1
|
Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat Microbiol 2021; 6:830-841. [PMID: 34045711 PMCID: PMC7611113 DOI: 10.1038/s41564-021-00911-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune clearance1. However, not all variants are equally fit in all environments2,3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here, we demonstrate this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm). A dominant surface antigen of S.Tm is its O-antigen: a long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase variation4,5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen-specific immunoglobulin A and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naive mice. Through the use of rationally designed oral vaccines, we induced immunoglobulin A responses blocking all of these trajectories. This selected for Salmonella mutants carrying deletions of the O-antigen polymerase gene wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents or complement) and predation (bacteriophages) and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.
Collapse
Affiliation(s)
- Médéric Diard
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Zoology, University of Oxford, Oxford, UK
| | - Verena Lentsch
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | | | | | - Daniel Hoces
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Selma Aslani
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Markus Arnoldini
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Flurina Böhi
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zürich, Zürich, Switzerland
| | - Kathrin Schumann-Moor
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Division of Surgical Research, University Hospital of Zürich, Zürich, Switzerland
| | - Jozef Adamcik
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas Donohue
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK.,Department of Orthopedics and Trauma, Medical University of Graz, Graz, Austria
| | - Marjan W van der Woude
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Alyson Hockenberry
- Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland.,Department of Environmental Sciences, ETH Zürich, Zürich, Switzerland
| | - Patrick H Viollier
- Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wüthrich
- Infection Biology, University Hospital of Basel, Basel, Switzerland
| | | | - Claude Loverdo
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Adrian Egli
- Infection Biology, University Hospital of Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Raffaele Mezzenga
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.,Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Otto Holst
- Forschungszentrum Borstel, Borstel, Germany
| | - Beat H Meier
- Institute for Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Emma Slack
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland. .,Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
2
|
Lends A, Ravotti F, Zandomeneghi G, Böckmann A, Ernst M, Meier BH. Direct amide 15N to 13C transfers for solid-state assignment experiments in deuterated proteins. J Biomol NMR 2018; 72:69-78. [PMID: 30206780 DOI: 10.1007/s10858-018-0207-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
The assignment of protein backbone and side-chain NMR chemical shifts is the first step towards the characterization of protein structure. The recent introduction of proton detection in combination with fast MAS has opened up novel opportunities for assignment experiments. However, typical 3D sequential-assignment experiments using proton detection under fast MAS lead to signal intensities much smaller than the theoretically expected ones due to the low transfer efficiency of some of the steps. Here, we present a selective 3D experiment for deuterated and (amide) proton back-exchanged proteins where polarization is directly transferred from backbone nitrogen to selected backbone or sidechain carbons. The proposed pulse sequence uses only 1H-15N cross-polarization (CP) transfers, which are, for deuterated proteins, about 30% more efficient than 1H-13C CP transfers, and employs a dipolar version of the INEPT experiment for N-C transfer. By avoiding HN-C (HN stands for amide protons) and C-C CP transfers, we could achieve higher selectivity and increased signal intensities compared to other pulse sequences containing long-range CP transfers. The REDOR transfer is designed with an additional selective π pulse, which enables the selective transfer of the polarization to the desired 13C spins.
Collapse
Affiliation(s)
- Alons Lends
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Francesco Ravotti
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Giorgia Zandomeneghi
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| |
Collapse
|
3
|
Gowda C, Zandomeneghi G, Zimmermann H, Schütz AK, Böckmann A, Ernst M, Meier BH. The conformation of the Congo-red ligand bound to amyloid fibrils HET-s(218-289): a solid-state NMR study. J Biomol NMR 2017; 69:207-213. [PMID: 29094285 DOI: 10.1007/s10858-017-0148-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 10/21/2017] [Indexed: 06/07/2023]
Abstract
We have previously shown that Congo red (CR) binds site specifically to amyloid fibrils formed by HET-s(218-289) with the long axis of the CR molecule almost parallel to the fibril axis. HADDOCK docking studies indicated that CR adopts a roughly planar conformation with the torsion angle ϕ characterizing the relative orientation of the two phenyl rings being a few degrees. In this study, we experimentally determine the torsion angle ϕ at the center of the CR molecule when bound to HET-s(218-289) amyloid fibrils using solid-state NMR tensor-correlation experiments. The method described here relies on the site-specific 13C labeling of CR and on the analysis of the two-dimensional magic-angle spinning tensor-correlation spectrum of 13C2-CR. We determined the torsion angle ϕ to be 19°.
Collapse
Affiliation(s)
| | | | - Herbert Zimmermann
- Department of Biomolecular Mechanisms, Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Anne K Schütz
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Anja Böckmann
- IBCP, UMR 5086 CNRS/Université de Lyon 1, 7 Passage du Vercors, 69367, Lyon, France
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
| |
Collapse
|
4
|
Hock A, Wilm B, Zandomeneghi G, Ampanozi G, Franckenberg S, Zoelch N, Wyss PO, De Zanche N, Nordmeyer-Maßner J, Kraemer T, Thali M, Ernst M, Kollias S, Henning A. Neurochemical profile of the human cervical spinal cord determined by MRS. NMR Biomed 2016; 29:1464-1476. [PMID: 27580498 DOI: 10.1002/nbm.3589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/14/2016] [Accepted: 06/29/2016] [Indexed: 06/06/2023]
Abstract
MRS enables insight into the chemical composition of central nervous system tissue. However, technical challenges degrade the data quality when applied to the human spinal cord. Therefore, to date detection of only the most prominent metabolite resonances has been reported in the healthy human spinal cord. The aim of this investigation is to provide an extended metabolic profile including neurotransmitters and antioxidants in addition to metabolites involved in the energy and membrane metabolism of the human cervical spinal cord in vivo. To achieve this, data quality was improved by using a custom-made, cervical detector array together with constructive averaging of a high number of echo signals, which is enabled by the metabolite cycling technique at 3T. In addition, the improved spinal cord spectra were extensively cross-validated, in vivo, post-mortem in situ and ex vivo. Reliable identification of up to nine metabolites was achieved in group analyses for the first time. Distinct features of the spinal cord neurochemical profile, in comparison with the brain neurotransmission system, include decreased concentrations of the sum of glutamate and glutamate and increased concentrations of aspartate, γ-amino-butyric acid, scyllo-inositol and the sum of myo-inositol and glycine.
Collapse
Affiliation(s)
- Andreas Hock
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland.
- Hospital of Psychiatry, Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zurich, Zurich, Switzerland.
| | - Bertram Wilm
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
| | | | - Garyfalia Ampanozi
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | - Niklaus Zoelch
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
| | - Patrik Oliver Wyss
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
- Institute of Neuroradiology, University Hospital of Zurich, Zurich, Switzerland
| | - Nicola De Zanche
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Thomas Kraemer
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Michael Thali
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | - Spyros Kollias
- Institute of Neuroradiology, University Hospital of Zurich, Zurich, Switzerland
| | - Anke Henning
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
- Max Plank Institute for Biological Cybernetics, Tuebingen, Baden-Württemberg, Germany
| |
Collapse
|
5
|
Ilg K, Zandomeneghi G, Rugarabamu G, Meier BH, Aebi M. HR-MAS NMR reveals a pH-dependent LPS alteration by de-O-acetylation at abequose in the O-antigen of Salmonella enterica serovar Typhimurium. Carbohydr Res 2013; 382:58-64. [PMID: 24211643 DOI: 10.1016/j.carres.2013.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 11/19/2022]
Abstract
NMR spectroscopy can detect biomolecules like lipopolysaccharide directly on the surface of the cell, thus avoiding isolation and purification, and providing a more realistic description than the one derived from in vitro studies. Here we present a high-resolution magic-angle spinning NMR study of the O-antigen of Salmonella enterica serovar Typhimurium (S. Typhimurium) performed directly on the cells showing the alteration of its acetylation state over time. The O-antigen region of S. Typhimurium consists of the repeating unit [→2)-α-d-Manp-(1→4)-α-l-Rhap-(1→3)-α-d-Galp-(1→] where Man stands for mannose, Rha for rhamnose, and Gal for galactose. Man is substituted with abequose (Abe) O-acetylated at carbon 2. Our studies revealed that the appearance of de-O-acetylated O-antigen in the stationary growth phase is due to the de-O-acetylation of already synthesized O-acetylated O-antigen and that this reaction is caused by the metabolism-induced basic pH of the growth medium. The labile O-acetylation of the O-antigen we observed in S. Typhimurium generates non-stoichiometric O-acetylation states and therefore changes the nature of an immunogenic epitope.
Collapse
Affiliation(s)
- Karin Ilg
- Institute of Microbiology, ETH Zurich, Department of Biology, HCI F407, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland
| | | | | | | | | |
Collapse
|
6
|
Zandomeneghi G, Maas W, Meier BH. Biological solid-state NMR at ETH Zurich. Chimia (Aarau) 2012; 66:798-800. [PMID: 23146268 DOI: 10.2533/chimia.2012.798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Solid-state Magnetic Resonance has been greatly developed over the past decade. Higher field spectrometers and other technical developments are expected to lead to further significant improvements.
Collapse
Affiliation(s)
- Giorgia Zandomeneghi
- Physical Chemistry ETH Zurich Wolfgang-Pauli-Strasse 10 CH-8093 Zurich, Switzerland
| | | | | |
Collapse
|
7
|
|
8
|
Affiliation(s)
| | - Karin Ilg
- Microbiology, ETH Zurich, Wolfgang-Pauli Str. 10, 8093 Zurich Switzerland
| | - Markus Aebi
- Microbiology, ETH Zurich, Wolfgang-Pauli Str. 10, 8093 Zurich Switzerland
| | - Beat H. Meier
- Physical Chemistry, ETH Zurich, Wolfgang-Pauli Str. 10, 8093 Zurich Switzerland
| |
Collapse
|
9
|
Junker K, Zandomeneghi G, Guo Z, Kissner R, Ishikawa T, Kohlbrecher J, Walde P. Mechanistic aspects of the horseradish peroxidase-catalysed polymerisation of aniline in the presence of AOT vesicles as templates. RSC Adv 2012. [DOI: 10.1039/c2ra20566a] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
10
|
Pizzanelli S, Forte C, Monti S, Zandomeneghi G, Hagarman A, Measey TJ, Schweitzer-Stenner R. Conformations of phenylalanine in the tripeptides AFA and GFG probed by combining MD simulations with NMR, FTIR, polarized Raman, and VCD spectroscopy. J Phys Chem B 2010; 114:3965-78. [PMID: 20184301 DOI: 10.1021/jp907502n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Conformational properties of small, flexible peptides are a matter of ongoing interest since they can be considered as models for unfolded proteins. However, the investigation of the conformations of small peptides is challenging as they are ensembles of rapidly interconverting conformers; moreover, the different methods used are prone to different approximations and errors. In order to obtain more reliable results, it is prudent to combine different techniques; here, molecular dynamics (MD) simulations together with nuclear magnetic resonance (NMR), Fourier transform IR (FTIR), polarized Raman, and vibrational circular dichroism (VCD) measurements were used to study the conformational propensity of phenylalanine in the tripeptides AFA and GFG, motivated by the relevance of phenylalanine for the self-aggregation of peptides. The results of this analysis indicate that the F residue predominantly populates the beta-strand (beta) and polyproline II (PPII) conformations in both AFA and GFG. However, while phenylalanine exhibits a propensity for beta-strand conformations in GFG (0.40 < or = beta population < or = 0.69 and 0.29 < or = PPII population < or = 0.42), the substitution of terminal glycines with alanine residues induces a higher population of PPII (0.31 < or = beta population < or = 0.50 and 0.37 < or = PPII population < or = 0.57).
Collapse
Affiliation(s)
- Silvia Pizzanelli
- Istituto per i Processi Chimico Fisici, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, via G. Moruzzi, 1 56124 Pisa, Italy.
| | | | | | | | | | | | | |
Collapse
|
11
|
Šišak D, McCusker L, Zandomeneghi G, Meier B, Bläser D, Boese R, Schweizer W, Gilmour R, Dunitz J. Die Kristallstruktur von D-Ribose - endlich! Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001266] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
12
|
Šišak D, McCusker L, Zandomeneghi G, Meier B, Bläser D, Boese R, Schweizer W, Gilmour R, Dunitz J. The Crystal Structure of D-Ribose-At Last! Angew Chem Int Ed Engl 2010; 49:4503-5. [DOI: 10.1002/anie.201001266] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
13
|
Riccò M, Pontiroli D, Mazzani M, Gianferrari F, Pagliari M, Goffredi A, Brunelli M, Zandomeneghi G, Meier BH, Shiroka T. Fullerenium Salts: A New Class of C60-Based Compounds. J Am Chem Soc 2010; 132:2064-8. [DOI: 10.1021/ja909614x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mauro Riccò
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Daniele Pontiroli
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Marcello Mazzani
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Fabio Gianferrari
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Massimo Pagliari
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Angelo Goffredi
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Michela Brunelli
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Giorgia Zandomeneghi
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Beat H. Meier
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| | - Toni Shiroka
- Dipartimento di Fisica, Università di Parma, Via G. Usberti 7/a, 43100 Parma, Italy, Institut Laue Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Physical Chemistry Laboratory, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland, and Laboratorium für Festkörperphysik, ETH-Zurich, Schafmattstrasse 16, CH-8093 Zurich, Switzerland
| |
Collapse
|
14
|
Zandomeneghi G, Zandomeneghi M. Determination of holo- and apo-riboflavin binding protein in avian egg whites through circular dichroism and fluorescence spectroscopy. J Agric Food Chem 2009; 57:6510-6517. [PMID: 19722562 DOI: 10.1021/jf901079n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The hen egg white contains proteins able to strongly bind, with a definite stoichiometry, small molecules such as biotin and riboflavin, or ions such as Cu2+ or Fe3+. The complexation process modifies the spectral properties of these low-molecular-weight species. On the basis of these changes, it is possible, in principle, to measure the quantity of the binding protein and to evaluate the protein-substrate interactions. Here, we present a method to determine the concentration of both the apo and holo forms of the riboflavin-binding protein (RFBP) present in avian egg white, by measuring the circular dichroism (CD) related to the controlled addition of riboflavin (or vitamin B2) to the egg white. At the same time, front-face fluorescence is used to confirm the concentration of apo-RFBP obtained from CD data. The method is based on data only from spectroscopy, and no process involving either extraction, chromatography, electrophoresis, or mass spectrometry is involved. We study the egg whites from four different avian species, reporting and comparing the concentration of the apo- and holo-RFBP and the molar circular dichroism spectra (Deltaepsilon) of riboflavin in the RFBP binding site. Finally, egg whites from different hen individuals are analyzed, and a surprising variation of the RFBP concentration is found.
Collapse
Affiliation(s)
- Giorgia Zandomeneghi
- Physical Chemistry, ETH-Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland
| | | |
Collapse
|
15
|
Williamson PTF, Zandomeneghi G, Barrantes FJ, Watts A, Meier BH. Structural and dynamic studies of the γ-M4 trans-membrane domain of the nicotinic acetylcholine receptor. Mol Membr Biol 2009; 22:485-96. [PMID: 16373320 DOI: 10.1080/09687860500370653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A structural characterization of a synthetic peptide corresponding to the fourth transmembrane domain (M4-TMD) of the gamma-subunit of the nicotinic acetylcholine receptor from Torpedo californica has been undertaken. Solid-state NMR and CD spectroscopy studies indicate that upon reconstitution into lipid vesicles or magnetically aligned lipid bilayers, the synthetic M4-TMD adopts a linear alpha-helical conformation with the helix aligned within 15 degrees of the membrane normal. Furthermore, analysis of the motional averaging of anisotropic interactions present in the solid-state NMR spectra of the reconstituted peptide, indicate that the dynamics of the peptide within the bilayer are highly sensitive to the phase adopted by the lipid bilayer, providing an insight into how the interaction of lipids with this domain may play a important role in the modulation of this receptor by its lipid environment.
Collapse
|
16
|
Zandomeneghi M, Carbonaro L, Zandomeneghi G. Biochemical fluorometric method for the determination of riboflavin in milk. J Agric Food Chem 2007; 55:5990-4. [PMID: 17590011 DOI: 10.1021/jf070811n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
UNLABELLED Methods of analysis of vitamin B2 in foods generally consist of the extraction of the sample, followed by enzymatic hydrolysis and quantitative measurement of the analyte, typically through RP-HPLC. The scope of our work here is to present a soft method to measure the free riboflavin content of a nontransparent and nonhomogeneous matrix such as milk, avoiding any extraction and separation of phases that are required in any published method for determination of the free RBF content in foods. We combine the front-face (FF) measurement of the light emission of milk with the ability of the apo-form of the riboflavin-binding protein (RBP) from chicken egg white to quench the riboflavin fluorescence. Thus, we titrate the RBF present in milk by gradually adding a solution of RBP to the milk sample and measuring, upon each addition, the FF residual emission due to uncomplexed RBF. The RBP binding capability has been measured in the same matrix of the analyte. Our results indicate a concentration of free RBF practically co-incident with the certified value for total B2 vitamin content in reference milk CRM 421. KEYWORDS Front-face fluorescence; riboflavin; apo-riboflavin-binding protein; milk fluorescence.
Collapse
Affiliation(s)
- Maurizio Zandomeneghi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
| | | | | |
Collapse
|
17
|
Zandomeneghi M, Carbonaro L, Zandomeneghi G. Comment on: Excitation-emission fluorescence spectroscopy combined with three-way methods of analysis as a complementary technique for olive oil characterization. J Agric Food Chem 2006; 54:5214-5. [PMID: 16819938 DOI: 10.1021/jf0605648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
|
18
|
Fändrich M, Zandomeneghi G, Krebs MRH, Kittler M, Buder K, Rossner A, Heinemann SH, Dobson CM, Diekmann S. Apomyoglobin reveals a random-nucleation mechanism in amyloid protofibril formation. Acta Histochem 2006; 108:215-9. [PMID: 16714052 DOI: 10.1016/j.acthis.2006.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Protofibrils (PFs) represent the earliest fibrillar species that occur in the course of amyloid fibril formation. Using apomyoglobin, we report here that PFs arise from a multi-step reaction and that they are preceded by an ensemble of non-fibrillar particles (NFPs). These intermediate aggregates encompass nascent elements of amyloid structure and can act as seeds in PF formation. Taken together with the observation that PFs often protrude from NFPs, our data suggest that PFs form by a random nucleation mechanism in which the polypeptide chains sample many different aggregated conformations. Once the appropriate structural characteristics are acquired, PFs are formed by addition of further polypeptide chains.
Collapse
Affiliation(s)
- Marcus Fändrich
- Institut für Molekulare Biotechnologie (IMB), Beutenbergstrasse 11, Postfach 100 813, D-07708 Jena, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Chandrasekhar I, van Gunsteren WF, Zandomeneghi G, Williamson PTF, Meier BH. Orientation and Conformational Preference of Leucine-Enkephalin at the Surface of a Hydrated Dimyristoylphosphatidylcholine Bilayer: NMR and MD Simulation. J Am Chem Soc 2005; 128:159-70. [PMID: 16390143 DOI: 10.1021/ja054785q] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The morphogenic opiate pentapeptide leucine-enkephalin (lenk) in a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer is studied using NMR spectroscopy and molecular dynamics simulation. Contrary to the frequent assumption that the peptide attains a single fixed conformation in the presence of membranes, we find that the lenk molecule is flexible, switching between specific bent conformations. The constraints to the orientation of the aromatic rings that are identified by the NMR experiment are found by the MD simulation to be related to the depth of the peptide in the bilayer. The motion of the N-H vectors of the peptide bonds with respect to the magnetic field direction as observed by MD largely explain the magnitude of the observed residual dipolar coupling (RDC), which are much reduced over the static (15)N-(1)H coupling. The measured RDCs are nevertheless significantly larger than the predicted ones, possibly due the absence of long-time motions in the simulations. The conformational behavior of lenk at the DMPC surface is compared to that in the aqueous solution, both in the neutral and in the zwitterionic forms.
Collapse
|
20
|
Zandomeneghi M, Zandomeneghi G. Comment on cluster analysis applied to the exploratory analysis of commercial spanish olive oils by means of excitation-emission fluorescence spectroscopy. J Agric Food Chem 2005; 53:5829-30. [PMID: 15998155 DOI: 10.1021/jf047797o] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
|
21
|
Christopeit T, Hortschansky P, Schroeckh V, Gührs K, Zandomeneghi G, Fändrich M. Mutagenic analysis of the nucleation propensity of oxidized Alzheimer's beta-amyloid peptide. Protein Sci 2005; 14:2125-31. [PMID: 15987892 PMCID: PMC2279324 DOI: 10.1110/ps.051470405] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The formation of polypeptide aggregates represents a nucleated polymerization reaction in which an initial nucleation event (lag phase) is followed by the extension of newly formed nuclei into larger aggregates, including fibrils (growth phase). The efficiencies of these reactions relate to the lag time (lag phase) and to the rate of aggregation (growth phase), which can be determined from experimental aggregation curves. Here we present a mutagenic analysis in which we replace valine 18 of the Alzheimer's Abeta (1-40) peptide with 17 different amino acids and determine its effect on the lag time, and therefore, on the propensity of nucleation. Comparison with various physico-chemical properties shows that nucleation is affected in a predictable manner depending on the beta-sheet propensity and hydrophobicity of residue 18. In addition, we observe a direct proportionality between the lag time and the rate of aggregation. These data imply that the two reactions, nucleation and polymerization, are governed by very similar physicochemical principles and that they involve the formation of the same types of noncovalent interactions.
Collapse
|
22
|
Hortschansky P, Schroeckh V, Christopeit T, Zandomeneghi G, Fändrich M. The aggregation kinetics of Alzheimer's beta-amyloid peptide is controlled by stochastic nucleation. Protein Sci 2005; 14:1753-9. [PMID: 15937275 PMCID: PMC2253354 DOI: 10.1110/ps.041266605] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We report here a recombinant expression system that allows production of large quantities of Alzheimer's Abeta(1-40) peptide. The material is competent to dissolve in water solutions with "random-coil properties," although its conformation and factual oligomerization state are determined by the physico-chemical solution conditions. When dissolved in 50 mM sodium phosphate buffer (pH 7.4) at 37 degrees C, the peptide is able to undergo a nucleated polymerization reaction. The aggregation profile is characteristically bipartite, consisting of lag and growth phase. From these curves we determined the lag time as well as the rate of aggregation. Both values were found to depend on peptide concentration and addition or formation of seeds. Moreover, they can vary considerably between apparently identical samples. These data imply that the nucleation event is under influence of a stochastic factor that can manifest itself in profound macroscopic differences in the aggregation kinetics of otherwise indistinguishable samples.
Collapse
|
23
|
Abstract
The presence of beta-sheets in the core of amyloid fibrils raised questions as to whether or not beta-sheet-containing proteins, such as transthyretin, are predisposed to form such fibrils. However, we show here that the molecular structure of amyloid fibrils differs more generally from the beta-sheets in native proteins. This difference is evident from the amide I region of the infrared spectrum and relates to the distribution of the phi/psi dihedral angles within the Ramachandran plot, the average number of strands per sheet, and possibly, the beta-sheet twist. These data imply that amyloid fibril formation from native beta-sheet proteins can involve a substantial structural reorganization.
Collapse
|
24
|
Zandomeneghi G, Meier BH. Adiabatic-passage cross polarization in N-15 NMR spectroscopy of peptides weakly associated to phospholipids: determination of large RDC. J Biomol NMR 2004; 30:303-309. [PMID: 15754056 DOI: 10.1007/s10858-004-3097-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Accepted: 08/03/2004] [Indexed: 05/24/2023]
Abstract
Structural information can be extracted from one-bond residual dipolar couplings (RDC) measured in NMR spectra of systems in field-ordered media. RDC can be on the order of J-couplings if the anisotropy of alignment is approximately 10(-2), 10-fold stronger than that typically used for structural studies of water-soluble proteins. In such systems the performance of (1)H--> (15)N polarization transfer methods of the INEPT type is not satisfactory. In this study we show the effectiveness of adiabatic-passage cross-polarization (APCP) in transferring the (1)H--> (15)N polarization in the bicelle-associated peptide Leucine Enkephalin (Lenk). APCP is efficient both in static samples and in samples spun at the magic angle (MAS) or any other angle of the spinning axis to the magnetic field (variable-angle spinning, VAS). The anisotropic spectrum of an aligned static sample and the isotropic spectrum of the sample under MAS provide a set of possible values for the (1)H-(15)N RDC of phospholipid-associated Lenk. The unambiguous determination of the (1)H-(15)N RDC was accomplished by means of VAS experiments.
Collapse
|
25
|
Zandomeneghi G, Tomaselli M, Williamson PTF, Meier BH. NMR of bicelles: orientation and mosaic spread of the liquid-crystal director under sample rotation. J Biomol NMR 2003; 25:113-123. [PMID: 12652120 DOI: 10.1023/a:1022236217018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Model-membrane systems composed of liquid-crystalline bicellar phases can be uniaxially oriented with respect to a magnetic field, thereby facilitating structural and dynamics studies of membrane-associated proteins. Here we quantitatively characterize a method that allows the manipulation of the direction of this uniaxial orientation. Bicelles formed from DMPC/DHPC are examined by (31)P NMR under variable-angle sample-spinning (VAS) conditions, confirming that the orientation of the liquid-crystalline director can be influenced by sample spinning. The director is perpendicular to the rotation axis when Theta (the angle between the sample-spinning axis and the magnetic field direction) is smaller than the magic angle, and is parallel to the rotation axis when Theta is larger than the magic angle. The new (31)P NMR VAS data presented are considerably more sensitive to the orientation of the bicelle than earlier (2)H studies and the analysis of the sideband pattern allows the determination of the orientation of the liquid-crystal director and its variation over the sample, i.e., the mosaic spread. Under VAS, the mosaic spread is small if Theta deviates significantly from the magic angle but becomes very large at the magic angle.
Collapse
|
26
|
Zandomeneghi G, Williamson PTF, Hunkeler A, Meier BH. Switched-angle spinning applied to bicelles containing phospholipid-associated peptides. J Biomol NMR 2003; 25:125-132. [PMID: 12652121 DOI: 10.1023/a:1022244025351] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In a model study, the proton NMR spectrum of the opioid pentapeptide leucine-enkephalin associated with bicelles is investigated. The spectral resolution for a static sample is limited due to the large number of anisotropic interactions, in particular strong proton-proton couplings, but resolution is greatly improved by magic-angle sample spinning. Here we present two-dimensional switched-angle spinning NMR experiments, which correlate the high-resolution spectrum of the membrane-bound peptide under magic-angle spinning with its anisotropic spectrum, leading to well-resolved spectra. The two-dimensional spectrum allows the exploitation of the high resolution of the isotropic spectrum, while retaining the structural information imparted by the anisotropic interactions in the static spectrum. Furthermore, switched-angle spinning techniques are demonstrated that allow one to record the proton spectrum of ordered bicellar phases as a function of the angle between the rotor axis and the magnetic field direction, thereby scaling the dipolar interactions by a predefined factor.
Collapse
|
27
|
Ouchi A, Zandomeneghi G, Zandomeneghi M. Complexation with albumins of chiral aromatic substrates and their chemistry in ground and excited states. Catalytic and chirality recognition properties of the protein in the cases of binaphthol, its photoisomers, and ketoprofen. Chirality 2002; 14:1-11. [PMID: 11748793 DOI: 10.1002/chir.10026] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The reactivity of organic molecules can be modified upon complexation with proteins: these changes can be different and more significant when the substrate is in an electronically excited state. Here we review UV, CD, and fluorescence spectroscopy studies on the photochemistry and on the chemistry of atropisomeric binaphthols and of ketoprofen, complexed to serum albumins. The chemical and photochemical properties of the organic substrates, complexed to the albumins or free in common solvents, are different. The role of the protein complexation is also evidenced in photoresolution processes of racemate-protein complexes. Catalytic effects due to serum albumins are also reported. In particular, the Arrhenius parameters for the rate of thermal isomerization of a metastable photoproduct of binaphthol in common solvents are compared with those of the bovine serum albumin catalyzed isomerization.
Collapse
Affiliation(s)
- Akihiko Ouchi
- National Institute of Materials and Chemical Research, Tsukuba, Japan
| | | | | |
Collapse
|
28
|
Zandomeneghi G, Tomaselli M, van Beek JD, Meier BH. Manipulation of the director in bicellar mesophases by sample spinning: a new tool for NMR spectroscopy. J Am Chem Soc 2001; 123:910-3. [PMID: 11456624 DOI: 10.1021/ja0019326] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is shown that bicellar nematic liquid-crystalline phases can be oriented with the director (the normal to the bicellar plane) at an arbitrary angle to the applied magnetic field by sample rotation around one axis (variable-angle sample spinning) or around two axes successively (switched-angle spinning). This promises to open novel possibilities for NMR studies of bicelles and proteins incorporated into bicelles or dissolved in a solution containing bicelles, including the correlation of several orientations in a two-dimensional NMR experiment.
Collapse
Affiliation(s)
- G Zandomeneghi
- Contribution from the Laboratory of Physical Chemistry, ETH-Zentrum, CH-8092 Zurich, Switzerland
| | | | | | | |
Collapse
|