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Khan S, Ansari A, Brachi M, Das D, El Housseini W, Minteer S, Miller AF. Structure, dynamics, and redox reactivity of an all-purpose flavodoxin. J Biol Chem 2024; 300:107122. [PMID: 38417793 PMCID: PMC10979112 DOI: 10.1016/j.jbc.2024.107122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024] Open
Abstract
The flavodoxin of Rhodopseudomonas palustris CGA009 (Rp9Fld) supplies highly reducing equivalents to crucial enzymes such as hydrogenase, especially when the organism is iron-restricted. By acquiring those electrons from photodriven electron flow via the bifurcating electron transfer flavoprotein, Rp9Fld provides solar power to vital metabolic processes. To understand Rp9Fld's ability to work with diverse partners, we solved its crystal structure. We observed the canonical flavodoxin (Fld) fold and features common to other long-chain Flds but not all the surface loops thought to recognize partner proteins. Moreover, some of the loops display alternative structures and dynamics. To advance studies of protein-protein associations and conformational consequences, we assigned the 19F NMR signals of all five tyrosines (Tyrs). Our electrochemical measurements show that incorporation of 3-19F-Tyr in place of Tyr has only a modest effect on Rp9Fld's redox properties even though Tyrs flank the flavin on both sides. Meanwhile, the 19F probes demonstrate the expected paramagnetic effect, with signals from nearby Tyrs becoming broadened beyond detection when the flavin semiquinone is formed. However, the temperature dependencies of chemical shifts and linewidths reveal dynamics affecting loops close to the flavin and regions that bind to partners in a variety of systems. These coincide with patterns of amino acid type conservation but not retention of specific residues, arguing against detailed specificity with respect to partners. We propose that the loops surrounding the flavin adopt altered conformations upon binding to partners and may even participate actively in electron transfer.
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Affiliation(s)
- Sharique Khan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Ahmadullah Ansari
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Monica Brachi
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Debarati Das
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | | | - Shelley Minteer
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA; Department of Chemistry, Kummer Institute Center for Resource Sustainability, Missouri University of Science and Technology, Rolla, Missouri, USA
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2
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de Amorim GC, Bardiaux B, Izadi-Pruneyre N. Structural Analysis of Proteins from Bacterial Secretion Systems and Their Assemblies by NMR Spectroscopy. Methods Mol Biol 2024; 2715:503-517. [PMID: 37930547 DOI: 10.1007/978-1-0716-3445-5_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Bacterial secretion systems are built up from proteins with different physicochemical characteristics, such as highly hydrophobic transmembrane polypeptides, and soluble periplasmic or intracellular domains. A single complex can be composed of more than ten proteins with distinct features, spreading through different cellular compartments. The membrane and multicompartment nature of the proteins, and their large molecular weight make their study challenging. However, information on their structure and assemblies is required to understand their mechanisms and interfere with them. An alternative strategy is to work with soluble domains and peptides corresponding to the regions of interest of the proteins.Here, we describe a simple and fast protocol to evaluate the stability, folding, and interaction of protein sub-complexes by using solution-state Nuclear Magnetic Resonance (NMR) spectroscopy. This technique is widely used for protein structure and protein-ligand interaction analysis in solution.
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Affiliation(s)
- Gisele Cardoso de Amorim
- Núcleo Multidisciplinar de Pesquisa em Biologia, Campus Duque de Caxias, Universidade Federal do Rio de Janeiro, Duque de Caxias, RJ, Brazil
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France.
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3
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Kerber PJ, Nuñez R, Jensen DR, Zhou AL, Peterson FC, Hill RB, Volkman BF, Smith BC. Fragment-based screening by protein-detected NMR spectroscopy. Methods Enzymol 2023; 690:285-310. [PMID: 37858532 PMCID: PMC10657026 DOI: 10.1016/bs.mie.2023.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Fragment-based drug discovery (FBDD) identifies low molecular weight compounds that can be developed into ligands with high affinity and selectivity for therapeutic targets. Screening fragment libraries (<10,000 molecules) with biophysical techniques against macromolecules provides information about novel chemical spaces that bind the macromolecule and scaffolds that can be modified to increase potency. A fragment-screening pipeline requires a standardized protocol for target selection, library assembly and maintenance, library screening, and hit validation to ensure hit integrity. Herein, the fundamental aspects of a fragment screening pipeline-focusing on protein-detected NMR data collection and analysis-are discussed in detail for researchers to use as a resource in their FBDD projects. Selected screening targets must undergo rigorous stability and buffer testing by NMR spectroscopy to ensure the protein structure is stable for the entire screen. Biophysical instrumentation that rapidly measures protein thermostability is helpful in buffer screening. Molecules in fragment libraries are analyzed computationally and physically, stored at appropriate temperatures, and multiplexed in well plates for library conservation. The screening protocol is streamlined using liquid handling robotics for sample preparation and customized Python scripts for protein-detected NMR data analysis. Molecules identified from the screen are titrated to determine their binding site(s) and Kd values and confirmed with an orthogonal biophysical assay. This detailed FBDD screening pipeline developed by the Program in Chemical Biology at the Medical College of Wisconsin has successfully screened many unrelated target proteins to identified novel molecules that selectively bind to these target proteins.
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Affiliation(s)
- Paul J Kerber
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Raymundo Nuñez
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Davin R Jensen
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Angela L Zhou
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
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4
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Rowlinson B, Crublet E, Kerfah R, Plevin MJ. Specific isotopic labelling and reverse labelling for protein NMR spectroscopy: using metabolic precursors in sample preparation. Biochem Soc Trans 2022; 50:1555-1567. [PMID: 36382942 DOI: 10.1042/bst20210586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2023]
Abstract
The study of protein structure, dynamics and function by NMR spectroscopy commonly requires samples that have been enriched ('labelled') with the stable isotopes 13C and/or 15N. The standard approach is to uniformly label a protein with one or both of these nuclei such that all C and/or N sites are in principle 'NMR-visible'. NMR spectra of uniformly labelled proteins can be highly complicated and suffer from signal overlap. Moreover, as molecular size increases the linewidths of NMR signals broaden, which decreases sensitivity and causes further spectral congestion. Both effects can limit the type and quality of information available from NMR data. Problems associated with signal overlap and signal broadening can often be alleviated though the use of alternative, non-uniform isotopic labelling patterns. Specific isotopic labelling 'turns on' signals at selected sites while the rest of the protein is NMR-invisible. Conversely, specific isotopic unlabelling (also called 'reverse' labelling) 'turns off' selected signals while the rest of the protein remains NMR-visible. Both approaches can simplify NMR spectra, improve sensitivity, facilitate resonance assignment and permit a range of different NMR strategies when combined with other labelling tools and NMR experiments. Here, we review methods for producing proteins with enrichment of stable NMR-visible isotopes, with particular focus on residue-specific labelling and reverse labelling using Escherichia coli expression systems. We also explore how these approaches can aid NMR studies of proteins.
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Affiliation(s)
- Benjamin Rowlinson
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, U.K
| | - Elodie Crublet
- NMR-Bio, World Trade Center- 5 Place Robert Schuman, 38025 Grenoble Cedex 1, France
| | - Rime Kerfah
- NMR-Bio, World Trade Center- 5 Place Robert Schuman, 38025 Grenoble Cedex 1, France
| | - Michael J Plevin
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, U.K
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Pérez Carrillo VH, Rose-Sperling D, Tran MA, Wiedemann C, Hellmich UA. Backbone NMR assignment of the nucleotide binding domain of the Bacillus subtilis ABC multidrug transporter BmrA in the post-hydrolysis state. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:81-86. [PMID: 34988902 PMCID: PMC9068644 DOI: 10.1007/s12104-021-10063-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 05/11/2023]
Abstract
ATP binding cassette (ABC) proteins are present in all phyla of life and form one of the largest protein families. The Bacillus subtilis ABC transporter BmrA is a functional homodimer that can extrude many different harmful compounds out of the cell. Each BmrA monomer is composed of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). While the TMDs of ABC transporters are sequentially diverse, the highly conserved NBDs harbor distinctive conserved motifs that enable nucleotide binding and hydrolysis, interdomain communication and that mark a protein as a member of the ABC superfamily. In the catalytic cycle of an ABC transporter, the NBDs function as the molecular motor that fuels substrate translocation across the membrane via the TMDs and are thus pivotal for the entire transport process. For a better understanding of the structural and dynamic consequences of nucleotide interactions within the NBD at atomic resolution, we determined the 1H, 13C and 15N backbone chemical shift assignments of the 259 amino acid wildtype BmrA-NBD in its post-hydrolytic, ADP-bound state.
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Affiliation(s)
- Victor Hugo Pérez Carrillo
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Dania Rose-Sperling
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Mai Anh Tran
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Christoph Wiedemann
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, 07743, Jena, Germany.
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6
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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7
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Napolitano S, Pokharna A, Glockshuber R, Gossert AD. The trans-to-cis proline isomerization in E. coli Trx folding is accelerated by trans prolines. Biophys J 2021; 120:5207-5218. [PMID: 34736898 DOI: 10.1016/j.bpj.2021.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/17/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022] Open
Abstract
The conserved fold of thioredoxin (Trx)-like thiol/disulfide oxidoreductases contains an invariant cis-proline residue (P76 in Escherichia coli Trx) that is essential for Trx function and that is responsible for the folding rate-limiting step. E. coli Trx contains four additional prolines, which are all in the trans conformation in the native state. Notably, a recent study revealed that replacement of all four trans prolines in Trx by alanines (Trx variant Trx1P) further slowed the rate-limiting step 25-fold, indicating that one or several of the four trans prolines accelerate the trans-to-cis transition of P76 in Trx wild-type (wt). Here, we characterized the folding kinetics of Trx variants containing cisP76 and one or several of the natural trans prolines of Trx wt with NMR spectroscopy. First, we demonstrate that the isomerization reaction in Trx1P is a pure two-state transition between two distinct tertiary structures, in which all observed NMR resonances changes follow the same first-order kinetics. Moreover, we show that trans-P68 is the critical residue responsible for the faster folding of wt Trx relative to the single-proline (P76) variant Trx1P, as the two-proline variant Trx2P(P76P68) already folds seven times faster than Trx1P. trans-P34 also accelerates trans-to-cis isomerization of P76, albeit to a smaller extent. Overall, the results demonstrate that trans prolines can significantly modulate the kinetics of rate-limiting trans-to-cis proline isomerization in protein folding. Finally, we discuss possible mechanisms of acceleration and the potential significance of a protein-internal folding acceleration mechanism for Trx in a living cell.
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Affiliation(s)
| | - Aditya Pokharna
- Institute of Molecular Biology and Biophysics, Zürich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Zürich, Switzerland.
| | - Alvar D Gossert
- Institute of Molecular Biology and Biophysics, Zürich, Switzerland; Biomolecular NMR Spectroscopy Platform, Department of Biology, ETH Zürich, Zürich, Switzerland.
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8
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Harnden KA, Roy A, Hosseinzadeh P. Overview of Methods for Purification and Characterization of Metalloproteins. Curr Protoc 2021; 1:e234. [PMID: 34436821 DOI: 10.1002/cpz1.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metalloproteins make up one third of all proteins and perform some of the most essential reactions on earth. The unique properties of the metal ions within these proteins, and in particular of redox-active metal ions, enables the use of a number of characterization techniques. It also necessitates unique considerations in terms of purification and characterization. In this overview, we describe the considerations and methods used for metalloprotein purification and characterization. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
| | - Anindya Roy
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, Washington
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9
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Chakraborty P, Rivière G, Liu S, de Opakua AI, Dervişoğlu R, Hebestreit A, Andreas LB, Vorberg IM, Zweckstetter M. Co-factor-free aggregation of tau into seeding-competent RNA-sequestering amyloid fibrils. Nat Commun 2021; 12:4231. [PMID: 34244499 PMCID: PMC8270918 DOI: 10.1038/s41467-021-24362-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/16/2021] [Indexed: 12/17/2022] Open
Abstract
Pathological aggregation of the protein tau into insoluble aggregates is a hallmark of neurodegenerative diseases. The emergence of disease-specific tau aggregate structures termed tau strains, however, remains elusive. Here we show that full-length tau protein can be aggregated in the absence of co-factors into seeding-competent amyloid fibrils that sequester RNA. Using a combination of solid-state NMR spectroscopy and biochemical experiments we demonstrate that the co-factor-free amyloid fibrils of tau have a rigid core that is similar in size and location to the rigid core of tau fibrils purified from the brain of patients with corticobasal degeneration. In addition, we demonstrate that the N-terminal 30 residues of tau are immobilized during fibril formation, in agreement with the presence of an N-terminal epitope that is specifically detected by antibodies in pathological tau. Experiments in vitro and in biosensor cells further established that co-factor-free tau fibrils efficiently seed tau aggregation, while binding studies with different RNAs show that the co-factor-free tau fibrils strongly sequester RNA. Taken together the study provides a critical advance to reveal the molecular factors that guide aggregation towards disease-specific tau strains.
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Affiliation(s)
| | - Gwladys Rivière
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Shu Liu
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Rıza Dervişoğlu
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alina Hebestreit
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Loren B Andreas
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ina M Vorberg
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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Muniyappan S, Lin Y, Lee YH, Kim JH. 17O NMR Spectroscopy: A Novel Probe for Characterizing Protein Structure and Folding. BIOLOGY 2021; 10:biology10060453. [PMID: 34064021 PMCID: PMC8223985 DOI: 10.3390/biology10060453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022]
Abstract
Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (17O), therefore, has been proposed as a useful probe that can provide detailed information about various physicochemical features of proteins. This is attributed to the facts that (1) 17O is an active isotope for nuclear magnetic resonance (NMR) spectroscopic approaches; (2) NMR spectroscopy is one of the most suitable tools for characterizing the structural and dynamical features of biomolecules under native-like conditions; and (3) oxygen atoms are frequently involved in essential hydrogen bonds for the structural and functional integrity of proteins or related biomolecules. Although 17O NMR spectroscopic investigations of biomolecules have been considerably hampered due to low natural abundance and the quadruple characteristics of the 17O nucleus, recent theoretical and technical developments have revolutionized this methodology to be optimally poised as a unique and widely applicable tool for determining protein structure and dynamics. In this review, we recapitulate recent developments in 17O NMR spectroscopy to characterize protein structure and folding. In addition, we discuss the highly promising advantages of this methodology over other techniques and explain why further technical and experimental advancements are highly desired.
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Affiliation(s)
- Srinivasan Muniyappan
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea;
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea;
- Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
- Research Headquarters, Korea Brain Research Institute, Daegu 41068, Korea
- Correspondence: (Y.-H.L.); (J.H.K.)
| | - Jin Hae Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
- Correspondence: (Y.-H.L.); (J.H.K.)
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11
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Varner TA, Mohamed-Raseek N, Miller AF. Assignments of 19F NMR resonances and exploration of dynamics in a long-chain flavodoxin. Arch Biochem Biophys 2021; 703:108839. [PMID: 33727041 DOI: 10.1016/j.abb.2021.108839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/23/2022]
Abstract
Flavodoxin is a small protein that employs a non-covalently bound flavin to mediate single-electron transfer at low potentials. The long-chain flavodoxins possess a long surface loop that is proposed to interact with partner proteins. We have incorporated 19F-labeled tyrosine in long-chain flavodoxin from Rhodopseudomonas palustris to gain a probe of possible loop dynamics, exploiting the presence of a Tyr in the long loop in addition to Tyr residues near the flavin. We report 19F resonance assignments for all four Tyrs, and demonstration of a pair of resonances in slow exchange, both corresponding to a Tyr adjacent to the flavin. We also provide evidence for dynamics affecting the Tyr in the long loop. Thus, we show that 19F NMR of 19F-Tyr labeled flavodoxin holds promise for monitoring possible changes in conformation upon binding to partner proteins.
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Affiliation(s)
- Taylor A Varner
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA
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12
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Magnesium magnetic isotope effects in microbiology. Arch Microbiol 2021; 203:1853-1861. [PMID: 33611633 DOI: 10.1007/s00203-021-02219-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/15/2020] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
Two main properties of atomic nuclei-mass and nuclear magnetic moments-are origin of many biological effects. Mass-dependent isotope effects have been studied for a long time. The effect of magnetic isotopes having a magnetic moment and spin was first shown in the early twenty-first century for the magnetic isotope magnesium 25Mg on enzymatic ATP synthesis. This stimulated the search for experimental evidence and theoretical justification of magnetic nuclei influence on biological processes. This review contains the results of scientific research on the magnesium magnetic isotope effects in microbiology. Microorganisms have been found to be sensitive to the presence of nuclear magnetic moment of magnesium isotope 25Mg compared with non-magnetic 24,26Mg isotopes.
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13
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Klein BA, Tkachuk DG, Terskikh VV, Michaelis VK. Expanding the NMR toolkit for biological solids: oxygen-17 enriched Fmoc-amino acids. NEW J CHEM 2021. [DOI: 10.1039/d1nj02847b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the solid-state 17O NMR parameters for five previously uncharacterized N-α-fluoren-9-yl-methoxycarbonyl-O-t-butyl (Fmoc) protected amino acids.
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14
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Immer C, Hacker C, Wöhnert J. Solution structure and RNA-binding of a minimal ProQ-homolog from Legionella pneumophila (Lpp1663). RNA (NEW YORK, N.Y.) 2020; 26:2031-2043. [PMID: 32989045 PMCID: PMC7668265 DOI: 10.1261/rna.077354.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/23/2020] [Indexed: 05/04/2023]
Abstract
Small regulatory RNAs (sRNAs) play an important role for posttranscriptional gene regulation in bacteria. sRNAs recognize their target messenger RNAs (mRNAs) by base-pairing, which is often facilitated by interactions with the bacterial RNA-binding proteins Hfq or ProQ. The FinO/ProQ RNA-binding protein domain was first discovered in the bacterial repressor of conjugation, FinO. Since then, the functional role of FinO/ProQ-like proteins in posttranscriptional gene regulation was extensively studied in particular in the enterobacteria E. coli and Salmonella enterica and a wide range of sRNA-targets was identified for these proteins. In addition, enterobacterial ProQ homologs also recognize and protect the 3'-ends of a number of mRNAs from exonucleolytic degradation. However, the RNA-binding properties of FinO/ProQ proteins with regard to the recognition of different RNA targets are not yet fully understood. Here, we present the solution NMR structure of the so far functionally uncharacterized ProQ homolog Lpp1663 from Legionella pneumophila as a newly confirmed member and a minimal model system of the FinO/ProQ protein family. In addition, we characterize the RNA-binding preferences of Lpp1663 with high resolution NMR spectroscopy and isothermal titration calorimetry (ITC). Our results suggest a binding preference for single-stranded uridine-rich RNAs in the vicinity of stable stem-loop structures. According to chemical shift perturbation experiments, the single-stranded U-rich RNAs interact mainly with a conserved RNA-binding surface on the concave site of Lpp1663.
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Affiliation(s)
- Carina Immer
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University, Frankfurt 60438, Germany
| | - Carolin Hacker
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University, Frankfurt 60438, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University, Frankfurt 60438, Germany
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15
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Lin B, Hung I, Gan Z, Chien PH, Spencer HL, Smith SP, Wu G. 17 O NMR Studies of Yeast Ubiquitin in Aqueous Solution and in the Solid State. Chembiochem 2020; 22:826-829. [PMID: 33058374 DOI: 10.1002/cbic.202000659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Indexed: 12/18/2022]
Abstract
We report a general method for amino acid-type specific 17 O-labeling of recombinant proteins in Escherichia coli. In particular, we have prepared several [1-13 C,17 O]-labeled yeast ubiquitin (Ub) samples including Ub-[1-13 C,17 O]Gly, Ub-[1-13 C,17 O]Tyr, and Ub-[1-13 C,17 O]Phe using the auxotrophic E. coli strain DL39 GlyA λDE3 (aspC- tyrB- ilvE- glyA- λDE3). We have also produced Ub-[η-17 O]Tyr, in which the phenolic group of Tyr59 is 17 O-labeled. We show for the first time that 17 O NMR signals from protein terminal residues and side chains can be readily detected in aqueous solution. We also reported solid-state 17 O NMR spectra for Ub-[1-13 C,17 O]Tyr and Ub-[1-13 C,17 O]Phe obtained at an ultrahigh magnetic field, 35.2 T (1.5 GHz for 1 H). This work represents a significant advance in the field of 17 O NMR studies of proteins.
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Affiliation(s)
- Binyang Lin
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ivan Hung
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Zhehong Gan
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Po-Hsiu Chien
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Holly L Spencer
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
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16
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Battistel MD, Freedberg DI. Dispersing the crowd: Adopting 13C direct detection for glycans. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106792. [PMID: 32759046 DOI: 10.1016/j.jmr.2020.106792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/08/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
As a direct consequence of technological advancements, the interest in direct detection of low-gamma/low-sensitivity heteronuclei for NMR experiments has been revived. Until recently, experimental development of 13C/15N detected experiments has been focused on protein NMR. In the present report, we extend the use of 13C-detected experiments to structural studies of glycans in natural abundance. The narrow 1H and wider 13C signal dispersion make glycans ideal candidates for heteronuclear detection. We show that 13C-detected HSQC offers a ten-fold increase in 13C dimension resolution compared to the analogous 1H-detected HSQC, when the experiments are acquired for the same amount of time. The enhanced resolution comes at the expense of 2 to 3-fold loss in SNR; however, the observed signal loss is a fraction of the theoretical 8-fold difference expected between experiments. Further, we show that by combining a 1H constant time element (CT), SMILE data reconstruction and 13C-direct detection, complete resonance assignments of highly degenerate glycan signals are possible. Finally, we demonstrate the potential of our strategy to aid in the assignment of complex glycans, by using a novel 13C-detected version of the CT-HSQC-TOCSY experiment performed on sialyl Lewis X pentasaccharide model system.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, United States.
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17
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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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18
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Chen JL, Wang X, Xiao YH, Su XC. Resonance Assignments of Lowly Populated and Unstable Enzyme Intermediate Complex under Real-Time Conditions. Chembiochem 2019; 20:2738-2742. [PMID: 31136055 DOI: 10.1002/cbic.201900240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Indexed: 11/08/2022]
Abstract
Unstable and low-abundance protein complexes represent a large family of transient protein complexes that are difficult to characterize, even by means of high-resolution NMR spectroscopy. A method to assign the NMR signals of these unstable complexes through a combination of selective isotope labeling of amino acids in a protein and site-specific labeling the protein with a paramagnetic tag is presented herein. By using this method, the resonances of unstable thioester intermediate complex (lifetime <5 h and highest concentration ≈20 μm) generated by Staphylococcus aureus sortase A and its peptide substrate under a real-time reaction have been assigned.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P.R. China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P.R. China
| | - Yu-Hao Xiao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P.R. China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P.R. China
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19
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Keller H, Kruse K, Averhoff B, Duchardt-Ferner E, Wöhnert J. NMR resonance assignments for the GSPII-C domain of the PilF ATPase from Thermus thermophilus in complex with c-di-GMP. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:361-366. [PMID: 31372934 DOI: 10.1007/s12104-019-09906-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
The natural transformation system of the thermophilic bacterium Thermus thermophilus is one of the most efficient DNA transport systems in terms of DNA uptake rate and promiscuity. The DNA transporter of T. thermophilus plays an important role in interdomain DNA transfer in hot environments. PilF is the traffic ATPase that provides the energy for the assembly of the DNA translocation machinery and the functionally linked type IV pilus system in T. thermophilus. In contrast to other known traffic ATPases, the N-terminal region of PilF harbors three consecutive domains with homology to general secretory pathway II (GSPII) domains. These GSPII-like domains influence pilus assembly, twitching motility and transformation efficiency. A structural homolog of the PilF GSPII-like domains, the N-terminal domain of the traffic ATPase MshE from Vibrio cholerae, was recently crystallized in complex with the bacterial second messenger c-di-GMP. In order to study the consequences of c-di-GMP binding on the three-dimensional architecture of PilF, we initiated structural studies on the PilF GSPII-like domains. Here, we present the 1H, 13C and 15N chemical shift assignments for the isolated PilF GSPII-C domain from T. thermophilus in complex with c-di-GMP. In addition, the structural dynamics of the complex was investigated in an {1H},15N-hetNOE experiment.
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Affiliation(s)
- Heiko Keller
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
| | - Kerstin Kruse
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Beate Averhoff
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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20
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Kaiser M, Hacker C, Duchardt-Ferner E, Wöhnert J. 1H, 13C, 15N backbone NMR resonance assignments for the rRNA methyltransferase Dim1 from the hyperthermophilic archaeon Pyrococcus horikoshii. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:309-314. [PMID: 31069720 DOI: 10.1007/s12104-019-09897-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
The protein dimethyladenosine transferase 1 (Dim1) is a highly conserved protein occurring in organisms ranging from bacteria such as E. coli where it is named KsgA to humans. Since Dim1 is involved in the biogenesis of the small ribosomal subunit it is an essential protein. During ribosome biogenesis Dim1 acts as an rRNA modification enzyme and dimethylates two adjacent adenosine residues of the small ribosomal subunit rRNA. In eukaryotes it is also required to ensure the proper endonucleolytic processing of the small ribosomal subunit rRNA precursor. Recently, a third function was proposed for eukaryotic Dim1. Karbstein and coworkers suggested that Dim1 interacts with the essential ribosome assembly factor Fap7 and that Fap7 is responsible for the dissociation of Dim1 from the nascent small ribosomal subunit. Here, we report the backbone 1H, 13C and 15N NMR resonance assignments for the 30.9 kDa Dim1 homologue from the hyperthermophilic archaeon Pyrococcus horikoshii (PhDim1) as a prerequisite for a detailed structural investigation of the PhDim1/PhFap7 interaction.
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Affiliation(s)
- Marco Kaiser
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
| | - Carolin Hacker
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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21
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Heiby JC, Goretzki B, Johnson CM, Hellmich UA, Neuweiler H. Methionine in a protein hydrophobic core drives tight interactions required for assembly of spider silk. Nat Commun 2019; 10:4378. [PMID: 31558722 PMCID: PMC6763431 DOI: 10.1038/s41467-019-12365-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023] Open
Abstract
Web spiders connect silk proteins, so-called spidroins, into fibers of extraordinary toughness. The spidroin N-terminal domain (NTD) plays a pivotal role in this process: it polymerizes spidroins through a complex mechanism of dimerization. Here we analyze sequences of spidroin NTDs and find an unusually high content of the amino acid methionine. We simultaneously mutate all methionines present in the hydrophobic core of a spidroin NTD from a nursery web spider’s dragline silk to leucine. The mutated NTD is strongly stabilized and folds at the theoretical speed limit. The structure of the mutant is preserved, yet its ability to dimerize is substantially impaired. We find that side chains of core methionines serve to mobilize the fold, which can thereby access various conformations and adapt the association interface for tight binding. Methionine in a hydrophobic core equips a protein with the capacity to dynamically change shape and thus to optimize its function. Spider silk is of interest in material science research. Here the authors show that the tight binding of a spider silk protein domain relies on the amino acid methionine, which is abundant in the domain core where it facilitates dynamic shape adaption of the binding interface.
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Affiliation(s)
- Julia C Heiby
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Benedikt Goretzki
- Institute for Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany.,Center for Biomolecular Magnetic Resonance, Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Christopher M Johnson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ute A Hellmich
- Institute for Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany. .,Center for Biomolecular Magnetic Resonance, Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
| | - Hannes Neuweiler
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074, Würzburg, Germany.
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22
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Toyama Y, Shimada I. Frequency selective coherence transfer NMR spectroscopy to study the structural dynamics of high molecular weight proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 304:62-77. [PMID: 31129430 DOI: 10.1016/j.jmr.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/05/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Multidimensional nuclear magnetic resonance (NMR) spectroscopy has enabled detailed characterizations of protein structures and dynamics that are closely linked to functions. However, it leads to a large sensitivity loss in applications to high molecular weight proteins, which is caused by spin relaxation during the frequency discrimination period in the indirect dimension. Here, we describe a selective coherence transfer scheme, which enables us to selectively observe 1H nuclei bonded to 15N or 13C nuclei with specified resonance frequencies. By utilizing this scheme, we achieved a 2.5- to 6-fold increase in signal height per unit of time with this scheme by avoiding the relaxation loss in the indirect dimension, as compared to the conventional two-dimensional heteronuclear correlation spectroscopy. We also demonstrated the effectiveness of this approach with applications to the membrane protein KirBac1.1, and characterized the functionally relevant conformational exchange process in both detergent micelles and a reconstituted membrane environment, corresponding to the apparent molecular masses of 220 kDa and 300 kDa, respectively.
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Affiliation(s)
- Yuki Toyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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23
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Löhr F, Gebel J, Henrich E, Hein C, Dötsch V. Towards complete polypeptide backbone NH assignment via combinatorial labeling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 302:50-63. [PMID: 30959416 DOI: 10.1016/j.jmr.2019.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Combinatorial selective isotope labeling is a valuable tool to facilitate polypeptide backbone resonance assignment in cases of low sensitivity or extensive chemical shift degeneracy. It involves recording of 15N-HSQC and 2D HN-projections of triple-resonance spectra on a limited set of samples containing different combinations of labeled and unlabeled amino acid types. Using labeling schemes in which the three backbone heteronuclei (amide nitrogen, α-carbon and carbonyl carbon) are enriched in 15N or 13C isotopes - individually as well as simultaneously - usually yields abundant amino-acid type information of consecutive residues i and i - 1. Although this results in a large number of anchor points that can be used in the sequential assignment process, for most amide signals the exact positioning of the corresponding residue the polypeptide sequence still relies on matching intra- and interresidual 13C chemical shifts obtained from 3D spectra. An obvious way to obtain more sequence-specific assignments directly with combinatorial labeling would be to increase the number of samples. This is, however, undesirable because of increased sample preparation efforts and costs. Irrespective of the number of samples, unambiguous assignments cannot be accomplished for i - 1/i pairs that are not unique in the sequence. Here we show that the ambiguity for non-unique pairs can be resolved by including information about the labeling state of residues i + 1 and i - 2. Application to a 35-residue peptide resulted in complete assignments of all detectable signals in the 15N HSQC which, due to its repetitive sequence and 13C chemical shift degeneracies, was difficult to achieve by other means. For a medium-sized protein (165 residues, rotational correlation time 8.2 ns) the improved protocol allowed the extent of backbone amide assignment to be expanded to 88% solely using a suite of 2D 1H-15N correlated spectra.
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Affiliation(s)
- Frank Löhr
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jakob Gebel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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24
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Henrich E, Löhr F, Mezhyrova J, Laguerre A, Bernhard F, Dötsch V. Synthetic Biology-Based Solution NMR Studies on Membrane Proteins in Lipid Environments. Methods Enzymol 2018; 614:143-185. [PMID: 30611423 DOI: 10.1016/bs.mie.2018.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although membrane proteins are in the focus of biochemical research for many decades the general knowledge of this important class is far behind soluble proteins. Despite several recent technical developments, the most challenging feature still is the generation of high-quality samples in environments suitable for the selected application. Reconstitution of membrane proteins into lipid bilayers will generate the most native-like environment and is therefore commonly desired. However, it poses tremendous problems to solution-state NMR analysis due to the dramatic increase in particle size resulting in high rotational correlation times. Nevertheless, a few promising strategies for the solution NMR analysis of membrane inserted proteins are emerging and will be discussed in this chapter. We focus on the generation of membrane protein samples in nanodisc membranes by cell-free systems and will describe the characteristic advantages of that platform in providing tailored protein expression and folding environments. We indicate frequent problems that have to be overcome in cell-free synthesis, nanodisc preparation, and customization for samples dedicated for solution-state NMR. Detailed instructions for sample preparation are given, and solution NMR approaches suitable for membrane proteins in bilayers are compiled. We further discuss the current strategies applied for signal detection from such difficult samples and describe the type of information that can be extracted from the various experiments. In summary, a comprehensive guideline for the analysis of membrane proteins in native-like membrane environments by solution-state NMR techniques will be provided.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Julija Mezhyrova
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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25
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Brockerman JA, Okon M, Withers SG, McIntosh LP. The pK a values of the catalytic residues in the retaining glycoside hydrolase T26H mutant of T4 lysozyme. Protein Sci 2018; 28:620-632. [PMID: 30537432 DOI: 10.1002/pro.3562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/24/2022]
Abstract
T4 phage lysozyme (T4L) is an enzyme that cleaves bacterial cell wall peptidoglycan. Remarkably, the single substitution of the active site Thr26 to a His (T26H) converts T4L from an inverting to a retaining glycoside hydrolase with transglycosylase activity. It has been proposed that T26H-T4L follows a double displacement mechanism with His26 serving as a nucleophile to form a covalent glycosyl-enzyme intermediate (Kuroki et al., PNAS 1999; 96:8949-8954). To gain further insights into this or alternative mechanisms, we used NMR spectroscopy to measure the acid dissociation constants (pKa values) and/or define the ionization states of the Asp, Glu, His, and Arg residues in the T4L mutant. Most notably, the pKa value of the putative nucleophile His26 is 6.8 ± 0.1, whereas that of the general acid Glu11 is 4.7 ± 0.1. If the proposed mechanism holds true, then T26H-T4L follows a reverse protonation pathway in which only a minor population of the free enzyme is in its catalytically competent ionization state with His26 deprotonated and Glu11 protonated. Our studies also confirm that all arginines in T26H-T4L, including the active site Arg145, are positively charged under neutral pH conditions. BRIEF STATEMENT: The replacement of a single amino acid changes T4 lysozyme from an inverting to a retaining glycoside hydrolase. Using NMR spectroscopy, we measured the pKa values of the ionizable residues in the active site of this mutant enzyme. Along with previously reported data, these results provide important constraints for understanding the catalytic mechanisms by which the wild-type and mutant form of T4 lysozyme cleave bacterial peptidoglycan.
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Affiliation(s)
- Jacob A Brockerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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26
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Asampille G, Verma BK, Swain M, Shettar A, Rosenzweig SA, Kondaiah P, Atreya HS. An ultra-stable redox-controlled self-assembling polypeptide nanotube for targeted imaging and therapy in cancer. J Nanobiotechnology 2018; 16:101. [PMID: 30526620 PMCID: PMC6286583 DOI: 10.1186/s12951-018-0427-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/24/2018] [Indexed: 01/10/2023] Open
Abstract
We introduce a self-assembling polypeptide-based nanotube system having the ability to specifically target cancer cells. The nanotubes target the cancer cell surface through integrin engagement with the help of multiple RGD units present along their surface. While the nanotubes are non-toxic towards cells in general, they can be loaded with suitable drugs to be released in a sustained manner in cancer cells. In addition, the nanotubes can be utilized for cellular imaging using any covalently tagged fluorescent dye. They are stable over a wide range of temperature due to intermolecular disulphide bonds formed during the self-assembly process. At the same time, presence of disulphide bonds provides a redox molecular switch for their degradation. Taken together this system provides a unique avenue for multimodal formulation in cancer therapy.
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Affiliation(s)
- Gitanjali Asampille
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India.,Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Brijesh Kumar Verma
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Monalisa Swain
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India.,Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012, India.,Basic Research Laboratory, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Abhijith Shettar
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.,Biotechnology Engineering, Ramaiah Institute of Technology, Bangalore, Karnataka, 560054, India
| | - Steven A Rosenzweig
- Department of Cell and Molecular Pharmacology, & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Paturu Kondaiah
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.
| | - Hanudatta S Atreya
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India.
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Stetz MA, Caro JA, Kotaru S, Yao X, Marques BS, Valentine KG, Wand AJ. Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation. Methods Enzymol 2018; 615:237-284. [PMID: 30638531 PMCID: PMC6364297 DOI: 10.1016/bs.mie.2018.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Recent studies suggest that the fast timescale motion of methyl-bearing side chains may play an important role in mediating protein activity. These motions have been shown to encapsulate the residual conformational entropy of the folded state that can potentially contribute to the energetics of protein function. Here, we provide an overview of how to characterize these motions using nuclear magnetic resonance (NMR) spin relaxation methods. The strengths and limitations of several techniques are highlighted in order to assist with experimental design. Particular emphasis is placed on the practical aspects of sample preparation, data collection, data fitting, and statistical analysis. Additionally, discussion of the recently refined "entropy meter" is presented and its use in converting NMR observables to conformational entropy is illustrated. Taken together, these methods should yield new insights into the complex interplay between structure and dynamics in protein function.
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Affiliation(s)
- Matthew A Stetz
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - José A Caro
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sravya Kotaru
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Xuejun Yao
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bryan S Marques
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kathleen G Valentine
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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28
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29
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Immer C, Hacker C, Wöhnert J. NMR resonance assignments for a ProQ homolog from Legionella pneumophila. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:319-322. [PMID: 29934867 DOI: 10.1007/s12104-018-9831-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/20/2018] [Indexed: 05/20/2023]
Abstract
Regulation of gene expression on a post-transcriptional level by small non-coding regulatory RNAs (sRNAs) is very common in bacteria. sRNAs base pair with sequences in their target messenger RNAs (mRNAs) and thereby regulate translation initiation or mRNA stability. Specialized RNA-binding proteins (RBPs) facilitate these regulatory sRNA/mRNA interactions by acting as RNA chaperones. A well-known example for such an RNA chaperone which is widespread in bacteria is the Hfq protein. Recently, the ProQ/FinO protein family was identified as a new class of RNA chaperones involved in sRNA based regulation. Only a few members of this protein family have been structurally characterized so far. In particular, the structural basis for RNA-binding and recognition has not yet been established for this class of proteins. Here, we report the 1H, 13C and 15N NMR resonance assignments for a ProQ homolog (Lpp 1663) from the gram-negative pathogenic bacterium Legionella pneumophila which will facilitate further structural and dynamic studies of this protein and its interaction with RNA targets.
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Affiliation(s)
- Carina Immer
- Institute for Molecular Biosciences, Goethe University Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
| | - Carolin Hacker
- Institute for Molecular Biosciences, Goethe University Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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30
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Hartmann JB, Zahn M, Burmann IM, Bibow S, Hiller S. Sequence-Specific Solution NMR Assignments of the β-Barrel Insertase BamA to Monitor Its Conformational Ensemble at the Atomic Level. J Am Chem Soc 2018; 140:11252-11260. [PMID: 30125090 DOI: 10.1021/jacs.8b03220] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
β-barrel outer membrane proteins (Omps) are key functional components of the outer membranes of Gram-negative bacteria, mitochondria, and plastids. In bacteria, their biogenesis requires the β-barrel-assembly machinery (Bam) with the central insertase BamA, but the exact translocation and insertion mechanism remains elusive. The BamA insertase features a loosely closed gating region between the first and last β-strand 16. Here, we describe ∼70% complete sequence-specific NMR resonance assignments of the transmembrane region of the BamA β-barrel in detergent micelles. On the basis of the assignments, NMR spectra show that the BamA barrel populates a conformational ensemble in slow exchange equilibrium, both in detergent micelles and lipid bilayer nanodiscs. Individual conformers can be selected from the ensemble by the introduction of a C-terminal strand extension, single-point mutations, or specific disulfide cross-linkings, and these modifications at the barrel seam are found to be allosterically coupled to sites at the entire barrel circumference. The resonance assignment provides a platform for mechanistic studies of BamA at atomic resolution, as well as for investigating interactions with potential antibiotic drugs and partner proteins.
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Affiliation(s)
| | - Michael Zahn
- Biozentrum , University of Basel , Klingelbergstrasse 70 , 4056 Basel , Switzerland
| | | | - Stefan Bibow
- Biozentrum , University of Basel , Klingelbergstrasse 70 , 4056 Basel , Switzerland
| | - Sebastian Hiller
- Biozentrum , University of Basel , Klingelbergstrasse 70 , 4056 Basel , Switzerland
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31
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Bergeron JRC, Brockerman JA, Vuckovic M, Deng W, Okon M, Finlay BB, McIntosh LP, Strynadka NCJ. Characterization of the two conformations adopted by the T3SS inner-membrane protein PrgK. Protein Sci 2018; 27:1680-1691. [PMID: 30095200 DOI: 10.1002/pro.3447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 11/07/2022]
Abstract
The pathogenic bacterium Salmonella enterica serovar Typhimurium utilizes two type III secretion systems (T3SS) to inject effector proteins into target cells upon infection. The T3SS secretion apparatus (the injectisome) is a large macromolecular assembly composed of over twenty proteins, many in highly oligomeric states. A sub-structure of the injectisome, termed the basal body, spans both membranes and the periplasmic space of the bacterium. It is primarily composed of three integral membranes proteins, InvG, PrgH, and PrgK, that form ring structures through which components are secreted. In particular, PrgK possesses a periplasmic region consisting of two globular domains joined by a linker polypeptide. We showed previously that in isolation, this region adopts two distinct conformations, of with only one is observed in the assembled basal body complex. Here, using NMR spectroscopy, we further characterize these two conformations. In particular, we demonstrate that the interaction of the linker region with the first globular domain, as found in the intact basal body, is dependent upon the cis conformation of the Leu77-Pro78 peptide. Furthermore, this interaction is pH-dependent due to coupling with hydrogen bond formation between Tyr75 and His42 in its neutral Nδ1 H tautomeric form. This pH-dependent interaction may play a role in the regulation of the secretion apparatus disassembly in the context of bacterial infection.
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Affiliation(s)
- Julien R C Bergeron
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jacob A Brockerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wanyin Deng
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - B Brett Finlay
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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32
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Accessing Structure, Dynamics and Function of Biological Macromolecules by NMR Through Advances in Isotope Labeling. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0085-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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Lacabanne D, Meier BH, Böckmann A. Selective labeling and unlabeling strategies in protein solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2018; 71:141-150. [PMID: 29197975 DOI: 10.1007/s10858-017-0156-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 06/07/2023]
Abstract
Selective isotope labeling is central in NMR experiments and often allows to push the limits on the systems investigated. It has the advantage to supply additional resolution by diminishing the number of signals in the spectra. This is particularly interesting when dealing with the large protein systems which are currently becoming accessible to solid-state NMR studies. Isotope labeled proteins for NMR experiments are most often expressed in E. coli systems, where bacteria are grown in minimal media supplemented with 15NH4Cl and 13C-glucose as sole source of nitrogen and carbon. For amino acids selective labeling or unlabeling, specific amino acids are supplemented in the minimal medium. The aim is that they will be incorporated in the protein by the bacteria. However, E. coli amino-acid anabolism and catabolism tend to interconnect different pathways, remnant of a subway system. These connections lead to inter conversion between amino acids, called scrambling. A thorough understanding of the involved pathways is thus important to obtain the desired labeling schemes, as not all combinations of amino acids are adapted. We present here a detailed overview of amino-acid metabolism in this context. Each amino-acid pathway is described in order to define accessible combinations for 13C or 15N specific labeling or unlabeling. Using as example the ABC transporter BmrA, a membrane protein of 600 residues, we demonstrate how these strategies can be applied. Indeed, even though there is no size limit in solid-state NMR, large (membrane) proteins are still a challenge due to heavy signal overlap. To initiate resonance assignment in these large systems, we describe how selectively labeled samples can be obtained with the addition of labeled or unlabeled amino acids in the medium. The reduced spectral overlap enabled us to identify typical spectral fingerprints and to initiate sequential assignment using the more sensitive 2D DARR experiments with long mixing time showing inter-residue correlations.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
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34
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Sugiki T, Furuita K, Fujiwara T, Kojima C. Amino Acid Selective 13C Labeling and 13C Scrambling Profile Analysis of Protein α and Side-Chain Carbons in Escherichia coli Utilized for Protein Nuclear Magnetic Resonance. Biochemistry 2018; 57:3576-3589. [PMID: 29924600 DOI: 10.1021/acs.biochem.8b00182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid selective isotope labeling is an important nuclear magnetic resonance technique, especially for larger proteins, providing strong bases for the unambiguous resonance assignments and information concerning the structure, dynamics, and intermolecular interactions. Amino acid selective 15N labeling suffers from isotope dilution caused by metabolic interconversion of the amino acids, resulting in isotope scrambling within the target protein. Carbonyl 13C atoms experience less isotope scrambling than the main-chain 15N atoms do. However, little is known about the side-chain 13C atoms. Here, the 13C scrambling profiles of the Cα and side-chain carbons were investigated for 15N scrambling-prone amino acids, such as Leu, Ile, Tyr, Phe, Thr, Val, and Ala. The level of isotope scrambling was substantially lower in 13Cα and 13C side-chain labeling than in 15N labeling. We utilized this reduced scrambling-prone character of 13C as a simple and efficient method for amino acid selective 13C labeling using an Escherichia coli cold-shock expression system and high-cell density fermentation. Using this method, the 13C labeling efficiency was >80% for Leu and Ile, ∼60% for Tyr and Phe, ∼50% for Thr, ∼40% for Val, and 30-40% for Ala. 1H-15N heteronuclear single-quantum coherence signals of the 15N scrambling-prone amino acid were also easily filtered using 15N-{13Cα} spin-echo difference experiments. Our method could be applied to the assignment of the 55 kDa protein.
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Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Kyoko Furuita
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Chojiro Kojima
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan.,Graduate School of Engineering Science , Yokohama National University , 79-5 Tokiwadai , Hodogaya-ku, Yokohama 240-8501 , Japan
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35
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Structure determination of protein-ligand complexes by NMR in solution. Methods 2018; 138-139:3-25. [DOI: 10.1016/j.ymeth.2018.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/24/2018] [Accepted: 01/29/2018] [Indexed: 11/18/2022] Open
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36
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Hoffmann B, Löhr F, Laguerre A, Bernhard F, Dötsch V. Protein labeling strategies for liquid-state NMR spectroscopy using cell-free synthesis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 105:1-22. [PMID: 29548364 DOI: 10.1016/j.pnmrs.2017.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 05/17/2023]
Abstract
Preparation of a protein sample for liquid-state nuclear magnetic resonance (NMR) spectroscopy analysis requires optimization of many parameters. This review describes labeling strategies for obtaining assignments of protein resonances. Particular emphasis is placed on the advantages of cell-free protein production, which enables exclusive labeling of the protein of interest, thereby simplifying downstream processing steps and increasing the availability of different labeling strategies for a target protein. Furthermore, proteins can be synthesized in milligram yields, and the open nature of the cell-free system allows the addition of stabilizers, scrambling inhibitors or hydrophobic solubilization environments directly during the protein synthesis, which is especially beneficial for membrane proteins. Selective amino acid labeling of the protein of interest, the possibility of addressing scrambling issues and avoiding the need for labile amino acid precursors have been key factors in enabling the introduction of new assignment strategies based on different labeling schemes as well as on new pulse sequences. Combinatorial selective labeling methods have been developed to reduce the number of protein samples necessary to achieve a complete backbone assignment. Furthermore, selective labeling helps to decrease spectral overlap and overcome size limitations for solution NMR analysis of larger complexes, oligomers, intrinsically disordered proteins and membrane proteins.
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Affiliation(s)
- Beate Hoffmann
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
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37
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Howard RJ, Carnevale V, Delemotte L, Hellmich UA, Rothberg BS. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:927-942. [PMID: 29258839 DOI: 10.1016/j.bbamem.2017.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/08/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022]
Abstract
Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Rebecca J Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden.
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden.
| | - Ute A Hellmich
- Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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38
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Wagner A, Diehl E, Krauth-Siegel RL, Hellmich UA. Backbone NMR assignments of tryparedoxin, the central protein in the hydroperoxide detoxification cascade of African trypanosomes, in the oxidized and reduced form. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:193-196. [PMID: 28573456 DOI: 10.1007/s12104-017-9746-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Tryparedoxin (Tpx) is a pivotal protein in the redox-metabolism of trypanosomatid parasites. Tpx has previously been identified as a potential target for drug development in the fight against human African sleeping sickness caused by Trypanosoma brucei. Tpx belongs to the thioredoxin superfamily and acts as an oxidoreductase in the parasite's cytoplasm. It contains a WCPPC active site motif, which enables the protein to undergo thiol-disulfide exchange. To promote future protein-drug interaction analyses, we report the 1H, 13C and 15N backbone chemical shift assignments for both the oxidized and reduced states of Tpx. The redox state of the protein has a significant impact on the chemical shifts of the residues at the active site of the protein, especially on the two redox active site cysteines. The NMR assignments presented here will be a prerequisite for investigating drug binding to Tpx in molecular detail and to drive further drug optimization.
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Affiliation(s)
- Annika Wagner
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Erika Diehl
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - R Luise Krauth-Siegel
- Biochemie-Zentrum, Universität Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Ute A Hellmich
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438, Frankfurt am Main, Germany.
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Perell GT, Mishra NK, Sudhamalla B, Ycas PD, Islam K, Pomerantz WCK. Specific Acetylation Patterns of H2A.Z Form Transient Interactions with the BPTF Bromodomain. Biochemistry 2017; 56:4607-4615. [PMID: 28771339 PMCID: PMC5779092 DOI: 10.1021/acs.biochem.7b00648] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational lysine acetylation of histone tails affects both chromatin accessibility and recruitment of multifunctional bromodomain-containing proteins for modulating transcription. The bromodomain- and PHD finger-containing transcription factor (BPTF) regulates transcription but has also been implicated in high gene expression levels in a variety of cancers. In this report, the histone variant H2A.Z, which replaces H2A in chromatin, is evaluated for its affinity for BPTF with a specific recognition pattern of acetylated lysine residues of the N-terminal tail region. Although BPTF immunoprecipitates H2A.Z-containing nucleosomes, a direct interaction with its bromodomain has not been reported. Using protein-observed fluorine nuclear magnetic resonance (PrOF NMR) spectroscopy, we identified a diacetylation of H2A.Z on lysine residues 4 and 11, with the highest affinity for BPTF with a Kd of 780 μM. A combination of subsequent 1H NMR Carr-Purcell-Meiboom-Gill experiments and photo-cross-linking further confirmed the specificity of the diacetylation pattern at lysines 4 and 11. Because of an adjacent PHD domain, this transient interaction may contribute to a higher-affinity bivalent interaction. Further evaluation of specificity toward a set of bromodomains, including two BET bromodomains (Brd4 and BrdT) and two Plasmodium falciparum bromodomains, resulted in one midmicromolar affinity binder, PfGCN5 (Kd = 650 μM). With these biochemical experiments, we have identified a direct interaction of histone H2A.Z with bromodomains with a specific acetylation pattern that further supports the role of H2A.Z in epigenetic regulation.
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Affiliation(s)
- Gabriella T. Perell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Neeraj K. Mishra
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Babu Sudhamalla
- Department of Chemistry, University of Pittsburgh, 1307 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Peter D. Ycas
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, 1307 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
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40
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Hein C, Löhr F, Schwarz D, Dötsch V. Acceleration of protein backbone NMR assignment by combinatorial labeling: Application to a small molecule binding study. Biopolymers 2017; 107. [PMID: 28035667 DOI: 10.1002/bip.23013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022]
Abstract
Selective labeling with stable isotopes has long been recognized as a valuable tool in protein NMR to alleviate signal overlap and sensitivity limitations. In this study, combinatorial 15 N-, 13 Cα -, and 13 C'-selective labeling has been used during the backbone assignment of human cyclophilin D to explore binding of an inhibitor molecule. Using a cell-free expression system, a scheme that involves 15 N, 1-13 C, 2-13 C, fully 15 N/13 C, and unlabeled amino acids was optimized to gain a maximum of assignment information from three samples. This scheme was combined with time-shared triple-resonance NMR experiments, which allows a fast and efficient backbone assignment by giving the unambiguous assignment of unique amino acid pairs in the protein, the identity of ambiguous pairs and information about all 19 non-proline amino acid types. It is therefore well suited for binding studies where de novo assignments of amide 1 H and 15 N resonances need to be obtained, even in cases where sensitivity is the limiting factor.
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Affiliation(s)
- Christopher Hein
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
| | - Daniel Schwarz
- Merck KGaA, Discovery Pharmacology, Global Research and Development, Darmstadt, 64293, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
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41
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Weiergräber OH, Schwarten M, Strodel B, Willbold D. Investigating Structure and Dynamics of Atg8 Family Proteins. Methods Enzymol 2016; 587:115-142. [PMID: 28253952 DOI: 10.1016/bs.mie.2016.09.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Atg8 family members were the first autophagy-related proteins to be investigated in structural detail and continue to be among the best-understood molecules of the pathway. In this review, we will first provide a concise outline of the major methods that are being applied for structural characterization of these proteins and the complexes they are involved in. This includes a discussion of the strengths and limitations associated with each method, along with guidelines for successful adoption to a specific problem. Subsequently, we will present examples illustrating the application of these techniques, with a particular focus on the complementarity of information they provide.
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Affiliation(s)
- O H Weiergräber
- Institute of Complex Systems, ICS-6 (Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - M Schwarten
- Institute of Complex Systems, ICS-6 (Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - B Strodel
- Institute of Complex Systems, ICS-6 (Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - D Willbold
- Institute of Complex Systems, ICS-6 (Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie und BMFZ, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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42
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Urick AK, Calle LP, Espinosa JF, Hu H, Pomerantz WCK. Protein-Observed Fluorine NMR Is a Complementary Ligand Discovery Method to 1H CPMG Ligand-Observed NMR. ACS Chem Biol 2016; 11:3154-3164. [PMID: 27627661 PMCID: PMC8325173 DOI: 10.1021/acschembio.6b00730] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To evaluate its potential as a ligand discovery tool, we compare a newly developed 1D protein-observed fluorine NMR (PrOF NMR) screening method with the well-characterized ligand-observed 1H CPMG NMR screen. We selected the first bromodomain of Brd4 as a model system to benchmark PrOF NMR because of the high ligandability of Brd4 and the need for small molecule inhibitors of related epigenetic regulatory proteins. We compare the two methods' hit sensitivity, triaging ability, experiment speed, material consumption, and the potential for false positives and negatives. To this end, we screened 930 fragment molecules against Brd4 in mixtures of five and followed up these studies with mixture deconvolution and affinity characterization of the top hits. In selected examples, we also compare the environmental responsiveness of the 19F chemical shift to 1H in 1D-protein observed 1H NMR experiments. To address concerns of perturbations from fluorine incorporation, ligand binding trends and affinities were verified via thermal shift assays and isothermal titration calorimetry. We conclude that for the protein understudy here, PrOF NMR and 1H CPMG have similar sensitivity, with both being effective tools for ligand discovery. In cases where an unlabeled protein can be used, 1D protein-observed 1H NMR may also be effective; however, the 19F chemical shift remains significantly more responsive.
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Affiliation(s)
- Andrew K. Urick
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Luis Pablo Calle
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Centro de Investigación Lilly, 28108 Alcobendas, Madrid, Spain
| | - Juan F. Espinosa
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Centro de Investigación Lilly, 28108 Alcobendas, Madrid, Spain
| | - Haitao Hu
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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43
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Malik N, Kumar A. Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state. JOURNAL OF BIOMOLECULAR NMR 2016; 66:21-35. [PMID: 27586017 DOI: 10.1007/s10858-016-0054-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
NMR resonance assignment of intrinsically disordered proteins poses a challenge because of the limited dispersion of amide proton chemical shifts. This becomes even more complex with the increase in the size of the system. Residue specific selective labeling/unlabeling experiments have been used to resolve the overlap, but require multiple sample preparations. Here, we demonstrate an assignment strategy requiring only a single sample of uniformly labeled (13)C,(15)N-protein. We have used a combinatorial approach, involving 3D-HNN, CC(CO)NH and 2D-MUSIC, which allowed us to assign a denatured centromeric protein Cse4 of 229 residues. Further, we show that even the less sensitive experiments, when used in an efficient manner can lead to the complete assignment of a complex system without the use of specialized probes in a relatively short time frame. The assignment of the amino acids discloses the presence of local structural propensities even in the denatured state accompanied by restricted motion in certain regions that provides insights into the early folding events of the protein.
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Affiliation(s)
- Nikita Malik
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ashutosh Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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44
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Neti SS, Eckert DM, Poulter CD. Construction of Functional Monomeric Type 2 Isopentenyl Diphosphate:Dimethylallyl Diphosphate Isomerase. Biochemistry 2016; 55:4229-38. [PMID: 27379573 DOI: 10.1021/acs.biochem.6b00564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the isoprenoid biosynthetic pathway. The enzyme from Streptomyces pneumoniae (spIDI-2) is a homotetramer in solution with behavior, including a substantial increase in the rate of FMN reduction by NADPH in the presence of IPP, suggesting that substrate binding at one subunit alters the kinetic and binding properties of another. We now report the construction of catalytically active monomeric spIDI-2. The monomeric enzyme contains a single-point mutation (N37A) and a six-residue C-terminal deletion that preserves the secondary structure of the subunits in the wild-type (wt) homotetramer. UV-vis spectra of the enzyme-bound flavin mononucleotide (FMN) cofactor in FMNox, FMNred, and FMNred·IPP/DMAPP states are the same for monomeric and wt homotetrameric spIDI-2. The mutations in monomeric IDI-2 lower the melting temperature of the protein by 20 °C and reduce the binding affinities of FMN and IDI by 40-fold but have a minimal effect on kcat. Stopped-flow kinetic studies of monomeric spIDI-2 showed that the rate of reduction of FMN by NADH (k = 1.64 × 10(-3) s(-1)) is substantially faster when IPP is added to the monomeric enzyme (k = 0.57 s(-1)), similar to behavior seen for wt-spIDI-2. Our results indicate that cooperative interactions among subunits in the wt homotetramer are not responsible for the increased rate of reduction of spIDI-2·FMN by NADH, and two possible scenarios for the enhancement are suggested.
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Affiliation(s)
- Syam Sundar Neti
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Debra M Eckert
- Department of Biochemistry, University of Utah School of Medicine , Salt Lake City, Utah 84112, United States
| | - C Dale Poulter
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
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45
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Kumar A, Balakrishna AM, Nartey W, Manimekalai MSS, Grüber G. Redox chemistry of Mycobacterium tuberculosis alkylhydroperoxide reductase E (AhpE): Structural and mechanistic insight into a mycoredoxin-1 independent reductive pathway of AhpE via mycothiol. Free Radic Biol Med 2016; 97:588-601. [PMID: 27417938 DOI: 10.1016/j.freeradbiomed.2016.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/07/2016] [Accepted: 07/09/2016] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has the ability to persist within the human host for a long time in a dormant stage and re-merges when the immune system is compromised. The pathogenic bacterium employs an elaborate antioxidant defence machinery composed of the mycothiol- and thioredoxin system in addition to a superoxide dismutase, a catalase, and peroxiredoxins (Prxs). Among the family of Peroxiredoxins, Mtb expresses a 1-cysteine peroxiredoxin, known as alkylhydroperoxide reductase E (MtAhpE), and defined as a potential tuberculosis drug target. The reduced MtAhpE (MtAhpE-SH) scavenges peroxides to become converted to MtAhpE-SOH. To provide continuous availability of MtAhpE-SH, MtAhpE-SOH has to become reduced. Here, we used NMR spectroscopy to delineate the reduced (MtAhpE-SH), sulphenic (MtAhpE-SOH) and sulphinic (MtAhpE-SO2H) states of MtAhpE through cysteinyl-labelling, and provide for the first time evidence of a mycothiol-dependent mechanism of MtAhpE reduction. This is confirmed by crystallographic studies, wherein MtAhpE was crystallized in the presence of mycothiol and the structure was solved at 2.43Å resolution. Combined with NMR-studies, the crystallographic structures reveal conformational changes of important residues during the catalytic cycle of MtAhpE. In addition, alterations of the overall protein in solution due to redox modulation are observed by small angle X-ray scattering (SAXS) studies. Finally, by employing SAXS and dynamic light scattering, insight is provided into the most probable physiological oligomeric state of MtAhpE necessary for activity, being also discussed in the context of concerted substrate binding inside the dimeric MtAhpE.
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Affiliation(s)
- Arvind Kumar
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Asha Manikkoth Balakrishna
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | | | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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46
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Buhr F, Jha S, Thommen M, Mittelstaet J, Kutz F, Schwalbe H, Rodnina MV, Komar AA. Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations. Mol Cell 2016; 61:341-351. [PMID: 26849192 DOI: 10.1016/j.molcel.2016.01.008] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/12/2015] [Accepted: 12/24/2015] [Indexed: 11/26/2022]
Abstract
In all genomes, most amino acids are encoded by more than one codon. Synonymous codons can modulate protein production and folding, but the mechanism connecting codon usage to protein homeostasis is not known. Here we show that synonymous codon variants in the gene encoding gamma-B crystallin, a mammalian eye-lens protein, modulate the rates of translation and cotranslational folding of protein domains monitored in real time by Förster resonance energy transfer and fluorescence-intensity changes. Gamma-B crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain different conformations, as indicated by altered in vivo stability and in vitro protease resistance. 2D NMR spectroscopic data suggest that structural differences are associated with different cysteine oxidation states of the purified proteins, providing a link between translation, folding, and the structures of isolated proteins. Thus, synonymous codons provide a secondary code for protein folding in the cell.
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Affiliation(s)
- Florian Buhr
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Sujata Jha
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio 44115, USA
| | - Michael Thommen
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Joerg Mittelstaet
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Felicitas Kutz
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio 44115, USA.,Department of Biochemistry and Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
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47
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Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins. Proc Natl Acad Sci U S A 2016; 113:E3461-7. [PMID: 27247408 DOI: 10.1073/pnas.1603799113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Absolute values of protein expression levels in cells are crucial information for understanding cellular biological systems. Precise quantification of proteins can be achieved by liquid chromatography (LC)-mass spectrometry (MS) analysis of enzymatic digests of proteins in the presence of isotope-labeled internal standards. Thus, development of a simple and easy way for the preparation of internal standards is advantageous for the analyses of multiple target proteins, which will allow systems-level studies. Here we describe a method, termed MS-based Quantification By isotope-labeled Cell-free products (MS-QBiC), which provides the simple and high-throughput preparation of internal standards by using a reconstituted cell-free protein synthesis system, and thereby facilitates both multiplexed and sensitive quantification of absolute amounts of target proteins. This method was applied to a systems-level dynamic analysis of mammalian circadian clock proteins, which consist of transcription factors and protein kinases that govern central and peripheral circadian clocks in mammals. Sixteen proteins from 20 selected circadian clock proteins were successfully quantified from mouse liver over a 24-h time series, and 14 proteins had circadian variations. Quantified values were applied to detect internal body time using a previously developed molecular timetable method. The analyses showed that single time-point data from wild-type mice can predict the endogenous state of the circadian clock, whereas data from clock mutant mice are not applicable because of the disappearance of circadian variation.
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48
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To V, Dzananovic E, McKenna SA, O’Neil J. The Dynamic Landscape of the Full-Length HIV-1 Transactivator of Transcription. Biochemistry 2016; 55:1314-25. [DOI: 10.1021/acs.biochem.5b01178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vu To
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Edis Dzananovic
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A. McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Joe O’Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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49
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Dubey A, Kadumuri RV, Jaipuria G, Vadrevu R, Atreya HS. Rapid NMR Assignments of Proteins by Using Optimized Combinatorial Selective Unlabeling. Chembiochem 2016; 17:334-40. [DOI: 10.1002/cbic.201500513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Abhinav Dubey
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
- IISc Mathematics Initiative; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| | - Rajashekar Varma Kadumuri
- Department of Biological Sciences; Birla Institute of Technology and Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Garima Jaipuria
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences; Birla Institute of Technology and Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Hanudatta S. Atreya
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
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50
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Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. PLoS One 2015; 10:e0139695. [PMID: 26437229 PMCID: PMC4593582 DOI: 10.1371/journal.pone.0139695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 01/18/2023] Open
Abstract
We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was the most productive method. Phage display selections were performed on 265 in vivo biotinylated antigen domains. High-affinity Fabs (<20nM) were obtained for 196. We constructed and optimized a new expression vector to produce in vivo biotinylated Fabs in E. coli. This increased average yields up to 10-fold, with an average yield of 4 mg/L. For 118 antigens, we identified Fabs that could immunoprecipitate their full-length endogenous targets from mammalian cell lysates. One Fab for each antigen was converted to a recombinant IgG and produced in mammalian cells, with an average yield of 15 mg/L. In summary, we have optimized each step of the pipeline to produce recombinant antibodies, significantly increasing both efficiency and yield, and also showed that these Fabs and IgGs can be generally useful for chromatin immunoprecipitation (ChIP) protocols.
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Affiliation(s)
- Nan Zhong
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Mani Ravichandran
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Maria Fenner
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Anandi Bhattacharya
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Michal Olszewski
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Evan Dowdell
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Haiming Huang
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Vincent Nadeem
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Sachdev S. Sidhu
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jack F. Greenblatt
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, MSB-4180, Toronto, ON M5S 1A8, Canada
| | - Edyta Marcon
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
- * E-mail:
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