1
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Jung E, Kraimps A, Dittmann S, Griesser T, Costafrolaz J, Mattenberger Y, Jurt S, Viollier PH, Sander P, Sievers S, Gademann K. Phenolic Substitution in Fidaxomicin: A Semisynthetic Approach to Antibiotic Activity Across Species. Chembiochem 2023; 24:e202300570. [PMID: 37728121 DOI: 10.1002/cbic.202300570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/21/2023]
Abstract
Fidaxomicin (Fdx) is a natural product antibiotic with potent activity against Clostridioides difficile and other Gram-positive bacteria such as Mycobacterium tuberculosis. Only a few Fdx derivatives have been synthesized and examined for their biological activity in the 50 years since its discovery. Fdx has a well-studied mechanism of action, namely inhibition of the bacterial RNA polymerase. Yet, the targeted organisms harbor different target protein sequences, which poses a challenge for the rational development of new semisynthetic Fdx derivatives. We introduced substituents on the two phenolic hydroxy groups of Fdx and evaluated the resulting trends in antibiotic activity against M. tuberculosis, C. difficile, and the Gram-negative model organism Caulobacter crescentus. As suggested by the target protein structures, we identified the preferable derivatisation site for each organism. The derivative ortho-methyl Fdx also exhibited activity against the Gram-negative C. crescentus wild type, a first for fidaxomicin antibiotics. These insights will guide the synthesis of next-generation fidaxomicin antibiotics.
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Affiliation(s)
- Erik Jung
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
| | - Anastassia Kraimps
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
| | - Silvia Dittmann
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Tizian Griesser
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Jordan Costafrolaz
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Yves Mattenberger
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Peter Sander
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Susanne Sievers
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Karl Gademann
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
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2
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Cucuzza S, Sitnik M, Jurt S, Michel E, Dai W, Müntener T, Ernst P, Häussinger D, Plückthun A, Zerbe O. Unexpected dynamics in femtomolar complexes of binding proteins with peptides. Nat Commun 2023; 14:7823. [PMID: 38016954 PMCID: PMC10684580 DOI: 10.1038/s41467-023-43596-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Ultra-tight binding is usually observed for proteins associating with rigidified molecules. Previously, we demonstrated that femtomolar binders derived from the Armadillo repeat proteins (ArmRPs) can be designed to interact very tightly with fully flexible peptides. Here we show for ArmRPs with four and seven sequence-identical internal repeats that the peptide-ArmRP complexes display conformational dynamics. These dynamics stem from transient breakages of individual protein-residue contacts that are unrelated to overall unbinding. The labile contacts involve electrostatic interactions. We speculate that these dynamics allow attaining very high binding affinities, since they reduce entropic losses. Importantly, only NMR techniques can pick up these local events by directly detecting conformational exchange processes without complications from changes in solvent entropy. Furthermore, we demonstrate that the interaction surface of the repeat protein regularizes upon peptide binding to become more compatible with the peptide geometry. These results provide novel design principles for ultra-tight binders.
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Affiliation(s)
- Stefano Cucuzza
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Malgorzata Sitnik
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Erich Michel
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Wenzhao Dai
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Thomas Müntener
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland.
| | - Oliver Zerbe
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland.
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3
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Baumann C, Chiang W, Valsecchi R, Jurt S, Deluigi M, Schuster M, Rosengren KJ, Plückthun A, Zerbe O. Side-chain dynamics of the α 1B -adrenergic receptor determined by NMR via methyl relaxation. Protein Sci 2023; 32:e4801. [PMID: 37805830 PMCID: PMC10593183 DOI: 10.1002/pro.4801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/17/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
G protein-coupled receptors (GPCRs) are medically important membrane proteins that sample inactive, intermediate, and active conformational states characterized by relatively slow interconversions (~μs-ms). On a faster timescale (~ps-ns), the conformational landscape of GPCRs is governed by the rapid dynamics of amino acid side chains. Such dynamics are essential for protein functions such as ligand recognition and allostery. Unfortunately, technical challenges have almost entirely precluded the study of side-chain dynamics for GPCRs. Here, we investigate the rapid side-chain dynamics of a thermostabilized α1B -adrenergic receptor (α1B -AR) as probed by methyl relaxation. We determined order parameters for Ile, Leu, and Val methyl groups in the presence of inverse agonists that bind orthosterically (prazosin, tamsulosin) or allosterically (conopeptide ρ-TIA). Despite the differences in the ligands, the receptor's overall side-chain dynamics are very similar, including those of the apo form. However, ρ-TIA increases the flexibility of Ile1764×56 and possibly of Ile2145×49 , adjacent to Pro2155×50 of the highly conserved P5×50 I3×40 F6×44 motif crucial for receptor activation, suggesting differences in the mechanisms for orthosteric and allosteric receptor inactivation. Overall, increased Ile side-chain rigidity was found for residues closer to the center of the membrane bilayer, correlating with denser packing and lower protein surface exposure. In contrast to two microbial membrane proteins, in α1B -AR Leu exhibited higher flexibility than Ile side chains on average, correlating with the presence of Leu in less densely packed areas and with higher protein-surface exposure than Ile. Our findings demonstrate the feasibility of studying receptor-wide side-chain dynamics in GPCRs to gain functional insights.
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Affiliation(s)
| | - Wan‐Chin Chiang
- Department of ChemistryUniversity of ZurichZurichSwitzerland
| | | | - Simon Jurt
- Department of ChemistryUniversity of ZurichZurichSwitzerland
| | - Mattia Deluigi
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | | | | | | | - Oliver Zerbe
- Department of ChemistryUniversity of ZurichZurichSwitzerland
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4
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Çalış İ, Ünlü A, Aydın ZU, Dönmez AA, Yusufoğlu HS, Jurt S, Linden A. Xanthones and Xanthone O-β-D-glucosides from the Roots of Polygala azizsancarii Dönmez. Chem Biodivers 2022; 19:e202200499. [PMID: 35797203 DOI: 10.1002/cbdv.202200499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022]
Abstract
Nine xanthone derivatives (1-9) were isolated from the roots of Polygala azizsancarii, which is a narrow endemic species for the flora of Türkiye. Based on all of the evidence, the structures of 1-9 were established as two previously undescribed xanthone O-glucosides, 3-O-β-D-glucopyranosyloxy-1,6-dihydroxy-2,5,7-trimethoxyxanthone (1), 3-O-β-D-glucopyranosyloxy-1,6-dihydroxy-2,7-dimethoxyxanthone (2), and seven previously described xanthones, 1,3,6-trihydroxy-2,5,7-trimethoxyxanthone (3), 1,3,6-trihydroxy-2,7-dimethoxyxanthone (4), 1,2,3,4,7-pentamethoxyxanthone (5), 1,3-dihydroxy-2,5,6,7-tetramethoxyxanthone (6), 1,3-dihydroxy-4,7-dimethoxyxanthone (7), 1,7-dihydroxy-3-methoxyxanthone (8), 1,7-dihydroxy-2,3-methylenedioxy-xanthone (9). The structures of the compounds were determined by spectroscopic methods, including 1D-NMR (1H NMR, 13C NMR, DEPT-135), 2D-NMR (COSY, NOESY, HSQC, HMBC, INADEQUATE), and HRMS. The solid-state structures of 1-4, including the absolute configurations of the stereogenic carbons of the sugar moiety in 1 and 2, were established by X-ray crystal-structure analyses. For the newly described compounds, the trivial names sancarosides A (1) and B (2) are proposed.
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Affiliation(s)
- İhsan Çalış
- Near East University: Yakin Dogu Universitesi, Department of Pharmacognosy, Faculty of Pharmacy, Near East Boulevard, 99138, Lefkoşa (Nicosia), TURKEY
| | - Ayşe Ünlü
- Hacettepe University: Hacettepe Universitesi, Department of Biology, Faculty of Science, Beytepe Campus, 06800, Ankara, TURKEY
| | - Zübeyde Uğurlu Aydın
- Hacettepe University: Hacettepe Universitesi, Department of Biology, Faculty of Science, Beytepe Campus, 06800, Ankara, TURKEY
| | - Ali A Dönmez
- Hacettepe University: Hacettepe Universitesi, Department of Biology, Faculty of Science, Beytepe Campus, 06800, Ankara, TURKEY
| | - Hasan Soliman Yusufoğlu
- Buraydah Private Colleges: Buraydah Colleges, Department of Pharmacognosy & Pharmaceutical Chemistry, College of Dentistry & Pharmacy, 51418, Buraydah, SAUDI ARABIA
| | - Simon Jurt
- University of Zurich: Universitat Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057, Zurich, SWITZERLAND
| | - Anthony Linden
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, Not Available, 8057, Zurich, SWITZERLAND
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5
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Migliavacca J, Kumar KS, Kopp L, Gries A, Yan S, Brunner C, Schuster M, Jurt S, Moehle K, Zerbe O, Schneider G, Grotzer M, Baumgartner M. TBIO-08. The molecular basis for rational targeting of FGFR-driven growth and invasiveness in pediatric brain tumors. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.690] [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: 11/12/2022] Open
Abstract
Abstract
The oncogenic activation of receptor tyrosine kinases (RTK) promotes growth, survival and dissemination in pediatric tumors including glioma, ependymoma and medulloblastoma (MB). Direct targeting of either the RTK or of downstream kinases can effectively block tumor promoting pathway functions. However, emergence of resistance is common. We hypothesized that alternative interference strategies that target protein-protein interactions (PPIs) instead of enzymatic activities could overcome the emergence of resistance. We characterized the molecular interactions downstream of the FGFR that regulate relevant growth and invasion-promoting mechanisms in MB cells, to identify potentially druggable PPIs. We found that the FRS2 protein is an essential up-stream effector of FGFR signaling towards invasiveness. Using a proteomics approach, we furthermore identified the Striatin 3 protein as a novel oncogenic effector of the FGFR pathway downstream of FRS2, as it integrates antagonistic growth and invasion signals downstream of FGFR. Mechanistically, Striatin 3 interacts with the Ser/Thr kinase MAP4K4, couples it to the protein phosphatase 2A, and thereby inactivates growth repressing activities of MAP4K4. In parallel, Striatin 3 enables MAP4K4-mediated phosphorylation of PKC-theta and VASP, which combined are necessary to promote tissue invasion. To selectively repress pro-invasive FGFR functions, we identified and functionally validated small molecule ligands of FRS2, that prevent FRS2 activation and downstream signaling. We demonstrate efficacy of these compounds in inhibiting invasion and growth promoting activities in vitro and in vivo, and identified potential off-target activities of the ligand using a proteome-wide interaction analysis. We propose inhibition of FRS2 by a small molecular PTB domain ligand as a strategy to repress FGF signaling in FGFR-driven tumors. The development of this ligand, and the de novo design of functional analogs thereof bear promise for further pre-clinical evaluation of these structures as anti-growth promoting and anti-metastatic therapeutics applicable to FGFR-driven tumors.
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Affiliation(s)
- Jessica Migliavacca
- University Children’s Hospital Zürich, Children’s Research Center, Pediatric Molecular Neuro-Oncology, Zürich, Switzerland
| | - Karthiga Santhana Kumar
- University Children’s Hospital Zürich, Children’s Research Center, Pediatric Molecular Neuro-Oncology, Zürich, Switzerland
| | - Levi Kopp
- University Children’s Hospital Zürich, Children’s Research Center, Pediatric Molecular Neuro-Oncology, Zürich, Switzerland
| | - Alexandre Gries
- University Children’s Hospital Zürich, Children’s Research Center, Pediatric Molecular Neuro-Oncology, Zürich, Switzerland
| | - Shen Yan
- University Children’s Hospital Zürich, Children’s Research Center, Pediatric Molecular Neuro-Oncology, Zürich, Switzerland
| | - Cyrill Brunner
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zürich, Switzerland
| | | | - Simon Jurt
- University of Zurich, Department of Chemistry, Zürich, Switzerland
| | - Kerstin Moehle
- University of Zurich, Department of Chemistry, Zürich, Switzerland
| | - Oliver Zerbe
- University of Zurich, Department of Chemistry, Zürich, Switzerland
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zürich, Switzerland
- ETH Singapore SEC Ltd , Singapore, Singapore , Singapore
| | - Michael Grotzer
- University Children’s Hospital Zürich, Department of Oncology, Zürich, Switzerland
| | - Martin Baumgartner
- University Children’s Hospital Zürich, Children’s Research Center, Pediatric Molecular Neuro-Oncology, Zürich, Switzerland
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6
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Kooijman L, Schuster M, Baumann C, Jurt S, Löhr F, Fürtig B, Güntert P, Zerbe O. Dynamics of Bacteriorhodopsin in the Dark‐Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Laurens Kooijman
- Department of Chemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Matthias Schuster
- Department of Chemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Christian Baumann
- Department of Chemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Simon Jurt
- Department of Chemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
| | - Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
- Laboratory of Physical Chemistry ETH Zürich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Oliver Zerbe
- Department of Chemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
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7
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Kooijman L, Schuster M, Baumann C, Jurt S, Löhr F, Fürtig B, Güntert P, Zerbe O. Dynamics of Bacteriorhodopsin in the Dark-Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy. Angew Chem Int Ed Engl 2020; 59:20965-20972. [PMID: 32726501 DOI: 10.1002/anie.202004393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/15/2020] [Indexed: 01/02/2023]
Abstract
To achieve efficient proton pumping in the light-driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark-adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays only 10 % residual proton pumping activity, are less well ordered, suggesting a link between side-chain dynamics on the cytosolic side of the bR cavity and proton pumping activity. In addition, slow conformational exchange, attributed to low frequency motions of aromatic rings, was indirectly observed for residues on the extracellular side of the bR cavity. This may be related to reorganization of the water network. These observations provide a detailed picture of previously undescribed equilibrium dynamics on different time scales for ground-state bR.
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Affiliation(s)
- Laurens Kooijman
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Christian Baumann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany.,Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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8
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Kooijman L, Ansorge P, Schuster M, Baumann C, Löhr F, Jurt S, Güntert P, Zerbe O. Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs. J Biomol NMR 2020; 74:45-60. [PMID: 31754899 PMCID: PMC7015963 DOI: 10.1007/s10858-019-00289-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/11/2019] [Indexed: 05/21/2023]
Abstract
Resonance assignments are challenging for membrane proteins due to the size of the lipid/detergent-protein complex and the presence of line-broadening from conformational exchange. As a consequence, many correlations are missing in the triple-resonance NMR experiments typically used for assignments. Herein, we present an approach in which correlations from these solution-state NMR experiments are supplemented by data from 13C unlabeling, single-amino acid type labeling, 4D NOESY data and proximity of moieties to lipids or water in combination with a structure of the protein. These additional data are used to edit the expected peaklists for the automated assignment protocol FLYA, a module of the program package CYANA. We demonstrate application of the protocol to the 262-residue proton pump from archaeal bacteriorhodopsin (bR) in lipid nanodiscs. The lipid-protein assembly is characterized by an overall correlation time of 44 ns. The protocol yielded assignments for 62% of all backbone (H, N, Cα, Cβ, C') resonances of bR, corresponding to 74% of all observed backbone spin systems, and 60% of the Ala, Met, Ile (δ1), Leu and Val methyl groups, thus enabling to assign a large fraction of the protein without mutagenesis data. Most missing resonances stem from the extracellular half, likely due intermediate exchange line-broadening. Further analysis revealed that missing information of the amino acid type of the preceding residue is the largest problem, and that 4D NOESY experiments are particularly helpful to compensate for that information loss.
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Affiliation(s)
- Laurens Kooijman
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Philipp Ansorge
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christian Baumann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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9
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Schmidt OP, Jurt S, Johannsen S, Karimi A, Sigel RKO, Luedtke NW. Concerted dynamics of metallo-base pairs in an A/B-form helical transition. Nat Commun 2019; 10:4818. [PMID: 31645548 PMCID: PMC6811676 DOI: 10.1038/s41467-019-12440-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 10/16/2018] [Accepted: 09/05/2019] [Indexed: 01/31/2023] Open
Abstract
Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-HgII-T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-HgII-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-HgII-(N4)C base pairs and greater A-form characteristics. Ten-fold different 1J coupling constants (15N,199Hg) are observed for (N3)C-HgII (114 Hz) versus (N4)C-HgII (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-HgII-T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding HgII, demonstrating that C-HgII-T has unique switching potential in DNA-based materials and devices.
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Affiliation(s)
- Olivia P Schmidt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Silke Johannsen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Ashkan Karimi
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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10
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Beil A, Jurt S, Walser R, Schönhut T, Güntert P, Palacios Ò, Atrian S, Capdevila M, Dallinger R, Zerbe O. The Solution Structure and Dynamics of Cd-Metallothionein from Helix pomatia Reveal Optimization for Binding Cd over Zn. Biochemistry 2019; 58:4570-4581. [DOI: 10.1021/acs.biochem.9b00830] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Beil
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Reto Walser
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Tanja Schönhut
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Òscar Palacios
- Departmento de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Silvia Atrian
- Departmento de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, E-08028 Barcelona, Spain
| | - Mercè Capdevila
- Departmento de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Reinhard Dallinger
- Institute of Zoology and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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11
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Salvati Manni L, Assenza S, Duss M, Vallooran JJ, Juranyi F, Jurt S, Zerbe O, Landau EM, Mezzenga R. Soft biomimetic nanoconfinement promotes amorphous water over ice. Nat Nanotechnol 2019; 14:609-615. [PMID: 30962546 DOI: 10.1038/s41565-019-0415-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Water is a ubiquitous liquid with unique physicochemical properties, whose nature has shaped our planet and life as we know it. Water in restricted geometries has different properties than in bulk. Confinement can prevent low-temperature crystallization of the molecules into a hexagonal structure and thus create a state of amorphous water. To understand the survival of life at subzero temperatures, it is essential to elucidate this behaviour in the presence of nanoconfining lipidic membranes. Here we introduce a family of synthetic lipids with designed cyclopropyl modifications in the hydrophobic chains that exhibit unique liquid-crystalline behaviour at low temperature, which enables the maintenance of amorphous water down to ~10 K due to nanoconfinement. The combination of experiments and molecular dynamics simulations unveils a complex lipid-water phase diagram in which bicontinuous cubic and lamellar liquid crystalline phases that contain subzero liquid, glassy or ice water emerge as a competition between the two components, each pushing towards its thermodynamically favoured state.
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Affiliation(s)
- Livia Salvati Manni
- Department of Chemistry, University of Zürich, Zürich, Switzerland
- Department of Health Sciences & Technology, ETH Zürich, Zürich, Switzerland
| | - Salvatore Assenza
- Department of Health Sciences & Technology, ETH Zürich, Zürich, Switzerland
| | - Michael Duss
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | - Jijo J Vallooran
- Department of Chemistry, University of Zürich, Zürich, Switzerland
- Department of Health Sciences & Technology, ETH Zürich, Zürich, Switzerland
| | - Fanni Juranyi
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | - Ehud M Landau
- Department of Chemistry, University of Zürich, Zürich, Switzerland.
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology, ETH Zürich, Zürich, Switzerland.
- Department of Materials, ETH Zürich, Zürich, Switzerland.
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12
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Simonelli L, Pedotti M, Bardelli M, Jurt S, Zerbe O, Varani L. Mapping Antibody Epitopes by Solution NMR Spectroscopy: Practical Considerations. Methods Mol Biol 2018; 1785:29-51. [PMID: 29714010 DOI: 10.1007/978-1-4939-7841-0_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Identifying an epitope, the region of the antigen in contact with an antibody, is useful in both basic and pharmaceutical research, as well as in vaccine design. Solution NMR spectroscopy is particularly well suited to the residue level characterization of intermolecular interfaces, including antibody-antigen interactions, and thus to epitope identification. Here, we describe the use of NMR for residue level characterization of protein epitopes, focusing on experimental protocols and practical considerations, highlighting advantages and drawbacks of the approach.
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Affiliation(s)
- Luca Simonelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Marco Bardelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland.
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13
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Wang J, Bardelli M, Espinosa DA, Pedotti M, Ng TS, Bianchi S, Simonelli L, Lim EXY, Foglierini M, Zatta F, Jaconi S, Beltramello M, Cameroni E, Fibriansah G, Shi J, Barca T, Pagani I, Rubio A, Broccoli V, Vicenzi E, Graham V, Pullan S, Dowall S, Hewson R, Jurt S, Zerbe O, Stettler K, Lanzavecchia A, Sallusto F, Cavalli A, Harris E, Lok SM, Varani L, Corti D. A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential. Cell 2017; 171:229-241.e15. [PMID: 28938115 PMCID: PMC5673489 DOI: 10.1016/j.cell.2017.09.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/14/2017] [Accepted: 08/31/2017] [Indexed: 11/15/2022]
Abstract
Zika virus (ZIKV), a mosquito-borne flavivirus, causes devastating congenital birth defects. We isolated a human monoclonal antibody (mAb), ZKA190, that potently cross-neutralizes multi-lineage ZIKV strains. ZKA190 is highly effective in vivo in preventing morbidity and mortality of ZIKV-infected mice. NMR and cryo-electron microscopy show its binding to an exposed epitope on DIII of the E protein. ZKA190 Fab binds all 180 E protein copies, altering the virus quaternary arrangement and surface curvature. However, ZIKV escape mutants emerged in vitro and in vivo in the presence of ZKA190, as well as of other neutralizing mAbs. To counter this problem, we developed a bispecific antibody (FIT-1) comprising ZKA190 and a second mAb specific for DII of E protein. In addition to retaining high in vitro and in vivo potencies, FIT-1 robustly prevented viral escape, warranting its development as a ZIKV immunotherapy.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/administration & dosage
- Antibodies, Viral/chemistry
- Antibodies, Viral/therapeutic use
- Cryoelectron Microscopy
- Epitopes
- Humans
- Magnetic Resonance Spectroscopy
- Mice
- Models, Molecular
- Sequence Alignment
- Viral Envelope Proteins/chemistry
- Zika Virus/chemistry
- Zika Virus/immunology
- Zika Virus Infection/therapy
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Affiliation(s)
- Jiaqi Wang
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Marco Bardelli
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Diego A Espinosa
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 185 Li Ka Shing Center, 1951 Oxford Street, Berkeley, California, 94720-3370, USA
| | - Mattia Pedotti
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Thiam-Seng Ng
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Siro Bianchi
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Luca Simonelli
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Elisa X Y Lim
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Mathilde Foglierini
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Martina Beltramello
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Guntur Fibriansah
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Jian Shi
- Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore; CryoEM unit, Department of Biological Sciences, National University of Singapore, Singapore 117557
| | - Taylor Barca
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 185 Li Ka Shing Center, 1951 Oxford Street, Berkeley, California, 94720-3370, USA
| | - Isabel Pagani
- Viral Pathogens and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Alicia Rubio
- Viral Pathogens and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Vania Broccoli
- Viral Pathogens and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; CNR-Institute of Neuroscience, Via Vanvitelli 32, 20129, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogens and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Victoria Graham
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Steven Pullan
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Stuart Dowall
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Karin Stettler
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Federica Sallusto
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Andrea Cavalli
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 185 Li Ka Shing Center, 1951 Oxford Street, Berkeley, California, 94720-3370, USA
| | - Shee-Mei Lok
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.
| | - Luca Varani
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.
| | - Davide Corti
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland.
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14
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Baumann C, Beil A, Jurt S, Niederwanger M, Palacios O, Capdevila M, Atrian S, Dallinger R, Zerbe O. Strukturanpassung eines Proteins an Metallbelastung: NMR-Struktur eines marinen Schnecken-Metallothioneins mit einer zusätzlichen Domäne. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Christian Baumann
- Institut für Chemie; Universität Zürich; Winterthurerstrasse 190 8057 Zürich Schweiz
| | - Andrea Beil
- Institut für Chemie; Universität Zürich; Winterthurerstrasse 190 8057 Zürich Schweiz
| | - Simon Jurt
- Institut für Chemie; Universität Zürich; Winterthurerstrasse 190 8057 Zürich Schweiz
| | - Michael Niederwanger
- Institut für Zoologie und Forschungsschwerpunkt für Molekulare Biowissenschaften; Universität Innsbruck; Technikerstraße 25 6020 Innsbruck Österreich
| | - Oscar Palacios
- Departament de Química; Universitat Autònoma de Barcelona; Spanien
| | - Mercè Capdevila
- Departament de Química; Universitat Autònoma de Barcelona; Spanien
| | - Sílvia Atrian
- Department of Genetics, Microbiology and Statistics; Faculty of Biology; University of Barcelona; Spanien
| | - Reinhard Dallinger
- Institut für Zoologie und Forschungsschwerpunkt für Molekulare Biowissenschaften; Universität Innsbruck; Technikerstraße 25 6020 Innsbruck Österreich
| | - Oliver Zerbe
- Institut für Chemie; Universität Zürich; Winterthurerstrasse 190 8057 Zürich Schweiz
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15
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Baumann C, Beil A, Jurt S, Niederwanger M, Palacios O, Capdevila M, Atrian S, Dallinger R, Zerbe O. Structural Adaptation of a Protein to Increased Metal Stress: NMR Structure of a Marine Snail Metallothionein with an Additional Domain. Angew Chem Int Ed Engl 2017; 56:4617-4622. [DOI: 10.1002/anie.201611873] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/03/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Christian Baumann
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Andrea Beil
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Simon Jurt
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Michael Niederwanger
- Institute of Zoology and Center for Molecular Biosciences; University of Innsbruck; Technikerstrasse 25 6020 Innsbruck Austria
| | - Oscar Palacios
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Cerdanyola del Vallès Barcelona Spain
| | - Mercè Capdevila
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Cerdanyola del Vallès Barcelona Spain
| | - Sílvia Atrian
- Department of Genetics, Microbiology and Statistics; Faculty of Biology; University of Barcelona; Av. Diagonal 643 08028 Barcelona Spain
| | - Reinhard Dallinger
- Institute of Zoology and Center for Molecular Biosciences; University of Innsbruck; Technikerstrasse 25 6020 Innsbruck Austria
| | - Oliver Zerbe
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
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16
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Poms M, Ansorge P, Martinez-Gil L, Jurt S, Gottstein D, Fracchiolla KE, Cohen LS, Güntert P, Mingarro I, Naider F, Zerbe O. NMR Investigation of Structures of G-protein Coupled Receptor Folding Intermediates. J Biol Chem 2016; 291:27170-27186. [PMID: 27864365 DOI: 10.1074/jbc.m116.740985] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 11/03/2016] [Indexed: 11/06/2022] Open
Abstract
Folding of G-protein coupled receptors (GPCRs) according to the two-stage model (Popot, J. L., and Engelman, D. M. (1990) Biochemistry 29, 4031-4037) is postulated to proceed in 2 steps: partitioning of the polypeptide into the membrane followed by diffusion until native contacts are formed. Herein we investigate conformational preferences of fragments of the yeast Ste2p receptor using NMR. Constructs comprising the first, the first two, and the first three transmembrane (TM) segments, as well as a construct comprising TM1-TM2 covalently linked to TM7 were examined. We observed that the isolated TM1 does not form a stable helix nor does it integrate well into the micelle. TM1 is significantly stabilized upon interaction with TM2, forming a helical hairpin reported previously (Neumoin, A., Cohen, L. S., Arshava, B., Tantry, S., Becker, J. M., Zerbe, O., and Naider, F. (2009) Biophys. J. 96, 3187-3196), and in this case the protein integrates into the hydrophobic interior of the micelle. TM123 displays a strong tendency to oligomerize, but hydrogen exchange data reveal that the center of TM3 is solvent exposed. In all GPCRs so-far structurally characterized TM7 forms many contacts with TM1 and TM2. In our study TM127 integrates well into the hydrophobic environment, but TM7 does not stably pack against the remaining helices. Topology mapping in microsomal membranes also indicates that TM1 does not integrate in a membrane-spanning fashion, but that TM12, TM123, and TM127 adopt predominantly native-like topologies. The data from our study would be consistent with the retention of individual helices of incompletely synthesized GPCRs in the vicinity of the translocon until the complete receptor is released into the membrane interior.
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Affiliation(s)
- Martin Poms
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Philipp Ansorge
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Luis Martinez-Gil
- the Department of Biochemistry and Molecular Biology, ERI BioTecMed, University of Valencia, E-46100 Burjassot, Spain
| | - Simon Jurt
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Gottstein
- the Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Katrina E Fracchiolla
- the Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, New York 10314, the Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Leah S Cohen
- the Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, New York 10314, the Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Peter Güntert
- the Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,the Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Ismael Mingarro
- the Department of Biochemistry and Molecular Biology, ERI BioTecMed, University of Valencia, E-46100 Burjassot, Spain
| | - Fred Naider
- the Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, New York 10314, the Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Oliver Zerbe
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland,
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17
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Moehle K, Kocherla H, Bacsa B, Jurt S, Zerbe K, Robinson JA, Zerbe O. Solution Structure and Dynamics of LptE from Pseudomonas aeruginosa. Biochemistry 2016; 55:2936-43. [DOI: 10.1021/acs.biochem.6b00313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kerstin Moehle
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Harsha Kocherla
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Bernadett Bacsa
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Katja Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - John A. Robinson
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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18
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Gutte PGM, Jurt S, Grütter MG, Zerbe O. Unusual structural features revealed by the solution NMR structure of the NLRC5 caspase recruitment domain. Biochemistry 2014; 53:3106-17. [PMID: 24815518 DOI: 10.1021/bi500177x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 01/22/2023]
Abstract
The cytosolic nucleotide-binding domain and leucine-rich repeat-containing receptors (NLRs) are key sensors for bacterial and viral invaders and endogenous stress signals. NLRs contain a varying N-terminal effector domain that regulates the downstream signaling events upon its activation and determines the subclass to which a NLR member belongs. NLRC5 contains an unclassified N-terminal effector domain that has been reported to interact downstream with the tandem caspase recruitment domain (CARD) of retinoic acid-inducible gene I (RIG-I). Here we report the solution structure of the N-terminal effector domain of NLRC5 and in vitro interaction experiments with the tandem CARD of RIG-I. The N-terminal effector domain of NLRC5 adopts a six α-helix bundle with a general death fold, though it displays specific structural features that are strikingly different from the CARD. Notably, α-helix 3 is replaced by an ordered loop, and α-helix 1 is devoid of the characteristic interruption. Detailed structural alignments between the N-terminal effector domains of NLRC5 with a representative of each death-fold subfamily showed that NLRC5 fits best to the CARD subfamily and can be called an atypical CARD. Due to the specific structural features, the atypical CARD also displays a different electrostatic surface. Because the shape and charge of the surface is crucial for the establishment of a homotypic CARD-CARD interaction, these specific structural features seem to have a significant effect on the interaction between the atypical CARD of NLRC5 and the tandem RIG-I CARD.
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Affiliation(s)
- Petrus G M Gutte
- Institute of Biochemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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19
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Jurt S, Zerbe O. A study on the influence of fast amide exchange on the accuracy of (15)N relaxation rate constants. J Biomol NMR 2012; 54:389-400. [PMID: 23143279 DOI: 10.1007/s10858-012-9682-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
(15)N relaxation rates of amide moieties provide insight both into global as well as local backbone dynamics of peptides and proteins. As the differences in the relaxation rates in general are small, their accurate determination is of prime importance. One potential source of error is fast amide exchange. It is well known that in its presence the effects of saturation transfer and H/D exchange may result in erroneous apparent relaxation rates R (1) and R (2). Here, the extent of these errors is rigorously examined. Theoretical considerations reveal that even when saturation effects are absent, H/D exchange will easily result in significant deviations from the true values. In particular overestimations of up to 10 % in R (1) and up to 5 % in R (2) are observed. An alternative scheme for fitting the relaxation data to the corresponding exponentials is presented that in the best cases not only delivers more accurate relaxation rates but also allows extracting estimates for the exchange rates. The theoretical computations were tested and verified for the case of ubiquitin.
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Affiliation(s)
- Simon Jurt
- Institute of Organic Chemistry, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
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20
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Pedersen SL, Bhatia VK, Jurt S, Paulsson JF, Pedersen MH, Jorgensen R, Holst B, Stamou D, Vrang N, Zerbe O, Jensen KJ. Improving membrane binding as a design strategy for amphipathic peptide hormones: 2-helix variants of PYY3-36. J Pept Sci 2012; 18:579-87. [DOI: 10.1002/psc.2436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/06/2012] [Indexed: 12/20/2022]
Affiliation(s)
- Søren L. Pedersen
- Department of Chemistry, Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
- The Lundbeck Foundation Center for Biomembranes in Nanomedicine; Unversity of Copenhagen; Denmark
| | - Vikram K. Bhatia
- Faculty of Health Sciences; University of Copenhagen; Blegdamsvej 3B 2200 Copenhagen N Denmark
- Novozymes A/S; Bagsvaerd Denmark
| | - Simon Jurt
- Institute of Organic Chemistry; University of Zurich; Winterthurerstrasse 190 CH 8057 Zurich Switzerland
| | | | - Maria H. Pedersen
- Department of Chemistry, Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | | | - Birgitte Holst
- Faculty of Health Sciences; University of Copenhagen; Blegdamsvej 3B 2200 Copenhagen N Denmark
| | - Dimitrios Stamou
- Department of Chemistry, Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
- The Lundbeck Foundation Center for Biomembranes in Nanomedicine; Unversity of Copenhagen; Denmark
| | - Niels Vrang
- gubra Aps; Agern Allé 1 2970 Hørsholm Denmark
| | - Oliver Zerbe
- Institute of Organic Chemistry; University of Zurich; Winterthurerstrasse 190 CH 8057 Zurich Switzerland
| | - Knud J. Jensen
- Department of Chemistry, Faculty of Science; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
- The Lundbeck Foundation Center for Biomembranes in Nanomedicine; Unversity of Copenhagen; Denmark
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21
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Wetzel SK, Ewald C, Settanni G, Jurt S, Plückthun A, Zerbe O. Residue-resolved stability of full-consensus ankyrin repeat proteins probed by NMR. J Mol Biol 2010; 402:241-58. [PMID: 20654623 DOI: 10.1016/j.jmb.2010.07.031] [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] [Received: 04/27/2010] [Revised: 07/10/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
Abstract
We investigated the stability determinants and the unfolding characteristics of full-consensus designed ankyrin repeat proteins (DARPins) by NMR. Despite the repeating sequence motifs, the resonances could be fully assigned using (2)H,(15)N,(13)C triple-labeled proteins. To remove further ambiguities, we attached paramagnetic spin labels to either end of these elongated proteins, which attenuate the resonances of the spatially closest residues. Deuterium exchange experiments of DARPins with two and three internal repeats between N- and C-terminal capping repeats (NI(2)C, NI(3)C) and NI(3)C_Mut5, where the C-cap had been reengineered, indicate that the stability of the full-consensus ankyrin repeat proteins is strongly dependent on the coupling between repeats, as the stabilized cap decreases the exchange rate throughout the whole protein. Some amide protons require more than a year to exchange at 37 degrees C, highlighting the extraordinary stability of the proteins. Denaturant-induced unfolding, followed by deuterium exchange, chemical shift change, and heteronuclear nuclear Overhauser effects, is consistent with an Ising-type description of equilibrium folding for NI(3)C_Mut5, while for native-state deuterium exchange, we postulate local fluctuations to dominate exchange as unfolding events are too slow in these very stable proteins. The location of extraordinarily slowly exchanging protons indicates a very stable core structure in the DARPins that combines hydrophobic shielding with favorable electrostatic interactions. These investigations help the understanding of repeat protein architecture and the further design of DARPins for biomedical applications where high stability is required.
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Affiliation(s)
- Svava K Wetzel
- Institute of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
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Jurt S, Aemissegger A, Güntert P, Zerbe O, Hilvert D. A Photoswitchable Miniprotein Based on the Sequence of Avian Pancreatic Polypeptide. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602084] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Jurt S, Aemissegger A, Güntert P, Zerbe O, Hilvert D. A Photoswitchable Miniprotein Based on the Sequence of Avian Pancreatic Polypeptide. Angew Chem Int Ed Engl 2006; 45:6297-300. [PMID: 16933352 DOI: 10.1002/anie.200602084] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Simon Jurt
- Institute of Organic Chemistry, University of Zurich, 8057 Zurich, Switzerland
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Abstract
Rider peaks are small peaks which are not well resolved from a large and asymmetrical neighbour but sit on its trailing side. The usual case is a large, tailed peak which is eluted just in front of the small peak, although the opposite situation can also occur (a small peak in front of a large peak with fronting). The common integration techniques. i.e. separating the peaks by vertical drop or by a tangent and determining area or height, give erroneous results. We propose a method for their quantification with low error. It is necessary to set up a "two-dimensional" calibration by varying both concentrations, i.e. of the large peak and of the rider. This leads to a series of linear equations which describe the rider size, as found by the integrator, as a function of the size of the large peak. The y-axis intercepts i of these equations show a linear relationship with the concentration x of the rider analyte, whereas the slopes s follow a quadratic relationship. These equations can be used to solve the equation y = s(x) x z + i(x) for x (y and z are the integrated peak size of the rider and the large peak, respectively). The procedure was tested with computer-generated peak pairs as well as with HPLC separations of 2,3-dimethylaniline (large tailing peak) and 2,3-dimethylphenol (symmetrical rider peak).
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Affiliation(s)
- S Jurt
- Department of Chemistry, University of Applied Sciences, Burgdorf, Switzerland
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