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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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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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Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics. PLoS One 2018; 13:e0200387. [PMID: 30044812 PMCID: PMC6059433 DOI: 10.1371/journal.pone.0200387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 06/25/2018] [Indexed: 11/19/2022] Open
Abstract
Given the increasing incidence of antibiotic resistance, antibiotics that employ new strategies are urgently needed. Bacterial survival is dependent on proper function of the signal recognition particle (SRP) and its receptor (FtsY). A unique set of interactions in FtsY:SRP-RNA represents a promising candidate for new antibiotic development as no antibiotic targets this complex and these interactions are functionally replaced by protein:protein interactions in eukaryotes. We used a Fragment Based Drug Design (FBDD) approach to search for new compounds that can bind FtsY, and have identified three lead fragments. In vitro and in vivo analyses have shown that despite a high micromolar binding affinity, one fragment has some antimicrobial properties. X-ray structures of E. coli FtsY:fragments reveal the fragments bind in the targeted RNA interaction site. Our results show that FBDD is a suitable approach for targeting FtsY:SRP-RNA for antibiotic development and opens the possibility of targeting protein:RNA interactions in general.
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Ahmad I, Nawaz N, Darwesh NM, ur Rahman S, Mustafa MZ, Khan SB, Patching SG. Overcoming challenges for amplified expression of recombinant proteins using Escherichia coli. Protein Expr Purif 2018; 144:12-18. [DOI: 10.1016/j.pep.2017.11.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 11/28/2022]
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Saidijam M, Karimi Dermani F, Sohrabi S, Patching SG. Efflux proteins at the blood-brain barrier: review and bioinformatics analysis. Xenobiotica 2017; 48:506-532. [PMID: 28481715 DOI: 10.1080/00498254.2017.1328148] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
1. Efflux proteins at the blood-brain barrier provide a mechanism for export of waste products of normal metabolism from the brain and help to maintain brain homeostasis. They also prevent entry into the brain of a wide range of potentially harmful compounds such as drugs and xenobiotics. 2. Conversely, efflux proteins also hinder delivery of therapeutic drugs to the brain and central nervous system used to treat brain tumours and neurological disorders. For bypassing efflux proteins, a comprehensive understanding of their structures, functions and molecular mechanisms is necessary, along with new strategies and technologies for delivery of drugs across the blood-brain barrier. 3. We review efflux proteins at the blood-brain barrier, classified as either ATP-binding cassette (ABC) transporters (P-gp, BCRP, MRPs) or solute carrier (SLC) transporters (OATP1A2, OATP1A4, OATP1C1, OATP2B1, OAT3, EAATs, PMAT/hENT4 and MATE1). 4. This includes information about substrate and inhibitor specificity, structural organisation and mechanism, membrane localisation, regulation of expression and activity, effects of diseases and conditions and the principal technique used for in vivo analysis of efflux protein activity: positron emission tomography (PET). 5. We also performed analyses of evolutionary relationships, membrane topologies and amino acid compositions of the proteins, and linked these to structure and function.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Fatemeh Karimi Dermani
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Sareh Sohrabi
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds , UK
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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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Hiruma-Shimizu K, Shimizu H, Thompson GS, Kalverda AP, Patching SG. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications. Mol Membr Biol 2016; 32:139-55. [DOI: 10.3109/09687688.2015.1125536] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Hiroki Shimizu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido, Japan,
| | - Gary S. Thompson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
| | - Arnout P. Kalverda
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
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Abraham SJ, Cheng RC, Chew TA, Khantwal CM, Liu CW, Gong S, Nakamoto RK, Maduke M. 13C NMR detects conformational change in the 100-kD membrane transporter ClC-ec1. JOURNAL OF BIOMOLECULAR NMR 2015; 61:209-26. [PMID: 25631353 PMCID: PMC4398623 DOI: 10.1007/s10858-015-9898-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/13/2015] [Indexed: 05/03/2023]
Abstract
CLC transporters catalyze the exchange of Cl(-) for H(+) across cellular membranes. To do so, they must couple Cl(-) and H(+) binding and unbinding to protein conformational change. However, the sole conformational changes distinguished crystallographically are small movements of a glutamate side chain that locally gates the ion-transport pathways. Therefore, our understanding of whether and how global protein dynamics contribute to the exchange mechanism has been severely limited. To overcome the limitations of crystallography, we used solution-state (13)C-methyl NMR with labels on methionine, lysine, and engineered cysteine residues to investigate substrate (H(+)) dependent conformational change outside the restraints of crystallization. We show that methyl labels in several regions report H(+)-dependent spectral changes. We identify one of these regions as Helix R, a helix that extends from the center of the protein, where it forms the part of the inner gate to the Cl(-)-permeation pathway, to the extracellular solution. The H(+)-dependent spectral change does not occur when a label is positioned just beyond Helix R, on the unstructured C-terminus of the protein. Together, the results suggest that H(+) binding is mechanistically coupled to closing of the intracellular access-pathway for Cl(-).
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Affiliation(s)
- Sherwin J. Abraham
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
| | - Ricky C. Cheng
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
| | - Thomas A. Chew
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
| | - Chandra M. Khantwal
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
| | - Corey W. Liu
- Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, 299 Campus Drive West, D105 Fairchild Science Building, Stanford, CA 94305
| | - Shimei Gong
- Department of Molecular Physiology and Biological Physics, University of Virginia, PO Box 10011, Charlottesville, VA 22906-0011
| | - Robert K. Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, PO Box 10011, Charlottesville, VA 22906-0011
| | - Merritt Maduke
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94035
- corresponding author, , tel (650)-723-9075, fax (650)-725-8021
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Hiruma-Shimizu K, Kalverda AP, Henderson PJF, Homans SW, Patching SG. Synthesis of uniformly deuteratedn-dodecyl-β-d-maltoside (d39-DDM) for solubilization of membrane proteins in TROSY NMR experiments. J Labelled Comp Radiopharm 2014; 57:737-43. [DOI: 10.1002/jlcr.3249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 10/21/2014] [Accepted: 11/06/2014] [Indexed: 01/07/2023]
Affiliation(s)
- Kazumi Hiruma-Shimizu
- School of Molecular and Cellular Biology; University of Leeds; Leeds UK
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds UK
- Waseda University; Tokyo Japan
| | - Arnout P. Kalverda
- School of Molecular and Cellular Biology; University of Leeds; Leeds UK
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds UK
| | - Peter J. F. Henderson
- School of Biomedical Sciences; University of Leeds; Leeds UK
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds UK
| | - Steve W. Homans
- School of Molecular and Cellular Biology; University of Leeds; Leeds UK
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds UK
- Newcastle University; Newcastle UK
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