1
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Popoff MR. Overview of Bacterial Protein Toxins from Pathogenic Bacteria: Mode of Action and Insights into Evolution. Toxins (Basel) 2024; 16:182. [PMID: 38668607 PMCID: PMC11054074 DOI: 10.3390/toxins16040182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/29/2024] Open
Abstract
Bacterial protein toxins are secreted by certain bacteria and are responsible for mild to severe diseases in humans and animals. They are among the most potent molecules known, which are active at very low concentrations. Bacterial protein toxins exhibit a wide diversity based on size, structure, and mode of action. Upon recognition of a cell surface receptor (protein, glycoprotein, and glycolipid), they are active either at the cell surface (signal transduction, membrane damage by pore formation, or hydrolysis of membrane compound(s)) or intracellularly. Various bacterial protein toxins have the ability to enter cells, most often using an endocytosis mechanism, and to deliver the effector domain into the cytosol, where it interacts with an intracellular target(s). According to the nature of the intracellular target(s) and type of modification, various cellular effects are induced (cell death, homeostasis modification, cytoskeleton alteration, blockade of exocytosis, etc.). The various modes of action of bacterial protein toxins are illustrated with representative examples. Insights in toxin evolution are discussed.
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Affiliation(s)
- Michel R Popoff
- Unité des Toxines Bactériennes, Institut Pasteur, Université Paris Cité, CNRS UMR 2001 INSERM U1306, F-75015 Paris, France
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2
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Sadi M, Carvalho N, Léger C, Vitorge B, Ladant D, Guijarro JI, Chenal A. B2LiVe, a label-free 1D-NMR method to quantify the binding of amphitropic peptides or proteins to membrane vesicles. CELL REPORTS METHODS 2023; 3:100624. [PMID: 37909050 PMCID: PMC10694493 DOI: 10.1016/j.crmeth.2023.100624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 08/03/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023]
Abstract
Amphitropic proteins and peptides reversibly partition from solution to membrane, a key process that regulates their functions. Experimental approaches classically used to measure protein partitioning into lipid bilayers, such as fluorescence and circular dichroism, are hardly usable when the peptides or proteins do not exhibit significant polarity and/or conformational changes upon membrane binding. Here, we describe binding to lipid vesicles (B2LiVe), a simple, robust, and widely applicable nuclear magnetic resonance (NMR) method to determine the solution-to-membrane partitioning of unlabeled proteins or peptides. B2LiVe relies on previously described proton 1D-NMR fast-pulsing techniques. Membrane partitioning induces a large line broadening, leading to a loss of protein signals; therefore, the decrease of the NMR signal directly measures the fraction of membrane-bound protein. The method uses low polypeptide concentrations and has been validated on several membrane-interacting polypeptides, ranging from 3 to 54 kDa, with membrane vesicles of different sizes and various lipid compositions.
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Affiliation(s)
- Mirko Sadi
- Institut Pasteur, Université de Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France; Université de Paris Cité, 75005 Paris, France
| | - Nicolas Carvalho
- Institut Pasteur, Université de Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France; Université de Paris Cité, 75005 Paris, France
| | - Corentin Léger
- Institut Pasteur, Université de Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France
| | - Bruno Vitorge
- Institut Pasteur, Université de Paris Cité, CNRS UMR3528, Biological NMR and HDX-MS Technological Platform, 75015 Paris, France
| | - Daniel Ladant
- Institut Pasteur, Université de Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France
| | - J Iñaki Guijarro
- Institut Pasteur, Université de Paris Cité, CNRS UMR3528, Biological NMR and HDX-MS Technological Platform, 75015 Paris, France.
| | - Alexandre Chenal
- Institut Pasteur, Université de Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France.
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3
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Rodnin MV, Vasques-Montes V, Kyrychenko A, Oliveira NFB, Kashipathy MM, Battaile KP, Douglas J, Lovell S, Machuqueiro M, Ladokhin AS. Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain. Toxins (Basel) 2023; 15:410. [PMID: 37505680 PMCID: PMC10467104 DOI: 10.3390/toxins15070410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/29/2023] Open
Abstract
Protonation of key histidine residues has been long implicated in the acid-mediated cellular action of the diphtheria toxin translocation (T-) domain, responsible for the delivery of the catalytic domain into the cell. Here, we use a combination of computational (constant-pH Molecular Dynamics simulations) and experimental (NMR, circular dichroism, and fluorescence spectroscopy along with the X-ray crystallography) approaches to characterize the initial stages of conformational change happening in solution in the wild-type T-domain and in the H223Q/H257Q double mutant. This replacement suppresses the acid-induced transition, resulting in the retention of a more stable protein structure in solutions at pH 5.5 and, consequently, in reduced membrane-disrupting activity. Here, for the first time, we report the pKa values of the histidine residues of the T-domain, measured by NMR-monitored pH titrations. Most peaks in the histidine side chain spectral region are titrated with pKas ranging from 6.2 to 6.8. However, the two most up-field peaks display little change down to pH 6, which is a limiting pH for this protein in solution at concentrations required for NMR. These peaks are absent in the double mutant, suggesting they belong to H223 and H257. The constant-pH simulations indicate that for the T-domain in solution, the pKa values for histidine residues range from 3.0 to 6.5, with those most difficult to protonate being H251 and H257. Taken together, our experimental and computational data demonstrate that previously suggested cooperative protonation of all six histidines in the T-domain does not occur.
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Affiliation(s)
- Mykola V. Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| | - Victor Vasques-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| | - Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 61022 Kharkiv, Ukraine
| | - Nuno F. B. Oliveira
- Institute of Biosystems and Integrative Sciences, University of Lisbon, 1749-016 Lisbon, Portugal (M.M.)
| | - Maithri M. Kashipathy
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66047, USA (S.L.)
| | | | - Justin Douglas
- COBRE Bio-NMR Laboratory, University of Kansas, Lawrence, KS 66045, USA;
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66047, USA (S.L.)
| | - Miguel Machuqueiro
- Institute of Biosystems and Integrative Sciences, University of Lisbon, 1749-016 Lisbon, Portugal (M.M.)
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
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4
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Ilangumaran Ponmalar I, Sarangi NK, Basu JK, Ayappa KG. Pore Forming Protein Induced Biomembrane Reorganization and Dynamics: A Focused Review. Front Mol Biosci 2021; 8:737561. [PMID: 34568431 PMCID: PMC8459938 DOI: 10.3389/fmolb.2021.737561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Pore forming proteins are a broad class of pathogenic proteins secreted by organisms as virulence factors due to their ability to form pores on the target cell membrane. Bacterial pore forming toxins (PFTs) belong to a subclass of pore forming proteins widely implicated in bacterial infections. Although the action of PFTs on target cells have been widely investigated, the underlying membrane response of lipids during membrane binding and pore formation has received less attention. With the advent of superresolution microscopy as well as the ability to carry out molecular dynamics (MD) simulations of the large protein membrane assemblies, novel microscopic insights on the pore forming mechanism have emerged over the last decade. In this review, we focus primarily on results collated in our laboratory which probe dynamic lipid reorganization induced in the plasma membrane during various stages of pore formation by two archetypal bacterial PFTs, cytolysin A (ClyA), an α-toxin and listeriolysin O (LLO), a β-toxin. The extent of lipid perturbation is dependent on both the secondary structure of the membrane inserted motifs of pore complex as well as the topological variations of the pore complex. Using confocal and superresolution stimulated emission depletion (STED) fluorescence correlation spectroscopy (FCS) and MD simulations, lipid diffusion, cholesterol reorganization and deviations from Brownian diffusion are correlated with the oligomeric state of the membrane bound protein as well as the underlying membrane composition. Deviations from free diffusion are typically observed at length scales below ∼130 nm to reveal the presence of local dynamical heterogeneities that emerge at the nanoscale-driven in part by preferential protein binding to cholesterol and domains present in the lipid membrane. Interrogating the lipid dynamics at the nanoscale allows us further differentiate between binding and pore formation of β- and α-PFTs to specific domains in the membrane. The molecular insights gained from the intricate coupling that occurs between proteins and membrane lipids and receptors during pore formation are expected to improve our understanding of the virulent action of PFTs.
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Affiliation(s)
| | - Nirod K. Sarangi
- School of Chemical Science, Dublin City University, Dublin, Ireland
| | - Jaydeep K. Basu
- Department of Physics, Indian Institute of Science, Bangalore, India
| | - K. Ganapathy Ayappa
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
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5
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Kinnun JJ, Scott HL, Ashkar R, Katsaras J. Biomembrane Structure and Material Properties Studied With Neutron Scattering. Front Chem 2021; 9:642851. [PMID: 33987167 PMCID: PMC8110834 DOI: 10.3389/fchem.2021.642851] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA, United States.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
| | - John Katsaras
- Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States.,Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, United States
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6
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Huang Y, Soliakov A, Le Brun AP, Macdonald C, Johnson CL, Solovyova AS, Waller H, Moore GR, Lakey JH. Helix N-Cap Residues Drive the Acid Unfolding That Is Essential in the Action of the Toxin Colicin A. Biochemistry 2019; 58:4882-4892. [PMID: 31686499 PMCID: PMC6899464 DOI: 10.1021/acs.biochem.9b00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Numerous bacterial toxins and other virulence factors
use low pH
as a trigger to convert from water-soluble to membrane-inserted states.
In the case of colicins, the pore-forming domain of colicin A (ColA-P)
has been shown both to undergo a clear acidic unfolding transition
and to require acidic lipids in the cytoplasmic membrane, whereas
its close homologue colicin N shows neither behavior. Compared to
that of ColN-P, the ColA-P primary structure reveals the replacement
of several uncharged residues with aspartyl residues, which upon replacement
with alanine induce an unfolded state at neutral pH. Here we investigate
ColA-P’s structural requirement for these critical aspartyl
residues that are largely situated at the N-termini of α helices.
As previously shown in model peptides, the charged carboxylate side
chain can act as a stabilizing helix N-Cap group by interacting with
free amide hydrogen bond donors. Because this could explain ColA-P
destabilization when the aspartyl residues are protonated or replaced
with alanyl residues, we test the hypothesis by inserting asparagine,
glutamine, and glutamate residues at these sites. We combine urea
(fluorescence and circular dichroism) and thermal (circular dichroism
and differential scanning calorimetry) denaturation experiments with 1H–15N heteronuclear single-quantum coherence
nuclear magnetic resonance spectroscopy of ColA-P at different pH
values to provide a comprehensive description of the unfolding process
and confirm the N-Cap hypothesis. Furthermore, we reveal that, in
urea, the single domain ColA-P unfolds in two steps; low pH destabilizes
the first step and stabilizes the second.
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Affiliation(s)
- Yan Huang
- Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , U.K.,College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Andrei Soliakov
- Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , U.K
| | - Anton P Le Brun
- Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , U.K.,Australian Centre for Neutron Scattering , Australian Nuclear Science and Technology Organisation , Kirrawee DC , NSW 2232 , Australia
| | - Colin Macdonald
- Department of Chemistry Centre for Structural & Molecular Biology, School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K
| | - Christopher L Johnson
- Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , U.K
| | - Alexandra S Solovyova
- Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , U.K
| | - Helen Waller
- Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , U.K
| | - Geoffrey R Moore
- Department of Chemistry Centre for Structural & Molecular Biology, School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , U.K
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7
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Pitard I, Malliavin TE. Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells. Toxins (Basel) 2019; 11:toxins11060369. [PMID: 31238550 PMCID: PMC6628625 DOI: 10.3390/toxins11060369] [Citation(s) in RCA: 5] [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: 05/28/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the functions and mechanisms of biological systems is an outstanding challenge. One way to overcome it is to combine together several approaches such as molecular modeling and experimental structural biology techniques. Indeed, the interplay between structural and dynamical properties of the system is crucial to unravel the function of molecular machinery’s. In this review, we focus on how molecular simulations along with structural information can aid in interpreting biological data. Here, we examine two different cases: (i) the endosomal translocation toxins (diphtheria, tetanus, botulinum toxins) and (ii) the activation of adenylyl cyclase inside the cytoplasm (edema factor, CyA, ExoY).
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Affiliation(s)
- Irène Pitard
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005 Paris, France.
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
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8
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Solid-State NMR Approaches to Study Protein Structure and Protein-Lipid Interactions. Methods Mol Biol 2019. [PMID: 31218633 DOI: 10.1007/978-1-4939-9512-7_23] [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
Solid-state NMR spectroscopy has been developed for the investigation of membrane-associated polypeptides and remains one of the few techniques to reveal high-resolution structural information in liquid-disordered phospholipid bilayers. In particular, oriented samples have been used to investigate the structure, dynamics and topology of membrane polypeptides. Much of the previous solid-state NMR work has been developed and performed on peptides but the technique is constantly expanding towards larger membrane proteins. Here, a number of protocols are presented describing among other the reconstitution of membrane proteins into oriented membranes, monitoring membrane alignment by 31P solid-state NMR spectroscopy, investigations of the protein by one- and two-dimensional 15N solid-state NMR and measurements of the lipid order parameters using 2H solid-state NMR spectroscopy. Using such methods solid-state NMR spectroscopy has revealed a detailed picture of the ensemble of both lipids and proteins and their mutual interdependence in the bilayer environment.
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9
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Clifton LA, Hall SCL, Mahmoudi N, Knowles TJ, Heinrich F, Lakey JH. Structural Investigations of Protein-Lipid Complexes Using Neutron Scattering. Methods Mol Biol 2019; 2003:201-251. [PMID: 31218621 DOI: 10.1007/978-1-4939-9512-7_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Neutron scattering has significant benefits for examining the structure of protein-lipid complexes. Cold (slow) neutrons are nondamaging and predominantly interact with the atomic nucleus, meaning that neutron beams can penetrate deeply into samples, which allows for flexibility in the design of samples studied. Most importantly, there is a strong difference in neutron scattering length (i.e., scattering power) between protium ([Formula: see text], 99.98% natural abundance) and deuterium ([Formula: see text] or D, 0.015%). Through the mixing of H2O and D2O in the samples and in some cases the deuterium labeling of the biomolecules, components within a complex can be hidden or enhanced in the scattering signal. This enables both the overall structure and the relative distribution of components within a complex to be resolved. Lipid-protein complexes are most commonly studied using neutron reflectometry (NR) and small angle neutron scattering (SANS). In this review the methodologies to produce and examine a variety of model biological membrane systems using SANS and NR are detailed. These systems include supported lipid bilayers derived from vesicle dispersions or Langmuir-Blodgett deposition, tethered bilayer systems, membrane protein-lipid complexes and polymer wrapped lipid nanodiscs. The three key stages of any SANS/NR study on model membrane systems-sample preparation, data collection, and analysis-are described together with some background on the techniques themselves.
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Affiliation(s)
- Luke A Clifton
- Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, Oxfordshire, UK.
| | - Stephen C L Hall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Najet Mahmoudi
- Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, Oxfordshire, UK
| | - Timothy J Knowles
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- National Institute of Standards and Technology Centre for Neutron Research, Gaithersburg, MD, USA
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK.
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10
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Membrane-Active Properties of an Amphitropic Peptide from the CyaA Toxin Translocation Region. Toxins (Basel) 2017; 9:toxins9110369. [PMID: 29135925 PMCID: PMC5705984 DOI: 10.3390/toxins9110369] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/28/2022] Open
Abstract
The adenylate cyclase toxin CyaA is involved in the early stages of infection by Bordetella pertussis, the causative agent of whooping cough. CyaA intoxicates target cells by a direct translocation of its catalytic domain (AC) across the plasma membrane and produces supraphysiological levels of cAMP, leading to cell death. The molecular process of AC translocation remains largely unknown, however. We have previously shown that deletion of residues 375–485 of CyaA selectively abrogates AC translocation into eukaryotic cells. We further identified within this “translocation region” (TR), P454 (residues 454–484), a peptide that exhibits membrane-active properties, i.e., is able to bind and permeabilize lipid vesicles. Here, we analyze various sequences from CyaA predicted to be amphipatic and show that although several of these peptides can bind membranes and adopt a helical conformation, only the P454 peptide is able to permeabilize membranes. We further characterize the contributions of the two arginine residues of P454 to membrane partitioning and permeabilization by analyzing the peptide variants in which these residues are substituted by different amino acids (e.g., A, K, Q, and E). Our data shows that both arginine residues significantly contribute, although diversely, to the membrane-active properties of P454, i.e., interactions with both neutral and anionic lipids, helix formation in membranes, and disruption of lipid bilayer integrity. These results are discussed in the context of the translocation process of the full-length CyaA toxin.
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11
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Mathematical modeling of mutant transferrin-CRM107 molecular conjugates for cancer therapy. J Theor Biol 2017; 416:88-98. [PMID: 28065783 DOI: 10.1016/j.jtbi.2017.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/19/2016] [Accepted: 01/05/2017] [Indexed: 11/20/2022]
Abstract
The transferrin (Tf) trafficking pathway is a promising mechanism for use in targeted cancer therapy due to the overexpression of transferrin receptors (TfRs) on cancerous cells. We have previously developed a mathematical model of the Tf/TfR trafficking pathway to improve the efficiency of Tf as a drug carrier. By using diphtheria toxin (DT) as a model toxin, we found that mutating the Tf protein to change its iron release rate improves cellular association and efficacy of the drug. Though this is an improvement upon using wild-type Tf as the targeting ligand, conjugated toxins like DT are unfortunately still highly cytotoxic at off-target sites. In this work, we address this hurdle in cancer research by developing a mathematical model to predict the efficacy and selectivity of Tf conjugates that use an alternative toxin. For this purpose, we have chosen to study a mutant of DT, cross-reacting material 107 (CRM107). First, we developed a mathematical model of the Tf-DT trafficking pathway by extending our Tf/TfR model to include intracellular trafficking via DT and DT receptors. Using this mathematical model, we subsequently investigated the efficacy of several conjugates in cancer cells: DT and CRM107 conjugated to wild-type Tf, as well as to our engineered mutant Tf proteins (K206E/R632A Tf and K206E/R534A Tf). We also investigated the selectivity of mutant Tf-CRM107 against non-neoplastic cells. Through the use of our mathematical model, we predicted that (i) mutant Tf-CRM107 exhibits a greater cytotoxicity than wild-type Tf-CRM107 against cancerous cells, (ii) this improvement was more drastic with CRM107 conjugates than with DT conjugates, and (iii) mutant Tf-CRM107 conjugates were selective against non-neoplastic cells. These predictions were validated with in vitro cytotoxicity experiments, demonstrating that mutant Tf-CRM107 conjugates is indeed a more suitable therapeutic agent. Validation from in vitro experiments also confirmed that such whole-cell kinetic models can be useful in cancer therapeutic design.
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12
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Koutsioubas A. Combined Coarse-Grained Molecular Dynamics and Neutron Reflectivity Characterization of Supported Lipid Membranes. J Phys Chem B 2016; 120:11474-11483. [DOI: 10.1021/acs.jpcb.6b05433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexandros Koutsioubas
- Jülich Centre for
Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, 85748 Garching, Germany
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13
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Rodrigo-Unzueta A, Martínez MA, Comino N, Alzari PM, Chenal A, Guerin ME. Molecular Basis of Membrane Association by the Phosphatidylinositol Mannosyltransferase PimA Enzyme from Mycobacteria. J Biol Chem 2016; 291:13955-13963. [PMID: 27189944 DOI: 10.1074/jbc.m116.723676] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 01/09/2023] Open
Abstract
Phosphatidyl-myo-inositol mannosyltransferase A (PimA) is an essential glycosyltransferase that initiates the biosynthetic pathway of phosphatidyl-myo-inositol mannoside, lipomannan, and lipoarabinomannan, which are key glycolipids/lipoglycans of the mycobacterial cell envelope. PimA belongs to a large family of membrane-associated glycosyltransferases for which the understanding of the molecular mechanism and conformational changes that govern substrate/membrane recognition and catalysis remains a major challenge. Here, we determined that PimA preferentially binds to negatively charged phosphatidyl-myo-inositol substrate and non-substrate membrane model systems (small unilamellar vesicle) through its N-terminal domain, inducing an important structural reorganization of anionic phospholipids. By using a combination of single-point mutagenesis, circular dichroism, and a variety of fluorescence spectroscopy techniques, we determined that this interaction is mainly mediated by an amphipathic α-helix (α2), which undergoes a substantial conformational change and localizes in the vicinity of the negatively charged lipid headgroups and the very first carbon atoms of the acyl chains, at the PimA-phospholipid interface. Interestingly, a flexible region within the N-terminal domain, which undergoes β-strand-to-α-helix and α-helix-to-β-strand transitions during catalysis, interacts with anionic phospholipids; however, the effect is markedly less pronounced to that observed for the amphipathic α2, likely reflecting structural plasticity/variability. Altogether, we propose a model in which conformational transitions observed in PimA might reflect a molten globule state that confers to PimA, a higher affinity toward the dynamic and highly fluctuating lipid bilayer.
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Affiliation(s)
- Ane Rodrigo-Unzueta
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain,; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Vizcaya, Spain
| | - Mariano A Martínez
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 and University Paris Diderot, Sorbonne Paris Cité, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Natalia Comino
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain,; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Vizcaya, Spain,; Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC-bioGUNE), Bizkaia Technology Park, 48160 Derio, Spain
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 and University Paris Diderot, Sorbonne Paris Cité, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Alexandre Chenal
- Unité de Biochimie des Interactions Macromoléculaires and CNRS UMR 3528, 28 Rue du Dr. Roux, 75724, Paris Cedex 15, France.
| | - Marcelo E Guerin
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain,; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Vizcaya, Spain,; Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC-bioGUNE), Bizkaia Technology Park, 48160 Derio, Spain,; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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Wacklin HP, Bremec BB, Moulin M, Rojko N, Haertlein M, Forsyth T, Anderluh G, Norton RS. Neutron reflection study of the interaction of the eukaryotic pore-forming actinoporin equinatoxin II with lipid membranes reveals intermediate states in pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:640-52. [DOI: 10.1016/j.bbamem.2015.12.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 11/02/2015] [Accepted: 12/15/2015] [Indexed: 01/07/2023]
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15
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Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Topography of the TH5 Segment in the Diphtheria Toxin T-Domain Channel. J Membr Biol 2015; 249:181-96. [PMID: 26645703 DOI: 10.1007/s00232-015-9859-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/18/2015] [Indexed: 10/22/2022]
Abstract
The translocation domain (T-domain) of diphtheria toxin contains 10 α helices in the aqueous crystal structure. Upon exposure to a planar lipid bilayer under acidic conditions, it inserts to form a channel and transport the attached amino-terminal catalytic domain across the membrane. The TH5, TH8, and TH9 helices form transmembrane segments in the open-channel state, with TH1-TH4 translocated across the membrane. The TH6-TH7 segment also inserts to form a constriction that occupies only a small portion of the total channel length. Here, we have examined the TH5 segment in more detail, using the substituted-cysteine accessibility method. We constructed a series of 23 mutant T-domains with single cysteine residues at positions in and near TH5, monitored their channel formation in planar lipid bilayers, and probed for an effect of thiol-specific reagents added to the solutions on either side of the membrane. For 15 of the mutants, the reagent caused a decrease in single-channel conductance, indicating that the introduced cysteine residue was exposed within the channel lumen. We also found that reaction caused large changes in ionic selectivity for some mutant channels. We determined whether reaction occurred in the open state or in the brief flicker-closed state of the channel. Finally, we compared the reaction rates from either side of the membrane. Our experiments are consistent with the hypotheses that the TH5 helix has a transmembrane orientation and remains helical in the open-channel state; they also indicate that the middle of the helix is aligned with the constriction in the channel.
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Labyntsev AJ, Korotkevych NV, Kolybo DV, Komisarenko SV. EFFECT OF DIPHTHERIA TOXIN T-DOMAIN ON ENDOSOMAL pH. UKRAINIAN BIOCHEMICAL JOURNAL 2015; 87:13-23. [PMID: 26547959 DOI: 10.15407/ubj87.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A key step in the mode of cytotoxic action of diphtheria toxin (DT) is the transfer of its catalytic domain (Cd) from endosomes into the cytosol. The main activity in this process is performed by the transport domain (Td), but the molecular mechanism of its action remains unknown. We have previously shown that Td can have some influence on the endosomal transport of DT The aim of this work was to study the effect of diphtheria toxin on the toxin compartmentalization in the intracellular transporting pathway and endosomal pH. We used recombinant fragments of DT which differed only by the presence of Td in their structure, fused with fluorescent proteins. It was shown that the toxin fragment with Td moved slower by the pathway early-late endosomes-lysosomes, and had a slightly different pattern of colocalization with endosomal markers than DT fragment without Td. In addition, endosomes containing DT fragments with Td had a constant pH of about 6.5 from the 10th to 50th minute of observation, for the same time endosomes containing DT fragments without Td demonstrated a decrease in pH from 6.3 to 5.5. These results indicate that Td inhibits acidification of endosomal medium. One of possible explanations for this may be the effect of the ion channel formed by the T-domain on the process of the endosomal acidification. This property of Td may not only inhibit maturation of endosomes but also inhibit activation of endosomal pH-dependent proteases, and this promotes successful transport of Cd into the cell cytosol.
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Flores-Canales JC, Maria K. Microsecond Simulations of the Diphtheria Toxin Translocation Domain in Association with Anionic Lipid Bilayers. J Phys Chem B 2015; 119:12074-85. [PMID: 26305016 PMCID: PMC4916650 DOI: 10.1021/acs.jpcb.5b07909] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diphtheria toxin translocation (T) domain undergoes conformational changes in acidic solution and associates with the lipid membranes, followed by refolding and transmembrane insertion of two nonpolar helices. This process is an essential step in delivery of the toxic catalytic domain of the diphtheria toxin to the infected cell, yet its molecular determinants are poorly characterized and understood. Therefore, an atomistic model of the T-domain-membrane interaction is needed to help characterize factors responsible for such association. In this work, we present atomistic model structures of T-domain membrane-bound conformations and investigate structural factors responsible for T-domain affinity with the lipid bilayer in acidic solution using all-atom molecular dynamics (MD) simulations. The initial models of the protein conformations and protein-membrane association that serve as starting points in the present work were developed using atomistic simulations of partial unfolding of the T-domain in acidic solution (Kurnikov, I. V.; et al. J. Mol. Biol. 2013, 425, 2752-2764), and coarse-grained simulations of the T-domain association with the membranes of various compositions (Flores-Canales, J. C.; et al. J. Membr. Biol. 2015, 248, 529-543). In this work we present atomistic level modeling of two distinct configurations of the T-domain in association with the anionic lipid bilayer. In microsecond-long MD simulations both conformations retain their compact structure and gradually penetrate deeper into the bilayer interface. One membrane-bound conformation is stabilized by the protein contacts with the lipid hydrophobic core. The second modeled conformation is initially inserted less deeply and forms multiple contacts with the lipid at the interface (headgroup) region. Such contacts are formed by the charged and hydrophilic groups of partially unfolded terminal helixes and loops. Neutralization of the acidic residues at the membrane interface allows for deeper insertion of the protein and reorientation of the protein at the membrane interface, which corroborates that acidic residue protonation as well as presence of the anionic lipids may play a role in the membrane association and further membrane insertion of the T-domain as implicated in experiments. All simulations reported in this work were performed using AMBER force-field on Anton supercomputer. To perform these reported simulations, we developed and carefully tested a force-field for the anionic 1-palmitoyl-2-oleoyl-phosphatidyl-glycerol (POPG) lipid, compatible with the Amber 99SB force-field and stable in microsecond-long MD simulations in isothermal-isobaric ensemble.
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Affiliation(s)
- Jose C. Flores-Canales
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kurnikova Maria
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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Labyntsev AI, Korotkevich NV, Manoĭlov KI, Kaberniuk AA, Kolibo DV, Komisarenko SV. [Recombinant fluorescent models for studying of diphtheria toxin]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 40:433-42. [PMID: 25898753 DOI: 10.1134/s1068162014040086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Diphtheria toxin is the main pathogenicity factor of causative agent of diphtheria Corynebacterium diphtheriae. Due to the small molecule size, it is of considerable interestfor the development of synthetic protein molecules with transporting function, e.g. immunotoxins. Expression and characterization of nontoxic recombinant fluorescent derivates of diphtheria toxin and its nontoxic mutant CRM 197 were described in this article. Obtained proteins may be applied in studies of receptor-binding and transporting functions of the toxin in cells, for determination of toxin receptor proHB-EGF expression level, immunization and antibody generation against the toxin and in development of diagnostic test-systems, detection of diphtheria toxin and antitoxic antibodies.
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20
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Varela Chavez C, Hoos S, Haustant GM, Chenal A, England P, Blondel A, Pauillac S, Lacy DB, Popoff MR. The catalytic domains of Clostridium sordellii lethal toxin and related large clostridial glucosylating toxins specifically recognize the negatively charged phospholipids phosphatidylserine and phosphatidic acid. Cell Microbiol 2015; 17:1477-93. [PMID: 25882477 DOI: 10.1111/cmi.12449] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/15/2015] [Indexed: 12/23/2022]
Abstract
Clostridium sordellii lethal toxin (TcsL) is a potent virulence factor belonging to the large clostridial glucosylating toxin family. TcsL enters target cells via receptor-mediated endocytosis and delivers the N-terminal catalytic domain (TcsL-cat) into the cytosol upon an autoproteolytic process. TcsL-cat inactivates small GTPases including Rac and Ras by glucosylation with uridine-diphosphate (UDP)-glucose as cofactor leading to drastic changes in cytoskeleton and cell viability. TcsL-cat was found to preferentially bind to phosphatidylserine (PS)-containing membranes and to increase the glucosylation of Rac anchored to lipid membrane. We here report binding affinity measurements of TcsL-cat for brain PS-containing membranes by surface plasmon resonance and enzyme-linked immunosorbent assay (ELISA). In addition, TcsL-cat bound to phosphatidic acid (PA) and, to a lesser extent, to other anionic lipids, but not to neutral lipids, sphingolipids or sterol. We further show that the lipid unsaturation status influenced TcsL-cat binding to phospholipids, PS with unsaturated acyl chains and PA with saturated acyl chains being the preferred bindingsubstrates. Phospholipid binding site is localized at the N-terminal four helical bundle structure (1-93 domain). However, TcsL-1-93 bound to a broad range of substrates, whereas TcsL-cat, which is the active domain physiologically delivered into the cytosol, selectively bound to PS and PA. Similar findings were observed with the other large clostridial glucosylating toxins from C. difficile, C. novyi and C. perfringens.
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Affiliation(s)
| | - Sylviane Hoos
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | | | - Alexandre Chenal
- Unité de Biochimie des Interactions Macromoléculaires, Institut Pasteur, Paris, France
| | - Patrick England
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Arnaud Blondel
- Unité de Bioinformatique Structurale, Institut Pasteur, Paris, France
| | - Serge Pauillac
- Unité des Bactéries anaérobies et Toxines, Institut Pasteur, Paris, France
| | - D Borden Lacy
- Unité de Bioinformatique Structurale, Institut Pasteur, Paris, France.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
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21
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Koh EH. Effect of Diphtheria Toxin on the Phospholipase D activity and Free Fatty Acid Release in HepG2 Cells. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2015. [DOI: 10.5012/jkcs.2015.59.1.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Flores-Canales JC, Vargas-Uribe M, Ladokhin AS, Kurnikova M. Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment. J Membr Biol 2015; 248:529-43. [PMID: 25650178 DOI: 10.1007/s00232-015-9771-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/02/2015] [Indexed: 12/01/2022]
Abstract
Diphtheria toxin translocation (T) domain inserts in lipid bilayers upon acidification of the environment. Computational and experimental studies have suggested that low pH triggers a conformational change of the T-domain in solution preceding membrane binding. The refolded membrane-competent state was modeled to be compact and mostly retain globular structure. In the present work, we investigate how this refolded state interacts with membrane interfaces in the early steps of T-domain's membrane association. Coarse-grained molecular dynamics simulations suggest two distinct membrane-bound conformations of the T-domain in the presence of bilayers composed of a mixture of zwitteronic and anionic phospholipids (POPC:POPG with a 1:3 molar ratio). Both membrane-bound conformations show a common near parallel orientation of hydrophobic helices TH8-TH9 relative to the membrane plane. The most frequently observed membrane-bound conformation is stabilized by electrostatic interactions between the N-terminal segment of the protein and the membrane interface. The second membrane-bound conformation is stabilized by hydrophobic interactions between protein residues and lipid acyl chains, which facilitate deeper protein insertion in the membrane interface. A theoretical estimate of a free energy of binding of a membrane-competent T-domain to the membrane is provided.
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Bychkova VE, Basova LV, Balobanov VA. How membrane surface affects protein structure. BIOCHEMISTRY (MOSCOW) 2015; 79:1483-514. [DOI: 10.1134/s0006297914130045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Li J, Rodnin MV, Ladokhin AS, Gross ML. Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain. Biochemistry 2014; 53:6849-56. [PMID: 25290210 PMCID: PMC4222528 DOI: 10.1021/bi500893y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.
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Affiliation(s)
- Jing Li
- Department of Chemistry, Washington University , St. Louis, Missouri 63130, United States
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Leka O, Vallese F, Pirazzini M, Berto P, Montecucco C, Zanotti G. Diphtheria toxin conformational switching at acidic pH. FEBS J 2014; 281:2115-22. [DOI: 10.1111/febs.12783] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/05/2014] [Accepted: 03/11/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Oneda Leka
- Department of Biomedical Sciences; University of Padua; Italy
| | | | - Marco Pirazzini
- Department of Biomedical Sciences; University of Padua; Italy
| | - Paola Berto
- Department of Biomedical Sciences; University of Padua; Italy
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Subrini O, Sotomayor-Pérez AC, Hessel A, Spiaczka-Karst J, Selwa E, Sapay N, Veneziano R, Pansieri J, Chopineau J, Ladant D, Chenal A. Characterization of a membrane-active peptide from the Bordetella pertussis CyaA toxin. J Biol Chem 2013; 288:32585-32598. [PMID: 24064217 PMCID: PMC3820891 DOI: 10.1074/jbc.m113.508838] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/09/2013] [Indexed: 12/27/2022] Open
Abstract
Bordetella pertussis, the pathogenic bacteria responsible for whooping cough, secretes several virulence factors, among which is the adenylate cyclase toxin (CyaA) that plays a crucial role in the early stages of human respiratory tract colonization. CyaA invades target cells by translocating its catalytic domain directly across the plasma membrane and overproduces cAMP, leading to cell death. The molecular process leading to the translocation of the catalytic domain remains largely unknown. We have previously shown that the catalytic domain per se, AC384, encompassing residues 1-384 of CyaA, did not interact with lipid bilayer, whereas a longer polypeptide, AC489, spanning residues 1-489, binds to membranes and permeabilizes vesicles. Moreover, deletion of residues 375-485 within CyaA abrogated the translocation of the catalytic domain into target cells. Here, we further identified within this region a peptidic segment that exhibits membrane interaction properties. A synthetic peptide, P454, corresponding to this sequence (residues 454-485 of CyaA) was characterized by various biophysical approaches. We found that P454 (i) binds to membranes containing anionic lipids, (ii) adopts an α-helical structure oriented in plane with respect to the lipid bilayer, and (iii) permeabilizes vesicles. We propose that the region encompassing the helix 454-485 of CyaA may insert into target cell membrane and induce a local destabilization of the lipid bilayer, thus favoring the translocation of the catalytic domain across the plasma membrane.
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Affiliation(s)
- Orso Subrini
- From the Institut Pasteur, CNRS UMR 3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Ana-Cristina Sotomayor-Pérez
- From the Institut Pasteur, CNRS UMR 3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Audrey Hessel
- From the Institut Pasteur, CNRS UMR 3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Johanna Spiaczka-Karst
- From the Institut Pasteur, CNRS UMR 3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Edithe Selwa
- the Institut Pasteur, CNRS UMR 3528, Unité de Bio-Informatique Structurale, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Nicolas Sapay
- the Commissariat à l'Energie Atomique, Direction des Sciences de la Vie, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Chimie et Biologie des Métaux, CEA Grenoble, 17 Rue des Martyrs, 38054 Grenoble, France
| | - Rémi Veneziano
- the Institut Charles Gerhardt, UMR 5253 CNRS/ENSCM/UM2/UM1, Equipe "Matériaux Avancés pour la Catalyse et la Santé", UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault-BP 14 491, 34093 Montpellier Cedex 05, France
| | - Jonathan Pansieri
- the Institut Charles Gerhardt, UMR 5253 CNRS/ENSCM/UM2/UM1, Equipe "Matériaux Avancés pour la Catalyse et la Santé", UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault-BP 14 491, 34093 Montpellier Cedex 05, France
| | - Joel Chopineau
- the Institut Charles Gerhardt, UMR 5253 CNRS/ENSCM/UM2/UM1, Equipe "Matériaux Avancés pour la Catalyse et la Santé", UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault-BP 14 491, 34093 Montpellier Cedex 05, France; the Université de Nîmes, Rue Docteur Georges Salan, 30021 Nîmes, France
| | - Daniel Ladant
- From the Institut Pasteur, CNRS UMR 3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France,.
| | - Alexandre Chenal
- From the Institut Pasteur, CNRS UMR 3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France,.
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pH-triggered conformational switching along the membrane insertion pathway of the diphtheria toxin T-domain. Toxins (Basel) 2013; 5:1362-80. [PMID: 23925141 PMCID: PMC3760040 DOI: 10.3390/toxins5081362] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 11/17/2022] Open
Abstract
The translocation (T)-domain plays a key role in the action of diphtheria toxin and is responsible for transferring the catalytic domain across the endosomal membrane into the cytosol in response to acidification. Deciphering the molecular mechanism of pH-dependent refolding and membrane insertion of the T-domain, which is considered to be a paradigm for cell entry of other bacterial toxins, reveals general physicochemical principles underlying membrane protein assembly and signaling on membrane interfaces. Structure-function studies along the T-domain insertion pathway have been affected by the presence of multiple conformations at the same time, which hinders the application of high-resolution structural techniques. Here, we review recent progress in structural, functional and thermodynamic studies of the T-domain archived using a combination of site-selective fluorescence labeling with an array of spectroscopic techniques and computer simulations. We also discuss the principles of conformational switching along the insertion pathway revealed by studies of a series of T-domain mutants with substitutions of histidine residues.
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28
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Le Brun A, Clifton LA, Halbert CE, Lin B, Meron M, Holden PJ, Lakey JH, Holt SA. Structural characterization of a model gram-negative bacterial surface using lipopolysaccharides from rough strains of Escherichia coli. Biomacromolecules 2013; 14:2014-22. [PMID: 23617615 PMCID: PMC3679557 DOI: 10.1021/bm400356m] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/18/2013] [Indexed: 12/29/2022]
Abstract
Lipopolysaccharides (LPS) make up approximately 75% of the Gram-negative bacterial outer membrane (OM) surface, but because of the complexity of the molecule, there are very few model OMs that include LPS. The LPS molecule consists of lipid A, which anchors the LPS within the OM, a core polysaccharide region, and a variable O-antigen polysaccharide chain. In this work we used RcLPS (consisting of lipid A plus the first seven sugars of the core polysaccharide) from a rough strain of Escherichia coli to form stable monolayers of LPS at the air-liquid interface. The vertical structure RcLPS monolayers were characterized using neutron and X-ray reflectometry, while the lateral structure was investigated using grazing incidence X-ray diffraction and Brewster angle microscopy. It was found that RcLPS monolayers at surface pressures of 20 mN m(-1) and above are resolved as hydrocarbon tails, an inner headgroup, and an outer headgroup of polysaccharide with increasing solvation from tails to outer headgroups. The lateral organization of the hydrocarbon lipid chains displays an oblique hexagonal unit cell at all surface pressures, with only the chain tilt angle changing with surface pressure. This is in contrast to lipid A, which displays hexagonal or, above 20 mN m(-1), distorted hexagonal packing. This work provides the first complete structural analysis of a realistic E. coli OM surface model.
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Affiliation(s)
- Anton
P. Le Brun
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Luke A. Clifton
- ISIS Neutron Facility, STFC Rutherford
Appleton Laboratory, Didcot, Oxfordshire
OX11 0QX, United Kingdom
| | - Candice E. Halbert
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
| | - Binhua Lin
- Consortium
of Advanced Radiation
Sources (CARS), University of Chicago,
Chicago, Illinois 60637, United States
| | - Mati Meron
- Consortium
of Advanced Radiation
Sources (CARS), University of Chicago,
Chicago, Illinois 60637, United States
| | - Peter J. Holden
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Jeremy H. Lakey
- Institute for Cell and Molecular
Biosciences, Newcastle University, Framlington
Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Stephen A. Holt
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
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Wang T, Yao H, Hong M. Determining the depth of insertion of dynamically invisible membrane peptides by gel-phase ¹H spin diffusion heteronuclear correlation NMR. JOURNAL OF BIOMOLECULAR NMR 2013; 56:139-148. [PMID: 23606274 PMCID: PMC3700645 DOI: 10.1007/s10858-013-9730-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 04/10/2013] [Indexed: 05/28/2023]
Abstract
Solid-state NMR determination of the depth of insertion of membrane peptides and proteins has so far utilized (1)H spin diffusion and paramagnetic relaxation enhancement experiments, which are typically conducted in the liquid-crystalline phase of the lipid bilayer. For membrane proteins or peptide assemblies that undergo intermediate-timescale motion in the liquid-crystalline membrane, these approaches are no longer applicable because the protein signals are broadened beyond detection. Here we show that the rigid-solid HETCOR experiment, with an additional spin diffusion period, can be used to determine the depth of proteins in gel-phase lipid membranes, where the proteins are immobilized to give high-intensity solid-state NMR spectra. Demonstration on two membrane peptides with known insertion depths shows that well-inserted peptides give rise to high lipid cross peak intensities and low water cross peaks within a modest spin diffusion mixing time, while surface-bound peptides have higher water than lipid cross peaks. Furthermore, well-inserted membrane peptides have nearly identical (1)H cross sections as the lipid chains, indicating equilibration of the peptide and lipid magnetization. Using this approach, we measured the membrane topology of the α-helical fusion peptide of the paramyxovirus, PIV5, in the anionic POPC/POPG membrane, in which the peptide undergoes intermediate-timescale motion at physiological temperature. The gel-phase HETCOR spectra indicate that the α-helical fusion peptide is well inserted into the POPC/POPG bilayer, spanning both leaflets. This insertion motif gives insight into the functional role of the α-helical PIV5 fusion peptide in virus-cell membrane fusion.
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Affiliation(s)
| | | | - M. Hong
- Corresponding author: Mei Hong Tel: 515-294-3521, Fax: 515-294-0105,
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30
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Aisenbrey C, Michalek M, Salnikov ES, Bechinger B. Solid-state NMR approaches to study protein structure and protein-lipid interactions. Methods Mol Biol 2013; 974:357-387. [PMID: 23404284 DOI: 10.1007/978-1-62703-275-9_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Solid-state NMR spectroscopy has been developed for the investigation of membrane-associated polypeptides and remains one of the few techniques to reveal high-resolution structural information in liquid-disordered phospholipid bilayers. In particular, oriented samples have been used to investigate the structure, dynamics, and topology of membrane polypeptides. Much of the previous solid-state NMR work has been developed and performed on peptides, but the technique is constantly expanding towards larger membrane proteins. Here, a number of protocols are presented describing among other the reconstitution of membrane proteins into oriented membranes, monitoring membrane alignment by (31)P solid-state NMR spectroscopy; investigations of the protein by one- and two-dimensional (15)N solid-state NMR; and measurements of the lipid order parameters using (2)H solid-state NMR spectroscopy. Using such methods solid-state NMR spectroscopy has revealed a detailed picture of the ensemble of both lipids and proteins and their mutual interdependence in the bilayer environment.
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31
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Abstract
Studying the structure of protein-lipid complexes, be they in vesicles, planar bilayers, monolayers, or nanodiscs, poses two particular challenges. Firstly such complexes are often dynamic. Secondly we need to resolve the lipid and protein structures within the complex. Neutron scattering is well placed to help in both respects since it deals with molecules in large, complex, dynamic structures and can easily differentiate between different molecular species. This comes from the great penetrating power of neutrons and their sensitivity to the difference between hydrogen (H) and deuterium (D). Both membrane proteins and lipids can be produced with varying degrees of deuteration, thus allowing us to dissect complexes with great accuracy. Two main scattering techniques are immediately applicable to the study of protein-lipid interactions. Neutron reflection exploits the constructive interference, which occurs when neutrons are reflected from different points in a layer. An everyday example is the rainbow of colors reflected from an oil film on water, which result from varying film thickness and the angle of reflection. Neutrons because of their short wavelengths (4-15 Å) and H/D sensitivity can, in reflectometry mode, provide accurate cross sections of lipid monolayers and bilayers. Small-angle neutron scattering (SANS) can resolve the structures of protein-lipid complexes if they are present as homogeneous dispersions. This is easiest with detergent micelles, but increasingly methods are being developed whereby vesicles, nanodiscs, etc., can be resolved. Again the ability to deuterate proteins and lipids enables SANS to resolve the inner structure of big, dynamic, lipid-protein complexes. The recent introduction of advanced neutron beam lines means that the technique is now within the grasp of a broad cross section of researchers.
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32
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Wadsäter M, Laursen T, Singha A, Hatzakis NS, Stamou D, Barker R, Mortensen K, Feidenhans'l R, Møller BL, Cárdenas M. Monitoring shifts in the conformation equilibrium of the membrane protein cytochrome P450 reductase (POR) in nanodiscs. J Biol Chem 2012; 287:34596-603. [PMID: 22891242 PMCID: PMC3464565 DOI: 10.1074/jbc.m112.400085] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 08/09/2012] [Indexed: 11/06/2022] Open
Abstract
Nanodiscs are self-assembled ∼50-nm(2) patches of lipid bilayers stabilized by amphipathic belt proteins. We demonstrate that a well ordered dense film of nanodiscs serves for non-destructive, label-free studies of isolated membrane proteins in a native like environment using neutron reflectometry (NR). This method exceeds studies of membrane proteins in vesicle or supported lipid bilayer because membrane proteins can be selectively adsorbed with controlled orientation. As a proof of concept, the mechanism of action of the membrane-anchored cytochrome P450 reductase (POR) is studied here. This enzyme is responsible for catalyzing the transfer of electrons from NADPH to cytochrome P450s and thus is a key enzyme in the biosynthesis of numerous primary and secondary metabolites in plants. Neutron reflectometry shows a coexistence of two different POR conformations, a compact and an extended form with a thickness of 44 and 79 Å, respectively. Upon complete reduction by NADPH, the conformational equilibrium shifts toward the compact form protecting the reduced FMN cofactor from engaging in unspecific electron transfer reaction.
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Affiliation(s)
- Maria Wadsäter
- From the Nano-Science Center and Institute of Chemistry, Faculty of Science, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Tomas Laursen
- the Plant Biochemistry Laboratory, Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Aparajita Singha
- the Bio-Nanotechnology Laboratory, Department of Neuroscience and Pharmacology, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Nikos S. Hatzakis
- the Bio-Nanotechnology Laboratory, Department of Chemistry, Department of Neuroscience and Pharmacology, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Dimitrios Stamou
- the Bio-Nanotechnology Laboratory, Department of Chemistry, Department of Neuroscience and Pharmacology, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Robert Barker
- the Institut Laue Langevin, 6 rue Jules Horowitz – BP 156, 38042 Grenoble Cedex 9, France, and
| | - Kell Mortensen
- the Nano-Science Center and Niels Bohr Institute, Universitetsparken 5, 2200 Copenhagen, Denmark
| | - Robert Feidenhans'l
- the Nano-Science Center and Niels Bohr Institute, Universitetsparken 5, 2200 Copenhagen, Denmark
| | - Birger Lindberg Møller
- the Plant Biochemistry Laboratory, Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Marité Cárdenas
- From the Nano-Science Center and Institute of Chemistry, Faculty of Science, University of Copenhagen, DK-2200 Copenhagen, Denmark
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33
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Fragneto G, Charitat T, Daillant J. Floating lipid bilayers: models for physics and biology. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:863-74. [PMID: 22825799 DOI: 10.1007/s00249-012-0834-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/01/2012] [Accepted: 06/14/2012] [Indexed: 10/28/2022]
Abstract
Progress in the determination of structure and fluctuation spectrum of a floating bilayer system, as well as potential applications for biological studies, is reviewed. The system described here was first introduced by Charitat et al. (Eur Phys J B 8:583-593, 1999) and consists of a planar bilayer floating at 2-3 nm away from an adsorbed one on a solid surface in contact with bulk water. This model has been widely used for surface scattering studies using both neutrons and synchrotron radiation and its use in studies of relevance for physics and biology research areas will be described, together with the progress towards the production of complex biomimetic samples for use with scattering techniques.
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Affiliation(s)
- Giovanna Fragneto
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042, Grenoble Cedex 9, France.
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34
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Karst JC, Barker R, Devi U, Swann MJ, Davi M, Roser SJ, Ladant D, Chenal A. Identification of a region that assists membrane insertion and translocation of the catalytic domain of Bordetella pertussis CyaA toxin. J Biol Chem 2012; 287:9200-12. [PMID: 22241477 DOI: 10.1074/jbc.m111.316166] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The adenylate cyclase (CyaA) toxin, one of the virulence factors secreted by Bordetella pertussis, the pathogenic bacteria responsible for whooping cough, plays a critical role in the early stages of respiratory tract colonization by this bacterium. The CyaA toxin is able to invade eukaryotic cells by translocating its N-terminal catalytic domain directly across the plasma membrane of the target cells, where, activated by endogenous calmodulin, it produces supraphysiological levels of cAMP. How the catalytic domain is transferred from the hydrophilic extracellular medium into the hydrophobic environment of the membrane and then to the cell cytoplasm remains an unsolved question. In this report, we have characterized the membrane-interacting properties of the CyaA catalytic domain. We showed that a protein covering the catalytic domain (AC384, encompassing residues 1-384 of CyaA) displayed no membrane association propensity. However, a longer polypeptide (AC489), encompassing residues 1-489 of CyaA, exhibited the intrinsic property to bind to membranes and to induce lipid bilayer destabilization. We further showed that deletion of residues 375-485 within CyaA totally abrogated the toxin's ability to increase intracellular cAMP in target cells. These results indicate that, whereas the calmodulin dependent enzymatic domain is restricted to the amino-terminal residues 1-384 of CyaA, the membrane-interacting, translocation-competent domain extends up to residue 489. This thus suggests an important role of the region adjacent to the catalytic domain of CyaA in promoting its interaction with and its translocation across the plasma membrane of target cells.
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Affiliation(s)
- Johanna C Karst
- Institut Pasteur, CNRS UMR 3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, Paris, France
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35
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Clifton LA, Johnson CL, Solovyova AS, Callow P, Weiss KL, Ridley H, Le Brun AP, Kinane CJ, Webster JRP, Holt SA, Lakey JH. Low resolution structure and dynamics of a colicin-receptor complex determined by neutron scattering. J Biol Chem 2011; 287:337-346. [PMID: 22081604 PMCID: PMC3249085 DOI: 10.1074/jbc.m111.302901] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Proteins that translocate across cell membranes need to overcome a significant hydrophobic barrier. This is usually accomplished via specialized protein complexes, which provide a polar transmembrane pore. Exceptions to this include bacterial toxins, which insert into and cross the lipid bilayer itself. We are studying the mechanism by which large antibacterial proteins enter Escherichia coli via specific outer membrane proteins. Here we describe the use of neutron scattering to investigate the interaction of colicin N with its outer membrane receptor protein OmpF. The positions of lipids, colicin N, and OmpF were separately resolved within complex structures by the use of selective deuteration. Neutron reflectivity showed, in real time, that OmpF mediates the insertion of colicin N into lipid monolayers. This data were complemented by Brewster Angle Microscopy images, which showed a lateral association of OmpF in the presence of colicin N. Small angle neutron scattering experiments then defined the three-dimensional structure of the colicin N-OmpF complex. This revealed that colicin N unfolds and binds to the OmpF-lipid interface. The implications of this unfolding step for colicin translocation across membranes are discussed.
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Affiliation(s)
- Luke A Clifton
- ISIS Spallation Neutron Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Christopher L Johnson
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Alexandra S Solovyova
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Phil Callow
- Partnership for Structural Biology, Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Kevin L Weiss
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Helen Ridley
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Anton P Le Brun
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Christian J Kinane
- ISIS Spallation Neutron Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - John R P Webster
- ISIS Spallation Neutron Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Stephen A Holt
- ISIS Spallation Neutron Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom.
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36
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Man P, Montagner C, Vitrac H, Kavan D, Pichard S, Gillet D, Forest E, Forge V. Accessibility Changes within Diphtheria Toxin T Domain upon Membrane Penetration Probed by Hydrogen Exchange and Mass Spectrometry. J Mol Biol 2011; 414:123-34. [DOI: 10.1016/j.jmb.2011.09.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 09/26/2011] [Indexed: 01/25/2023]
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37
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Nanoscale structural and mechanical effects of beta-amyloid (1–42) on polymer cushioned membranes: A combined study by neutron reflectometry and AFM Force Spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2646-55. [DOI: 10.1016/j.bbamem.2011.07.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 07/06/2011] [Accepted: 07/19/2011] [Indexed: 11/20/2022]
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38
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Westphal D, Dewson G, Czabotar PE, Kluck RM. Molecular biology of Bax and Bak activation and action. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:521-31. [PMID: 21195116 DOI: 10.1016/j.bbamcr.2010.12.019] [Citation(s) in RCA: 378] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 12/17/2010] [Accepted: 12/19/2010] [Indexed: 12/26/2022]
Abstract
Bax and Bak are two nuclear-encoded proteins present in higher eukaryotes that are able to pierce the mitochondrial outer membrane to mediate cell death by apoptosis. Thus, organelles recruited by nucleated cells to supply energy can be recruited by Bax and Bak to kill cells. The two proteins lie in wait in healthy cells where they adopt a globular α-helical structure, seemingly as monomers. Following a variety of stress signals, they convert into pore-forming proteins by changing conformation and assembling into oligomeric complexes in the mitochondrial outer membrane. Proteins from the mitochondrial intermembrane space then empty into the cytosol to activate proteases that dismantle the cell. The arrangement of Bax and Bak in membrane-bound complexes, and how the complexes porate the membrane, is far from being understood. However, recent data indicate that they first form symmetric BH3:groove dimers which can be linked via an interface between the α6-helices to form high order oligomers. Here, we review how Bax and Bak change conformation and oligomerize, as well as how oligomers might form a pore. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.
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41
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Membrane association and pore formation by alpha-helical peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 677:24-30. [PMID: 20687478 DOI: 10.1007/978-1-4419-6327-7_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Membrane-active peptides exhibit antimicrobial, channel-forming and transport activities and have therefore early on been interesting targets for biophysical investigations. When the peptide-lipid interactions are studied a dynamic view emerges in which the peptides change conformation upon membrane insertion, can adopt a variety of topologies and change the macroscopic phase properties of the membrane locally or globally. Interestingly several proteins have been identified that also interact with the membrane in a dynamic fashion and where the lessons learned from peptides may add to our understanding of the ways these proteins function.
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42
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Wang J, London E. The membrane topography of the diphtheria toxin T domain linked to the a chain reveals a transient transmembrane hairpin and potential translocation mechanisms. Biochemistry 2009; 48:10446-56. [PMID: 19780588 DOI: 10.1021/bi9014665] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The diphtheria toxin T domain helps translocate the A chain of the toxin across membranes. To gain insight into translocation, the membrane topography of key residues in T domain attached to the A chain (AT protein) was compared to that in the isolated T domain using fluorescence techniques. This study demonstrates that residues in T domain hydrophobic helices (TH5-TH9) tended to be less exposed to aqueous solution in the AT protein than in the isolated T domain. Under conditions in which the loop connecting TH5 to TH6/7 is located stably on the cis (insertion) side of the membrane in the isolated T domain, it moves between the cis and trans sides of the membrane in the AT protein. This is indicative of the formation of a dynamic, transient transmembrane hairpin topography by TH5-TH7 in the AT protein. Since TH8 and TH9 also form a transmembrane hairpin, this means that TH5-TH9 may form a cluster of transmembrane helices. These helices have a nonpolar surface likely to face the lipid bilayer in a helix cluster and a surface rich in uncharged hydrophilic residues which in a helix cluster would likely be facing inward (and perhaps be pore-lining). This uncharged hydrophilic surface could play a crucial role in translocation, interacting transiently with the translocating A chain. A similar motif can be found in, and may be important for, other protein translocation systems.
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Affiliation(s)
- Jie Wang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
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