 DOI: 10.1021/acs.chemrev.0c00195] [Citation(s) in RCA: 235] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chiral π-conjugated molecules provide new materials with outstanding features for current and perspective applications, especially in the field of optoelectronic devices. In thin films, processes such as charge conduction, light absorption, and emission are governed not only by the structure of the individual molecules but also by their supramolecular structures and intermolecular interactions to a large extent. Electronic circular dichroism, ECD, and its emission counterpart, circularly polarized luminescence, CPL, provide tools for studying aggregated states and the key properties to be sought for designing innovative devices. In this review, we shall present a comprehensive coverage of chiroptical properties measured on thin films of organic π-conjugated molecules. In the first part, we shall discuss some general concepts of ECD, CPL, and other chiroptical spectroscopies, with a focus on their applications to thin film samples. In the following, we will overview the existing literature on chiral π-conjugated systems whose thin films have been characterized by ECD and/or CPL, as well other chiroptical spectroscopies. Special emphasis will be put on systems with large dissymmetry factors (gabs and glum) and on the application of ECD and CPL to derive structural information on aggregated states.
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Affiliation(s)
- Gianluigi Albano
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
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10
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Enzyme-Ligand Interaction Monitored by Synchrotron Radiation Circular Dichroism. Methods Mol Biol 2019. [PMID: 31773649 DOI: 10.1007/978-1-0716-0163-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
CD spectroscopy is the essential tool to quickly ascertain in the far-UV region the global conformational changes, the secondary structure content, and protein folding and in the near-UV region the local tertiary structure changes probed by the local environment of the aromatic side chains, prosthetic groups (hemes, flavones, carotenoids), the dihedral angle of disulfide bonds, and the ligand chromophore moieties, the latter occurring as a result of protein-ligand binding interaction. Qualitative and quantitative investigations into ligand-binding interactions in both the far- and near-UV regions using CD spectroscopy provide unique and direct information whether induced conformational changes upon ligand binding occur and of what nature that are unattainable with other techniques such as fluorescence, ITC, SPR, and AUC.This chapter provides an overview of how to perform circular dichroism (CD) experiments, detailing methods, hints and tips for successful CD measurements. Descriptions of different experimental designs are discussed using CD to investigate ligand-binding interactions. This includes standard qualitative CD measurements conducted in both single-measurement mode and high-throughput 96-well plate mode, CD titrations, and UV protein denaturation assays with and without ligand.The highly collimated micro-beam available at B23 beamline for synchrotron radiation circular dichroism (SRCD) at Diamond Light Source (DLS) offers many advantages to benchtop instruments. The synchrotron light source is ten times brighter than a standard xenon arc light source of benchtop instruments. The small diameter of the synchrotron beam can be up to 160 times smaller than that of benchtop light beams; this has enabled the use of small aperture cuvette cells and flat capillary tubes reducing substantially the amount of volume sample to be investigated. Methods, hints and tips, and golden rules to measure good quality, artifact-free SRCD and CD data will be described in this chapter in particular for the study of protein-ligand interactions and protein photostability.
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Kwan TOC, Reis R, Siligardi G, Hussain R, Cheruvara H, Moraes I. Selection of Biophysical Methods for Characterisation of Membrane Proteins. Int J Mol Sci 2019; 20:E2605. [PMID: 31137900 PMCID: PMC6566885 DOI: 10.3390/ijms20102605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 02/01/2023] Open
Abstract
Over the years, there have been many developments and advances in the field of integral membrane protein research. As important pharmaceutical targets, it is paramount to understand the mechanisms of action that govern their structure-function relationships. However, the study of integral membrane proteins is still incredibly challenging, mostly due to their low expression and instability once extracted from the native biological membrane. Nevertheless, milligrams of pure, stable, and functional protein are always required for biochemical and structural studies. Many modern biophysical tools are available today that provide critical information regarding to the characterisation and behaviour of integral membrane proteins in solution. These biophysical approaches play an important role in both basic research and in early-stage drug discovery processes. In this review, it is not our objective to present a comprehensive list of all existing biophysical methods, but a selection of the most useful and easily applied to basic integral membrane protein research.
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Affiliation(s)
- Tristan O C Kwan
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Rosana Reis
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Harish Cheruvara
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
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Abstract
Binding of calcium - and small molecules in general - often induce conformational changes in large molecules and complexes. The degree and type of change varies, but the resulting shift in specific affinities ultimately induces a physiological response. It is therefore important for our understanding of responses at the cellular level to define coupled changes at the molecular level.Calumenin, a six-EF-hand calcium-binding protein localized in the endoplasmic reticulum, undergoes substantial calcium-induced rearrangement. We have demonstrated how calumenin changes from being unfolded in the absence of calcium to a compact trilobal fold in the presence of calcium (Mazzorana et al., PLoS One 11:e0151547, 2016).Here, we describe protocols for the expression and purification of calumenin and calmodulin, another EF-hand protein modulated by calcium, along with protocols for biophysical techniques used to characterize calcium-induced changes to protein conformation. Analytical size-exclusion chromatography in the presence and absence of calcium provides an informed indication of any larger conformational movements. Circular dichroism spectroscopy reveals alterations to the secondary or tertiary structure, while small-angle X-ray scattering explores changes further providing low-resolution conformational details.Surface plasmon resonance estimates binding kinetics and affinities completing the biophysical description of these events.
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Affiliation(s)
- Marco Mazzorana
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
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13
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Albano G, Górecki M, Pescitelli G, Di Bari L, Jávorfi T, Hussain R, Siligardi G. Electronic circular dichroism imaging (CDi) maps local aggregation modes in thin films of chiral oligothiophenes. NEW J CHEM 2019. [DOI: 10.1039/c9nj02746g] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A detailed investigation of the circular dichroism imaging (CDi) technique on thin films of a chiral 1,4-dialkoxyphenylene-based oligothiophene with outstanding chiroptical features revealed the primary role of local supramolecular structures.
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Affiliation(s)
- Gianluigi Albano
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
| | - Marcin Górecki
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
- Institute of Organic Chemistry
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
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14
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Siligardi G, Hughes CS, Hussain R. Characterisation of sensor kinase by CD spectroscopy: golden rules and tips. Biochem Soc Trans 2018; 46:1627-1642. [PMID: 30514767 PMCID: PMC6299240 DOI: 10.1042/bst20180222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 01/22/2023]
Abstract
This is a review that describes the golden rules and tips on how to characterise the molecular interactions of membrane sensor kinase proteins with ligands using mainly circular dichroism (CD) spectroscopy. CD spectroscopy is essential for this task as any conformational change observed in the far-UV (secondary structures (α-helix, β-strands, poly-proline of type II, β-turns, irregular and folding) and near-UV regions [local environment of the aromatic side-chains of amino acid residues (Phe, Tyr and Trp) and ligands (drugs) and prosthetic groups (porphyrins, cofactors and coenzymes (FMN, FAD, NAD))] upon ligand addition to the protein can be used to determine qualitatively and quantitatively ligand-binding interactions. Advantages of using CD versus other techniques will be discussed. The difference CD spectra of the protein-ligand mixtures calculated subtracting the spectra of the ligand at various molar ratios can be used to determine the type of conformational changes induced by the ligand in terms of the estimated content of the various elements of protein secondary structure. The highly collimated microbeam and high photon flux of Diamond Light Source B23 beamline for synchrotron radiation circular dichroism (SRCD) enable the use of minimal amount of membrane proteins (7.5 µg for a 0.5 mg/ml solution) for high-throughput screening. Several examples of CD titrations of membrane proteins with a variety of ligands are described herein including the protocol tips that would guide the choice of the appropriate parameters to conduct these titrations by CD/SRCD in the best possible way.
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Affiliation(s)
- Giuliano Siligardi
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, U.K
| | - Charlotte S Hughes
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, U.K
| | - Rohanah Hussain
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, U.K.
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15
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Hussain R, Longo E, Siligardi G. UV-Denaturation Assay to Assess Protein Photostability and Ligand-Binding Interactions Using the High Photon Flux of Diamond B23 Beamline for SRCD. Molecules 2018; 23:molecules23081906. [PMID: 30065161 PMCID: PMC6222506 DOI: 10.3390/molecules23081906] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/20/2022] Open
Abstract
Light irradiation with high photon flux in the vacuum and far-UV region is known to denature the conformation of biopolymers. Measures are in place at Diamond Light Source B23 beamline for Synchrotron Radiation Circular Dichroism (SRCD) to control and make this effect negligible. However, UV denaturation of proteins can also be exploited as a novel method for assessing biopolymer photostability as well as ligand-binding interactions. Usually, host–ligand binding interactions can be assessed monitoring CD changes of the host biopolymer upon ligand addition. The novel method of identifying ligand binding monitoring the change of relative rate of UV denaturation using SRCD is especially important when there are very little or insignificant secondary structure changes of the host protein upon ligand binding. The temperature study, another method used to determine molecular interactions, can often be inconclusive when the thermal effect associated with the displacement of the bound solvent molecules by the ligand is also small, making the determination of the binding interaction inconclusive. Herein we present a review on the UV-denaturation assay as a novel method to determine the relative photostability of protein formulations as well as the screening of ligand-binding interactions using the high photon flux Diamond B23 beamline for SRCD.
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Affiliation(s)
- Rohanah Hussain
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot OX11 0DE, UK.
| | - Edoardo Longo
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot OX11 0DE, UK.
| | - Giuliano Siligardi
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot OX11 0DE, UK.
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16
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Ojea-Jiménez I, Capomaccio R, Osório I, Mehn D, Ceccone G, Hussain R, Siligardi G, Colpo P, Rossi F, Gilliland D, Calzolai L. Rational design of multi-functional gold nanoparticles with controlled biomolecule adsorption: a multi-method approach for in-depth characterization. NANOSCALE 2018; 10:10173-10181. [PMID: 29786727 DOI: 10.1039/c8nr00973b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multi-functionalized nanoparticles are of great interest in biotechnology and biomedicine, especially for diagnostic and therapeutic purposes. However, at the moment the characterization of complex, multi-functional nanoparticles is still challenging and this hampers the development of advanced nanomaterials for biological applications. In this work, we have designed a model system consisting of gold nanoparticles functionalized with two differentially-terminated poly(ethylene oxide) ligands, providing both "stealth" properties and protein-binding capabilities to the nanoparticles. We use a combination of techniques (Centrifugal Liquid Sedimentation, Dynamic Light Scattering, Flow Field Flow Fractionation, Transmission Electron Microscopy, and Circular Dichroism) to: (i) monitor and quantify the ratios of ligand molecules per nanoparticle; (ii) determine the effect of coating density on non-specific protein adsorption; (iii) to assess the number and structure of the covalently-bound proteins. This article aims at comparing the complementary outcomes from typical and orthogonal techniques used in nanoparticle characterization by employing a versatile nanoparticle-ligands-biomolecule model system.
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Affiliation(s)
- Isaac Ojea-Jiménez
- European Commission, DG-Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy.
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17
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Domingo-Espín J, Nilsson O, Bernfur K, Del Giudice R, Lagerstedt JO. Site-specific glycations of apolipoprotein A-I lead to differentiated functional effects on lipid-binding and on glucose metabolism. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2822-2834. [PMID: 29802959 DOI: 10.1016/j.bbadis.2018.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 02/06/2023]
Abstract
Prolonged hyperglycemia in poorly controlled diabetes leads to an increase in reactive glucose metabolites that covalently modify proteins by non-enzymatic glycation reactions. Apolipoprotein A-I (apoA-I) of high-density lipoprotein (HDL) is one of the proteins that becomes glycated in hyperglycemia. The impact of glycation on apoA-I protein structure and function in lipid and glucose metabolism were investigated. ApoA-I was chemically glycated by two different glucose metabolites (methylglyoxal and glycolaldehyde). Synchrotron radiation and conventional circular dichroism spectroscopy were used to study apoA-I structure and stability. The ability to bind lipids was measured by lipid-clearance assay and native gel analysis, and cholesterol efflux was measured by using lipid-laden J774 macrophages. Diet induced obese mice with established insulin resistance, L6 rat and C2C12 mouse myocytes, as well as INS-1E rat insulinoma cells, were used to determine in vivo and in vitro glucose uptake and insulin secretion. Site-specific, covalent modifications of apoA-I (lysines or arginines) led to altered protein structure, reduced lipid binding capability and a reduced ability to catalyze cholesterol efflux from macrophages, partly in a modification-specific manner. The stimulatory effects of apoA-I on the in vivo glucose clearance were negatively affected when apoA-I was modified with methylglyoxal, but not with glycolaldehyde. The in vitro data showed that both glucose uptake in muscle cells and insulin secretion from beta cells were affected. Taken together, glycation modifications impair the apoA-I protein functionality in lipid and glucose metabolism, which is expected to have implications for diabetes patients with poorly controlled blood glucose.
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Affiliation(s)
- Joan Domingo-Espín
- Department of Experimental Medical Science, Lund University, S-221 84 Lund, Sweden
| | - Oktawia Nilsson
- Department of Experimental Medical Science, Lund University, S-221 84 Lund, Sweden
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Lund University, S-221 84 Lund, Sweden
| | - Rita Del Giudice
- Department of Experimental Medical Science, Lund University, S-221 84 Lund, Sweden
| | - Jens O Lagerstedt
- Department of Experimental Medical Science, Lund University, S-221 84 Lund, Sweden.
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18
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Yasinska IM, Gonçalves Silva I, Sakhnevych SS, Ruegg L, Hussain R, Siligardi G, Fiedler W, Wellbrock J, Bardelli M, Varani L, Raap U, Berger S, Gibbs BF, Fasler-Kan E, Sumbayev VV. High mobility group box 1 (HMGB1) acts as an "alarmin" to promote acute myeloid leukaemia progression. Oncoimmunology 2018; 7:e1438109. [PMID: 29872582 PMCID: PMC5980411 DOI: 10.1080/2162402x.2018.1438109] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 02/08/2023] Open
Abstract
High mobility group box 1 (HMGB1) is a non-histone protein localised in the cell nucleus, where it interacts with DNA and promotes nuclear transcription events. HMGB1 levels are elevated during acute myeloid leukaemia (AML) progression followed by participation of this protein in triggering signalling events in target cells as a pro-inflammatory stimulus. This mechanism was hypothesised to be employed as a survival pathway by malignant blood cells and our aims were therefore to test this hypothesis experimentally. Here we report that HMGB1 triggers the release of tumour necrosis factor alpha (TNF-α) by primary human AML cells. TNF-α induces interleukin 1 beta (IL-1β) production by healthy leukocytes, leading to IL-1β-induced secretion of stem cell factor (SCF) by competent cells (for example endothelial cells). These results were verified in mouse bone marrow and primary human AML blood plasma samples. In addition, HMGB1 was found to induce secretion of angiogenic vascular endothelial growth factor (VEGF) and this process was dependent on the immune receptor Tim-3. We therefore conclude that HMGB1 is critical for AML progression as a ligand of Tim-3 and other immune receptors thus supporting survival/proliferation of AML cells and possibly the process of angiogenesis.
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Affiliation(s)
- Inna M Yasinska
- Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham Maritime, United Kingdom
| | - Isabel Gonçalves Silva
- Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham Maritime, United Kingdom
| | - Svetlana S Sakhnevych
- Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham Maritime, United Kingdom
| | - Laura Ruegg
- Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham Maritime, United Kingdom
| | | | | | - Walter Fiedler
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Jasmin Wellbrock
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Marco Bardelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Ulrike Raap
- Department of Medicine (Dermatology and Allergology), University of Oldenburg, Germany
| | - Steffen Berger
- Department of Pediatric Surgery and Department of Biomedical Research, Children's Hospital, Inselspital, University of Bern, Switzerland
| | - Bernhard F Gibbs
- Department of Medicine (Dermatology and Allergology), University of Oldenburg, Germany
- Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham Maritime, United Kingdom
| | - Elizaveta Fasler-Kan
- Department of Pediatric Surgery and Department of Biomedical Research, Children's Hospital, Inselspital, University of Bern, Switzerland
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Vadim V Sumbayev
- Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham Maritime, United Kingdom
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19
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Hussain R, Hughes CS, Jávorfi T, Siligardi G, Williams P, Bonev BB. To Boil an Egg: Substrate Binding Affects Critical Stability in Thermal Unfolding of Proteins. J Phys Chem B 2018; 122:2213-2218. [PMID: 29401389 DOI: 10.1021/acs.jpcb.7b10643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thermal unfolding of proteins is used extensively in screening of drug candidates because molecular interactions with ligands and substrates affect strongly protein stability, transition temperature, and cooperativity. We use synchrotron radiation circular dichroism to monitor the thermal evolution of secondary structure in proteins as they approach the melting point and the impact of substrate on their thermal behavior. Using Landau free energy expansion, we quantify transition strength and proximity to a critical point through the relative separation τ+ between the transition temperature Tm and the spinodal T+, obtained from the equation of state. The weakest transition was observed in lysozyme with τ+ = -0.0167 followed by holo albumin with τ+ = -0.0208 with the strongest transition in monomeric apo albumin τ+ = -0.0242. A structural transition at 45 °C in apo albumin leads to a noncooperative melt with τ+ = -0.00532 and amyloidogenic increase in beta content.
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Affiliation(s)
- Rohanah Hussain
- Diamond Light Source Ltd. , Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, U.K
| | - Charlotte S Hughes
- Diamond Light Source Ltd. , Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, U.K
| | - Tamás Jávorfi
- Diamond Light Source Ltd. , Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, U.K
| | - Giuliano Siligardi
- Diamond Light Source Ltd. , Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, U.K
| | - Paul Williams
- School of Life Sciences, University of Nottingham , Queen's Medical Centre, Nottingham NG7 2UH, U.K
| | - Boyan B Bonev
- School of Life Sciences, University of Nottingham , Queen's Medical Centre, Nottingham NG7 2UH, U.K
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20
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Synchrotron radiation circular dichroism spectroscopy reveals structural divergences in HDL-bound apoA-I variants. Sci Rep 2017; 7:13540. [PMID: 29051568 PMCID: PMC5648894 DOI: 10.1038/s41598-017-13878-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/03/2017] [Indexed: 12/15/2022] Open
Abstract
Apolipoprotein A-I (apoA-I) in high-density lipoprotein (HDL) provides cardiovascular protection. Synchrotron radiation circular dichroism (SRCD) spectroscopy was used to analyze the dynamic solution structure of the apoA-I protein in the apo- and HDL-states and the protein structure conversion in HDL formation. Wild-type apoA-I protein was compared to human variants that either are protective (R173C, Milano) or lead to increased risk for ischaemic heart disease (A164S). Comparable secondary structure distributions in the HDL particles, including significant levels of beta strand/turn, were observed. ApoA-I Milano in HDL displayed larger size heterogeneity, increased protein flexibility, and an altered lipid-binding profile, whereas the apoA-I A164S in HDL showed decrease thermal stability, potentially linking the intrinsic HDL propensities of the variants to disease risk.
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21
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Del Giudice R, Domingo-Espín J, Iacobucci I, Nilsson O, Monti M, Monti DM, Lagerstedt JO. Structural determinants in ApoA-I amyloidogenic variants explain improved cholesterol metabolism despite low HDL levels. Biochim Biophys Acta Mol Basis Dis 2017; 1863:3038-3048. [PMID: 28887204 DOI: 10.1016/j.bbadis.2017.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 11/19/2022]
Abstract
Twenty Apolipoprotein A-I (ApoA-I) variants are responsible for a systemic hereditary amyloidosis in which protein fibrils can accumulate in different organs, leading to their failure. Several ApoA-I amyloidogenic mutations are also associated with hypoalphalipoproteinemia, low ApoA-I and high-density lipoprotein (HDL)-cholesterol plasma levels; however, subjects affected by ApoA-I-related amyloidosis do not show a higher risk of cardiovascular diseases (CVD). The structural features, the lipid binding properties and the functionality of four ApoA-I amyloidogenic variants were therefore inspected in order to clarify the paradox observed in the clinical phenotype of the affected subjects. Our results show that ApoA-I amyloidogenic variants are characterized by a different oligomerization pattern and that the position of the mutation in the ApoA-I sequence affects the molecular structure of the formed HDL particles. Although lipidation increases ApoA-I proteins stability, all the amyloidogenic variants analyzed show a lower affinity for lipids, both in vitro and in ex vivo mouse serum. Interestingly, the lower efficiency at forming HDL particles is compensated by a higher efficiency at catalysing cholesterol efflux from macrophages. The decreased affinity of ApoA-I amyloidogenic variants for lipids, together with the increased efficiency in the cholesterol efflux process, could explain why, despite the unfavourable lipid profile, patients affected by ApoA-I related amyloidosis do not show a higher CVD risk.
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Affiliation(s)
- Rita Del Giudice
- Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden.
| | - Joan Domingo-Espín
- Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden
| | - Ilaria Iacobucci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Oktawia Nilsson
- Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden
| | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | - Daria Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | - Jens O Lagerstedt
- Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden.
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22
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Quality control and biophysical characterisation data of VanSA. Data Brief 2017; 14:41-47. [PMID: 28765830 PMCID: PMC5526436 DOI: 10.1016/j.dib.2017.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/13/2017] [Accepted: 07/10/2017] [Indexed: 11/21/2022] Open
Abstract
This data article presents the results from quality control experiments including N-terminal sequencing, SEC-MALS and Mass Spectrometry for purified VanSA used in experiments described in (Hughes et al., 2017) [1]; in addition to ligand interaction measurements and thermal melting curves of VanSA in the presence of screened ligands from circular dichroism measurements as well as UV–vis absorbance spectra for the binding interaction of VanSA in the presence of screened ligands.
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23
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Hughes CS, Longo E, Phillips-Jones MK, Hussain R. Characterisation of the selective binding of antibiotics vancomycin and teicoplanin by the VanS receptor regulating type A vancomycin resistance in the enterococci. Biochim Biophys Acta Gen Subj 2017; 1861:1951-1959. [PMID: 28511809 PMCID: PMC5482315 DOI: 10.1016/j.bbagen.2017.05.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 02/04/2023]
Abstract
A-type resistance towards "last-line" glycopeptide antibiotic vancomycin in the leading hospital acquired infectious agent, the enterococci, is the most common in the UK. Resistance is regulated by the VanRASA two-component system, comprising the histidine sensor kinase VanSA and the partner response regulator VanRA. The nature of the activating ligand for VanSA has not been identified, therefore this work sought to identify and characterise ligand(s) for VanSA. In vitro approaches were used to screen the structural and activity effects of a range of potential ligands with purified VanSA protein. Of the screened ligands (glycopeptide antibiotics vancomycin and teicoplanin, and peptidoglycan components N-acetylmuramic acid, D-Ala-D-Ala and Ala-D-y-Glu-Lys-D-Ala-D-Ala) only glycopeptide antibiotics vancomycin and teicoplanin were found to bind VanSA with different affinities (vancomycin 70μM; teicoplanin 30 and 170μM), and were proposed to bind via exposed aromatic residues tryptophan and tyrosine. Furthermore, binding of the antibiotics induced quicker, longer-lived phosphorylation states for VanSA, proposing them as activators of type A vancomycin resistance in the enterococci.
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Affiliation(s)
- C S Hughes
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom; Membranes, Membrane Proteins & Peptides Research Group, School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom
| | - E Longo
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom
| | - M K Phillips-Jones
- Membranes, Membrane Proteins & Peptides Research Group, School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom.
| | - R Hussain
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom.
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24
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Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions. Biochem Soc Trans 2017; 44:810-23. [PMID: 27284046 PMCID: PMC4900758 DOI: 10.1042/bst20160023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/20/2023]
Abstract
This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developed at Leeds alongside Professor Steve Baldwin to whom this review is dedicated. It also reviews two biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins–synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs.
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25
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Membrane remodeling by the M2 amphipathic helix drives influenza virus membrane scission. Sci Rep 2017; 7:44695. [PMID: 28317901 PMCID: PMC5357790 DOI: 10.1038/srep44695] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 02/13/2017] [Indexed: 02/07/2023] Open
Abstract
Membrane scission is a crucial step in all budding processes, from endocytosis to viral budding. Many proteins have been associated with scission, though the underlying molecular details of how scission is accomplished often remain unknown. Here, we investigate the process of M2-mediated membrane scission during the budding of influenza viruses. Residues 50–61 of the viral M2 protein bind membrane and form an amphipathic α-helix (AH). Membrane binding requires hydrophobic interactions with the lipid tails but not charged interactions with the lipid headgroups. Upon binding, the M2AH induces membrane curvature and lipid ordering, constricting and destabilizing the membrane neck, causing scission. We further show that AHs in the cellular proteins Arf1 and Epsin1 behave in a similar manner. Together, they represent a class of membrane-induced AH domains that alter membrane curvature and fluidity, mediating the scission of constricted membrane necks in multiple biological pathways.
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26
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Townsend D, Hughes E, Hussain R, Siligardi G, Baldock S, Madine J, Middleton DA. Heparin and Methionine Oxidation Promote the Formation of Apolipoprotein A-I Amyloid Comprising α-Helical and β-Sheet Structures. Biochemistry 2017; 56:1632-1644. [DOI: 10.1021/acs.biochem.6b01120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David Townsend
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Eleri Hughes
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot OX11 0DE, Oxon, England
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot OX11 0DE, Oxon, England
| | - Sarah Baldock
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Jillian Madine
- Department of Biochemistry, Institute
of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - David A. Middleton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
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27
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Zinna F, Resta C, Górecki M, Pescitelli G, Di Bari L, Jávorfi T, Hussain R, Siligardi G. Circular Dichroism Imaging: Mapping the Local Supramolecular Order in Thin Films of Chiral Functional Polymers. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02590] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Francesco Zinna
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi
13, 56124 Pisa, Italy
| | - Claudio Resta
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi
13, 56124 Pisa, Italy
| | - Marcin Górecki
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi
13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi
13, 56124 Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi
13, 56124 Pisa, Italy
| | - Tamás Jávorfi
- Diamond Light
Source, Ltd., Chilton, Didcot OX11 0DE, United Kingdom
| | - Rohanah Hussain
- Diamond Light
Source, Ltd., Chilton, Didcot OX11 0DE, United Kingdom
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28
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Fuller A, Wall A, Crowther MD, Lloyd A, Zhurov A, Sewell AK, Cole DK, Beck K. Thermal Stability of Heterotrimeric pMHC Proteins as Determined by Circular Dichroism Spectroscopy. Bio Protoc 2017; 7:e2366. [PMID: 28748203 DOI: 10.21769/bioprotoc.2366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
T cell receptor (TCR) recognition of foreign peptide fragments, presented by peptide major histocompatibility complex (pMHC), governs T-cell mediated protection against pathogens and cancer. Many factors govern T-cell sensitivity, including the affinity of the TCR-pMHC interaction and the stability of pMHC on the surface of antigen presenting cells. These factors are particularly relevant for the peptide vaccination field, in which more stable pMHC interactions could enable more effective protection against disease. Here, we discuss a method for the determination of pMHC stability that we have used to investigate HIV immune escape, T-cell sensitivity to cancer antigens and mechanisms leading to autoimmunity.
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Affiliation(s)
- Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Aaron Wall
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Michael D Crowther
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Angharad Lloyd
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Alexei Zhurov
- Cardiff University School of Dentistry, Heath Park, Cardiff, UK
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Konrad Beck
- Cardiff University School of Dentistry, Heath Park, Cardiff, UK
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Hussain R, Jávorfi T, Rudd TR, Siligardi G. High-throughput SRCD using multi-well plates and its applications. Sci Rep 2016; 6:38028. [PMID: 28004702 PMCID: PMC5177961 DOI: 10.1038/srep38028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 11/03/2016] [Indexed: 12/03/2022] Open
Abstract
The sample compartment for high-throughput synchrotron radiation circular dichroism (HT-SRCD) has been developed to satisfy an increased demand of protein characterisation in terms of folding and binding interaction properties not only in the traditional field of structural biology but also in the growing research area of material science with the potential to save time by 80%. As the understanding of protein behaviour in different solvent environments has increased dramatically the development of novel functions such as recombinant proteins modified to have different functions from harvesting solar energy to metabolonics for cleaning heavy and metal and organic molecule pollutions, there is a need to characterise speedily these system.
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Affiliation(s)
- Rohanah Hussain
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Tamás Jávorfi
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Timothy R Rudd
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Giuliano Siligardi
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
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30
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Gold nanoparticles increases UV and thermal stability of human serum albumin. Biointerphases 2016; 11:04B310. [PMID: 27984858 DOI: 10.1116/1.4972113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ultraviolet (UV) radiation, temperature, and time can degrade proteins. Here, the authors show that gold nanoparticles significantly protect human serum albumin from denaturation when exposed to "stressing" conditions such as UV irradiation and sustained exposure in suboptimal conditions. In particular, the authors show that gold nanoparticles significantly reduce the decrease in secondary structure induced by UV irradiation or extended exposure to ambient temperature.
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31
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Ruzza P, Vitale RM, Hussain R, Biondi B, Amodeo P, Sechi G, Siligardi G. Interactions of GFAP with ceftriaxone and phenytoin: SRCD and molecular docking and dynamic simulation. Biochim Biophys Acta Gen Subj 2016; 1860:2239-48. [DOI: 10.1016/j.bbagen.2016.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/14/2016] [Accepted: 04/27/2016] [Indexed: 01/28/2023]
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32
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Mehmood S, Corradi V, Choudhury HG, Hussain R, Becker P, Axford D, Zirah S, Rebuffat S, Tieleman DP, Robinson CV, Beis K. Structural and Functional Basis for Lipid Synergy on the Activity of the Antibacterial Peptide ABC Transporter McjD. J Biol Chem 2016; 291:21656-21668. [PMID: 27555327 DOI: 10.1074/jbc.m116.732107] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/08/2016] [Indexed: 11/06/2022] Open
Abstract
The lipid bilayer is a dynamic environment that consists of a mixture of lipids with different properties that regulate the function of membrane proteins; these lipids are either annular, masking the protein hydrophobic surface, or specific lipids, essential for protein function. In this study, using tandem mass spectrometry, we have identified specific lipids associated with the Escherichia coli ABC transporter McjD, which translocates the antibacterial peptide MccJ25. Using non-denaturing mass spectrometry, we show that McjD in complex with MccJ25 survives the gas phase. Partial delipidation of McjD resulted in reduced ATPase activity and thermostability as shown by circular dichroism, both of which could be restored upon addition of defined E. coli lipids. We have resolved a phosphatidylglycerol lipid associated with McjD at 3.4 Å resolution, whereas molecular dynamic simulations carried out in different lipid environments assessed the binding of specific lipids to McjD. Combined, our data show a synergistic effect of zwitterionic and negatively charged lipids on the activity of McjD; the zwitterionic lipids provide structural stability to McjD, whereas the negatively charged lipids are essential for its function.
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Affiliation(s)
- Shahid Mehmood
- From the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Valentina Corradi
- the Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Hassanul G Choudhury
- the Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom.,the Membrane Protein Lab.,the Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom, and
| | - Rohanah Hussain
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, United Kingdom
| | - Patrick Becker
- the Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom.,the Membrane Protein Lab.,the Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom, and
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, United Kingdom
| | - Severine Zirah
- the Communication Molecules and Adaptation of Microorganisms Laboratory (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - Sylvie Rebuffat
- the Communication Molecules and Adaptation of Microorganisms Laboratory (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - D Peter Tieleman
- the Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Carol V Robinson
- From the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom,
| | - Konstantinos Beis
- the Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom, .,the Membrane Protein Lab.,the Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom, and
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Cole DK, Bulek AM, Dolton G, Schauenberg AJ, Szomolay B, Rittase W, Trimby A, Jothikumar P, Fuller A, Skowera A, Rossjohn J, Zhu C, Miles JJ, Peakman M, Wooldridge L, Rizkallah PJ, Sewell AK. Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. J Clin Invest 2016; 126:2191-204. [PMID: 27183389 PMCID: PMC4887163 DOI: 10.1172/jci85679] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/10/2016] [Indexed: 12/11/2022] Open
Abstract
The cross-reactivity of T cells with pathogen- and self-derived peptides has been implicated as a pathway involved in the development of autoimmunity. However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide–major histocompatibility complexes (pMHC) are unclear. Here, we studied multiligand discrimination by a human, preproinsulin reactive, MHC class-I–restricted CD8+ T cell clone (1E6) that can recognize over 1 million different peptides. We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. Evaluation of these structures demonstrated that binding was stabilized through a conserved lock-and-key–like minimal binding footprint that enables 1E6 TCR to tolerate vast numbers of substitutions outside of this so-called hotspot. Highly potent antigens of the 1E6 TCR engaged with a strong antipathogen-like binding affinity; this engagement was governed though an energetic switch from an enthalpically to entropically driven interaction compared with the natural autoimmune ligand. Together, these data highlight how T cell cross-reactivity with pathogen-derived antigens might break self-tolerance to induce autoimmune disease.
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Affiliation(s)
- David K. Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Anna M. Bulek
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Andrea J. Schauenberg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Barbara Szomolay
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
| | - William Rittase
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Andrew Trimby
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Prithiviraj Jothikumar
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Ania Skowera
- Department of Immunobiology, King’s College London, London, United Kingdom
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Jamie Rossjohn
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Cheng Zhu
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - John J. Miles
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark Peakman
- Department of Immunobiology, King’s College London, London, United Kingdom
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Linda Wooldridge
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Pierre J. Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Andrew K. Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
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Hussain R, Siligardi G. Characterisation of Conformational and Ligand Binding Properties of Membrane Proteins Using Synchrotron Radiation Circular Dichroism (SRCD). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:43-59. [PMID: 27553234 PMCID: PMC6126569 DOI: 10.1007/978-3-319-35072-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Membrane proteins are notoriously difficult to crystallise for use in X-ray crystallographic structural determination, or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour in solution. The advantage of synchrotron radiation circular dichroism (SRCD) measured with synchrotron beamlines compared to the CD from benchtop instruments is the extended spectral far-UV region that increases the accuracy of secondary structure estimations, in particular under high ionic strength conditions. Membrane proteins are often available in small quantities, and for this SRCD measured at the Diamond B23 beamline has successfully facilitated molecular recognition studies. This was done by probing the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells (1-5 cm) of small volume capacity (70 μl-350 μl). In this chapter we describe the use of SRCD to qualitatively and quantitatively screen ligand binding interactions (exemplified by Sbma, Ace1 and FsrC proteins); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by FsrC); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by inositol transporters) as well as the stability of membrane proteins (exemplified by GalP, Ace1). The importance of the in solution characterisation of the conformational behaviour and ligand binding properties of proteins in both far- andnear-UV regions and the use of high-throughput CD (HT-CD) using 96- and 384-well multiplates to study the folding effects in various protein crystallisation buffers are also discussed.
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Affiliation(s)
- Rohanah Hussain
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
| | - Giuliano Siligardi
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
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35
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De Santis E, Edwards AA, Alexander BD, Holder SJ, Biesse-Martin AS, Nielsen BV, Mistry D, Waters L, Siligardi G, Hussain R, Faure S, Taillefumier C. Selective complexation of divalent cations by a cyclic α,β-peptoid hexamer: a spectroscopic and computational study. Org Biomol Chem 2016; 14:11371-11380. [DOI: 10.1039/c6ob01954d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The first report on metal binding ability of a cyclic α,β-peptoid hexamer towards a selection of metal cations is presented.
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Affiliation(s)
- E. De Santis
- Medway School of Pharmacy
- Universities of Kent and Greenwich at Medway
- Chatham Maritime
- UK
| | - A. A. Edwards
- Medway School of Pharmacy
- Universities of Kent and Greenwich at Medway
- Chatham Maritime
- UK
| | | | - S. J. Holder
- Functional Materials Group
- School of Physical Sciences
- University of Kent
- Canterbury
- UK
| | - A.-S. Biesse-Martin
- Université Clermont Auvergne
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand
- F-63000 Clermont-Ferrand
- France
| | - B. V. Nielsen
- School of Science
- University of Greenwich
- Chatham Maritime
- UK
| | - D. Mistry
- Division of Pharmacy and Pharmaceutical Sciences
- University of Huddersfield
- Huddersfield
- UK
| | - L. Waters
- Division of Pharmacy and Pharmaceutical Sciences
- University of Huddersfield
- Huddersfield
- UK
| | | | | | - S. Faure
- Université Clermont Auvergne
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand
- F-63000 Clermont-Ferrand
- France
| | - C. Taillefumier
- Université Clermont Auvergne
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand
- F-63000 Clermont-Ferrand
- France
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Bürck J, Roth S, Windisch D, Wadhwani P, Moss D, Ulrich AS. UV-CD12: synchrotron radiation circular dichroism beamline at ANKA. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:844-52. [PMID: 25931105 PMCID: PMC4416691 DOI: 10.1107/s1600577515004476] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/03/2015] [Indexed: 05/25/2023]
Abstract
Synchrotron radiation circular dichroism (SRCD) is a rapidly growing technique for structure analysis of proteins and other chiral biomaterials. UV-CD12 is a high-flux SRCD beamline installed at the ANKA synchrotron, to which it had been transferred after the closure of the SRS Daresbury. The beamline covers an extended vacuum-UV to near-UV spectral range and has been open for users since October 2011. The current end-station allows for temperature-controlled steady-state SRCD spectroscopy, including routine automated thermal scans of microlitre volumes of water-soluble proteins down to 170 nm. It offers an excellent signal-to-noise ratio over the whole accessible spectral range. The technique of oriented circular dichroism (OCD) was recently implemented for determining the membrane alignment of α-helical peptides and proteins in macroscopically oriented lipid bilayers as mimics of cellular membranes. It offers improved spectral quality <200 nm compared with an OCD setup adapted to a bench-top instrument, and accelerated data collection by a factor of ∼3. In addition, it permits investigations of low hydrated protein films down to 130 nm using a rotatable sample cell that avoids linear dichroism artifacts.
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Affiliation(s)
- Jochen Bürck
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Siegmar Roth
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Dirk Windisch
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - David Moss
- ANKA Synchrotron Radiation Facility, Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
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Hussain R, Benning K, Javorfi T, Longo E, Rudd TR, Pulford B, Siligardi G. CDApps: integrated software for experimental planning and data processing at beamline B23, Diamond Light Source. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:465-8. [PMID: 25723950 PMCID: PMC4344363 DOI: 10.1107/s1600577514028161] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/26/2014] [Indexed: 05/28/2023]
Abstract
The B23 Circular Dichroism beamline at Diamond Light Source has been operational since 2009 and has seen visits from more than 200 user groups, who have generated large amounts of data. Based on the experience of overseeing the users' progress at B23, four key areas requiring the most assistance are identified: planning of experiments and note-keeping; designing titration experiments; processing and analysis of the collected data; and production of experimental reports. To streamline these processes an integrated software package has been developed and made available for the users. The subsequent article summarizes the main features of the software.
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Affiliation(s)
- Rohanah Hussain
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Kristian Benning
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tamas Javorfi
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Edoardo Longo
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Timothy R. Rudd
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Bill Pulford
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Giuliano Siligardi
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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Hagelueken G, Clarke BR, Huang H, Tuukkanen A, Danciu I, Svergun DI, Hussain R, Liu H, Whitfield C, Naismith JH. A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide. Nat Struct Mol Biol 2015; 22:50-56. [PMID: 25504321 PMCID: PMC4650267 DOI: 10.1038/nsmb.2935] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/20/2014] [Indexed: 11/22/2022]
Abstract
Long-chain bacterial polysaccharides have important roles in pathogenicity. In Escherichia coli O9a, a model for ABC transporter-dependent polysaccharide assembly, a large extracellular carbohydrate with a narrow size distribution is polymerized from monosaccharides by a complex of two proteins, WbdA (polymerase) and WbdD (terminating protein). Combining crystallography and small-angle X-ray scattering, we found that the C-terminal domain of WbdD contains an extended coiled-coil that physically separates WbdA from the catalytic domain of WbdD. The effects of insertions and deletions in the coiled-coil region were analyzed in vivo, revealing that polymer size is controlled by varying the length of the coiled-coil domain. Thus, the coiled-coil domain of WbdD functions as a molecular ruler that, along with WbdA:WbdD stoichiometry, controls the chain length of a model bacterial polysaccharide.
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Affiliation(s)
- Gregor Hagelueken
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Bradley R. Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Hexian Huang
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Anne Tuukkanen
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestraße 85, 22603 Hamburg, Germany
| | - Iulia Danciu
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestraße 85, 22603 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestraße 85, 22603 Hamburg, Germany
| | | | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
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39
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Longo E, Santis ED, Hussain R, van der Walle CF, Casas-Finet J, Uddin S, Santos AD, Siligardi G. The effect of palmitoylation on the conformation and physical stability of a model peptide hormone. Int J Pharm 2014; 472:156-64. [PMID: 24928136 DOI: 10.1016/j.ijpharm.2014.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/04/2014] [Accepted: 06/07/2014] [Indexed: 02/08/2023]
Abstract
Peptides are ideal drug candidates due to their potency and specificity, but suffer from a short half-life and low membrane permeability. Acylation can overcome these limitations but the consequences to stability under different formulation conditions and stresses are largely unreported. Using synchrotron radiation circular dichroism (SRCD), we show that palmitoylation of a 28 amino acid peptide hormone (pI 9.82) induced a structural transition from 310-helix to α-helix, irrespective of buffer type and pH investigated (5.5-8.0) when compared to the non acylated analogues. These conformational preferences were retained in the presence of non-ionic micelles but not anionic micelles, which induced an α-helical structure for all peptides. Palmitoylation promoted an irreversible peptide denaturation under thermal stress at pH ≥ 6.5 and increased the propensity for loss of helical structure under high photon flux (here used as a novel accelerated photostability test). The presence of either ionic or non-ionic micelles did not recover these conformational changes over the same irradiation period. These results demonstrate that acylation can change peptide conformation and decrease thermal-/photo-stability, with important consequences for drug-development strategies.
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Affiliation(s)
- Edoardo Longo
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Emiliana De Santis
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom.
| | | | - Jose Casas-Finet
- MedImmune LLC, Analytical Biochemistry, Gaithersburg, MD 20878, USA
| | - Shahid Uddin
- MedImmune Ltd., Formulation Sciences, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Ana Dos Santos
- MedImmune Ltd., Formulation Sciences, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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Functional characterization of SbmA, a bacterial inner membrane transporter required for importing the antimicrobial peptide Bac7(1-35). J Bacteriol 2013; 195:5343-51. [PMID: 24078610 DOI: 10.1128/jb.00818-13] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SbmA is an inner membrane protein of Gram-negative bacteria that is involved in the internalization of glycopeptides and prokaryotic and eukaryotic antimicrobial peptides, as well as of peptide nucleic acid (PNA) oligomers. The SbmA homolog BacA is required for the development of Sinorhizobium meliloti bacteroids within plant cells and favors chronic infections with Brucella abortus and Mycobacterium tuberculosis in mice. Here, we investigated functional features of SbmA/BacA using the proline-rich antimicrobial peptide Bac7(1-35) as a substrate. Circular dichroism and affinity chromatography studies were used to investigate the ability of SbmA to bind the peptide, and a whole-cell transport assay with fluorescently labeled peptide allowed the determination of transport kinetic parameters with a calculated Km value of 6.95 ± 0.89 μM peptide and a Vmax of 53.91 ± 3.17 nmol/min/mg SbmA. Use of a bacterial two-hybrid system coupled to SEC-MALLS (size exclusion chromatography coupled with multiangle laser light scattering) analyses established that SbmA is a homodimer in the membrane, and treatment of the cells with arsenate or ionophores indicated that the peptide transport mediated by SbmA is driven by the electrochemical gradient. Overall, these results shed light on the SbmA-mediated internalization of peptide substrates and suggest that the transport of an unknown substrate(s) represents the function of this protein.
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Siligardi G, Hussain R, Patching SG, Phillips-Jones MK. Ligand- and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:34-42. [PMID: 23811229 DOI: 10.1016/j.bbamem.2013.06.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 11/15/2022]
Abstract
A great number of membrane proteins have proven difficult to crystallise for use in X-ray crystallographic structural determination or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour. In this review examples of the applications of CD and synchrotron radiation CD (SRCD) to membrane protein ligand binding interaction studies are discussed. The availability of SRCD has been an important advancement in recent progress, most particularly because it can be used to extend the spectral region in the far-UV region (important for increasing the accuracy of secondary structure estimations) and for working with membrane proteins available in only small quantities for which SRCD has facilitated molecular recognition studies. Such studies have been accomplished by probing in the near-UV region the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells of small volume capacity. In particular, this review describes the most recent use of the technique in the following areas: to obtain quantitative data on ligand binding (exemplified by the FsrC membrane sensor kinase receptor); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by secretory phospholipase A2); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by the antiseptic transporter SugE). Finally, the importance of characterising in solution the conformational behaviour and ligand binding properties of proteins in both far- and near-UV regions is discussed. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Giuliano Siligardi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; School of Biological Sciences, University of Liverpool, Liverpool, UK.
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Phillips-Jones MK, Patching SG, Edara S, Nakayama J, Hussain R, Siligardi G. Interactions of the intact FsrC membrane histidine kinase with the tricyclic peptideinhibitor siamycin I revealed through synchrotron radiation circular dichroism. Phys Chem Chem Phys 2013. [DOI: 10.1039/c2cp43722h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Réfrégiers M, Wien F, Ta HP, Premvardhan L, Bac S, Jamme F, Rouam V, Lagarde B, Polack F, Giorgetta JL, Ricaud JP, Bordessoule M, Giuliani A. DISCO synchrotron-radiation circular-dichroism endstation at SOLEIL. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:831-835. [PMID: 22898965 DOI: 10.1107/s0909049512030002] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 07/01/2012] [Indexed: 06/01/2023]
Abstract
The new synchrotron-radiation circular-dichroism (SRCD) endstation on the UV-visible synchrotron beamline DISCO has been commissioned at the SOLEIL synchrotron. The design has been focused on preservation of a high degree of linear polarization at high flux and moderate resolving power covering the vacuum ultraviolet to visible spectral range (125-600 nm). The beam dimensions have been set to 4 mm × 4 mm at 1 nm bandwidth for lower sample degradation. The nitrogen-purged sample chamber fits three types of sample holders accommodating conventional round cell mounting, automated rotation of the samples, as well as a microfluidic set-up. Automated temperature-controlled data collection on microvolumes is now available to the biology and chemistry communities. Macromolecules including membrane proteins, soluble proteins, bio-nanotubes, sugars, DNA and RNAs are now routinely investigated.
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Interactions of the intact FsrC membrane histidine kinase with its pheromone ligand GBAP revealed through synchrotron radiation circular dichroism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1595-602. [DOI: 10.1016/j.bbamem.2012.02.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 02/08/2012] [Accepted: 02/10/2012] [Indexed: 11/22/2022]
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De Santis E, Hjelmgaard T, Caumes C, Faure S, Alexander BD, Holder SJ, Siligardi G, Taillefumier C, Edwards AA. Effect of capping groups at the N- and C-termini on the conformational preference of α,β-peptoids. Org Biomol Chem 2012; 10:1108-22. [DOI: 10.1039/c1ob06386c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Laera S, Ceccone G, Rossi F, Gilliland D, Hussain R, Siligardi G, Calzolai L. Measuring protein structure and stability of protein-nanoparticle systems with synchrotron radiation circular dichroism. NANO LETTERS 2011; 11:4480-4484. [PMID: 21932791 DOI: 10.1021/nl202909s] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We measure the structural and stability changes of proteins at nanomolar concentration upon interaction with nanoparticles. Using synchrotron radiation circular dichroism (SRCD), we measure a decrease of 6 °C in the thermal unfolding of human serum albumin upon interaction with silver nanoparticles while this does not happen with gold. The use of SRCD allows measuring critical parameters on protein-nanoparticle interactions, and it will provide experimental data on the relative stability of key biological proteins for nanotoxicology.
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Affiliation(s)
- Stefania Laera
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection I-21027, Ispra (VA), Italy
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De Santis E, Hjelmgaard T, Faure S, Roy O, Didierjean C, Alexander BD, Siligardi G, Hussain R, Jávorfi T, Edwards AA, Taillefumier C. Cyclic α,β-peptoid octamers with differing side chain patterns: synthesis and conformational investigation. Amino Acids 2011; 41:663-72. [DOI: 10.1007/s00726-011-0887-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 03/08/2011] [Indexed: 11/28/2022]
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