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Mekkattu Tharayil S, Mahawaththa MC, Feintuch A, Maleckis A, Ullrich S, Morewood R, Maxwell MJ, Huber T, Nitsche C, Goldfarb D, Otting G. Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:169-182. [PMID: 37904871 PMCID: PMC10539774 DOI: 10.5194/mr-3-169-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 11/01/2023]
Abstract
The paramagnetism of a lanthanoid tag site-specifically installed on a protein provides a rich source of structural information accessible by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy. Here we report a lanthanoid tag for selective reaction with cysteine or selenocysteine with formation of a (seleno)thioether bond and a short tether between the lanthanoid ion and the protein backbone. The tag is assembled on the protein in three steps, comprising (i) reaction with 4-fluoro-2,6-dicyanopyridine (FDCP); (ii) reaction of the cyano groups with α -cysteine, penicillamine or β -cysteine to complete the lanthanoid chelating moiety; and (iii) titration with a lanthanoid ion. FDCP reacts much faster with selenocysteine than cysteine, opening a route for selective tagging in the presence of solvent-exposed cysteine residues. Loaded with Tb 3 + and Tm 3 + ions, pseudocontact shifts were observed in protein NMR spectra, confirming that the tag delivers good immobilisation of the lanthanoid ion relative to the protein, which was also manifested in residual dipolar couplings. Completion of the tag with different 1,2-aminothiol compounds resulted in different magnetic susceptibility tensors. In addition, the tag proved suitable for measuring distance distributions in double electron-electron resonance experiments after titration with Gd 3 + ions.
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Affiliation(s)
| | - Mithun C. Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michael J. Maxwell
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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2
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Feichtinger M, Beier A, Migotti M, Schmid M, Bokhovchuk F, Chène P, Konrat R. Long-range structural preformation in yes-associated protein precedes encounter complex formation with TEAD. iScience 2022; 25:104099. [PMID: 35378854 PMCID: PMC8976148 DOI: 10.1016/j.isci.2022.104099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/25/2022] [Accepted: 03/15/2022] [Indexed: 11/22/2022] Open
Abstract
Yes-associated protein (YAP) is a partly intrinsically disordered protein (IDP) that plays a major role as the downstream element of the Hippo pathway. Although the structures of the complex between TEA domain transcription factors (TEADs) and the TEAD-binding domain of YAP are already well characterized, its apo state and the binding mechanism with TEADs are still not clearly defined. Here we characterize via a combination of different NMR approaches with site-directed mutagenesis and affinity measurements the intrinsically disordered solution state of apo YAP. Our results provide evidence that the apo state of YAP adopts several compact conformations that may facilitate the formation of the YAP:TEAD complex. The interplay between local secondary structure element preformation and long-range co-stabilization of these structured elements precedes the encounter complex formation with TEAD and we, therefore, propose that TEAD binding proceeds largely via conformational selection of the preformed compact substates displaying at least nanosecond lifetimes. Secondary structure elements are preformed in apo YAP Preformation of secondary structure elements is co-dependent Apo YAP exhibits long-range structural compaction YAP compaction has a kinetic contribution to the YAP:TEAD formation
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Affiliation(s)
- Michael Feichtinger
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Andreas Beier
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Mario Migotti
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Matthias Schmid
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Fedir Bokhovchuk
- Ichnos Sciences SA, Route de la Corniche 5A, 1066 Epalinges, Switzerland
| | - Patrick Chène
- Novartis Pharma AG, Postfach WSJ 386.4, 4002 Basel, Switzerland
| | - Robert Konrat
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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Vida I, Fazekas Z, Gyulai G, Nagy‐Fazekas D, Pálfy G, Stráner P, Kiss É, Perczel A. Bacterial fermentation and isotope labelling optimized for amyloidogenic proteins. Microb Biotechnol 2021; 14:1107-1119. [PMID: 33739615 PMCID: PMC8085922 DOI: 10.1111/1751-7915.13778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 11/30/2022] Open
Abstract
We developed a cost sensitive isotope labelling procedure using a fed-batch fermentation method and tested its efficiency producing the 15 N-, 13 C- and 15 N/13 C-labelled variants of an amyloidogenic miniprotein (E5: EEEAVRLYIQWLKEGGPSSGRPPPS). E5 is a surface active protein, which forms amyloids in solution. Here, we confirm, using both PM-IRRAS and AFM measurements, that the air-water interface triggers structural rearrangement and promotes the amyloid formation of E5, and thus it is a suitable test protein to work out efficient isotope labelling schemes even for such difficult sequences. E. coli cells expressing the recombinant, ubiquitin-fused miniprotein were grown in minimal media containing either unlabelled nutrients, or 15 N-NH4 Cl and/or 13 C-D-Glc. The consumption rates of NH4 Cl and D-Glc were quantitatively monitored during fermentation and their ratio was established to be 1:5 (for NH4 Cl: D-Glc). One- and two-step feeding schemes were custom-optimized to enhance isotope incorporation expressing five different E5 miniprotein variants. With the currently optimized protocols we could achieve a 1.5- to 5-fold increase of yields of several miniproteins coupled to a similar magnitude of cost reduction as compared to flask labelling protocols.
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Affiliation(s)
- István Vida
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
- Hevesy György PhD School of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
| | - Zsolt Fazekas
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
- Hevesy György PhD School of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
| | - Gergő Gyulai
- Laboratory of Interfaces and NanostructuresInstitute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
| | - Dóra Nagy‐Fazekas
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
- Hevesy György PhD School of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
- MTA‐ELTE Protein Modeling Research Group, Eötvös Loránd Research Network (ELKH)Institute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
| | - Pál Stráner
- MTA‐ELTE Protein Modeling Research Group, Eötvös Loránd Research Network (ELKH)Institute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
| | - Éva Kiss
- Laboratory of Interfaces and NanostructuresInstitute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
- MTA‐ELTE Protein Modeling Research Group, Eötvös Loránd Research Network (ELKH)Institute of ChemistryEötvös Loránd UniversityPázmány P. stny. 1/ABudapestH‐1117Hungary
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Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
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Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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Canonica F, Klose D, Ledermann R, Sauer MM, Abicht HK, Quade N, Gossert AD, Chesnov S, Fischer HM, Jeschke G, Hennecke H, Glockshuber R. Structural basis and mechanism for metallochaperone-assisted assembly of the Cu A center in cytochrome oxidase. SCIENCE ADVANCES 2019; 5:eaaw8478. [PMID: 31392273 PMCID: PMC6669012 DOI: 10.1126/sciadv.aaw8478] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
The mechanisms underlying the biogenesis of the structurally unique, binuclear Cu1.5+•Cu1.5+ redox center (CuA) on subunit II (CoxB) of cytochrome oxidases have been a long-standing mystery. Here, we reconstituted the CoxB•CuA center in vitro from apo-CoxB and the holo-forms of the copper transfer chaperones ScoI and PcuC. A previously unknown, highly stable ScoI•Cu2+•CoxB complex was shown to be rapidly formed as the first intermediate in the pathway. Moreover, our structural data revealed that PcuC has two copper-binding sites, one each for Cu1+ and Cu2+, and that only PcuC•Cu1+•Cu2+ can release CoxB•Cu2+ from the ScoI•Cu2+•CoxB complex. The CoxB•CuA center was then formed quantitatively by transfer of Cu1+ from a second equivalent of PcuC•Cu1+•Cu2+ to CoxB•Cu2+. This metalation pathway is consistent with all available in vivo data and identifies the sources of the Cu ions required for CuA center formation and the order of their delivery to CoxB.
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Affiliation(s)
- Fabia Canonica
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Maximilian M. Sauer
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Helge K. Abicht
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nick Quade
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Alvar D. Gossert
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Serge Chesnov
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | | | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Hauke Hennecke
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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7
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Azatian SB, Kaur N, Latham MP. Increasing the buffering capacity of minimal media leads to higher protein yield. JOURNAL OF BIOMOLECULAR NMR 2019; 73:11-17. [PMID: 30613903 PMCID: PMC6441617 DOI: 10.1007/s10858-018-00222-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/22/2018] [Indexed: 05/03/2023]
Abstract
We describe a general and simple modification to the standard M9 minimal medium recipe that leads to an approximate twofold increase in the yield of heterologously expressed proteins in Escherichia coli BL21(DE3) bacteria. We monitored the growth of bacteria transformed with plasmids for three different test proteins in five minimal media with different concentrations of buffering salts and/or initial media pH. After purification of the over-expressed proteins, we found a clear correlation between the protein yield and change in media pH over time, where the minimal media that were the most buffered and therefore most resistant to change in pH produced the most protein. And in all three test protein cases, the difference in yield was nearly twofold between the best and worst buffering media. Thus, we propose that increasing the buffering capacity of M9 minimal media will generally lead to a similar increase for most of the proteins currently produced by this standard protein expression protocol. Moreover, we have qualitatively found that this effect also extends to deuterated M9 minimal media growths, which could lead to significant cost savings in these preparations.
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Affiliation(s)
- Stephan B Azatian
- Department of Chemistry and Biochemistry, Texas Tech University, 1204 Boston Ave., Lubbock, TX, 79423-1061, USA
| | - Navneet Kaur
- Department of Chemistry and Biochemistry, Texas Tech University, 1204 Boston Ave., Lubbock, TX, 79423-1061, USA
| | - Michael P Latham
- Department of Chemistry and Biochemistry, Texas Tech University, 1204 Boston Ave., Lubbock, TX, 79423-1061, USA.
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8
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Boisbouvier J, Kay LE. Advanced isotopic labeling for the NMR investigation of challenging proteins and nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2018; 71:115-117. [PMID: 30043256 DOI: 10.1007/s10858-018-0199-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Medicine, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
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