1
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Klein A, Vasa SK, Söldner B, Grohe K, Linser R. Unambiguous Side-Chain Assignments for Solid-State NMR Structure Elucidation of Nondeuterated Proteins via a Combined 5D/4D Side-Chain-to-Backbone Experiment. J Phys Chem Lett 2022; 13:1644-1651. [PMID: 35147439 DOI: 10.1021/acs.jpclett.1c04075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Owing to fast-magic-angle-spinning technology, proton-detected solid-state NMR has been facilitating the analysis of insoluble, crystalline, sedimented, and membrane proteins. However, potential applications have been largely restricted by limited access to side-chain resonances. The recent availability of spinning frequencies exceeding 100 kHz in principle now allows direct probing of all protons without the need for partial deuteration. This potentiates both the number of accessible target proteins and possibilities to exploit side-chain protons as reporters on distances and interactions. Their low dispersion, however, has severely compromised their chemical-shift assignment, which is a prerequisite for their use in downstream applications. Herein, we show that unambiguous correlations are obtained from 5D methodology by which the side-chain resonances are directly connected with the backbone. When further concatenated with simultaneous 4D intra-side-chain correlations, this yields comprehensive assignments in the side chains and hence allows a high density of distance restraints for high-resolution structure calculation from minimal amounts of protein.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Benedikt Söldner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Kristof Grohe
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
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2
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Klein A, Vasa SK, Linser R. Automated projection spectroscopy in solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2018; 72:163-170. [PMID: 30430291 DOI: 10.1007/s10858-018-0215-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Given that solid-state NMR is being used for protein samples of increasing molecular weight and complexity, higher-dimensionality methods are likely to be more and more indispensable for unambiguous chemical shift assignments in the near future. In addition, solid-state NMR spectral properties are increasingly comparable with solution NMR, allowing adaptation of more sophisticated solution NMR strategies for the solid state in addition to the conventional methodology. Assessing first principles, here we demonstrate the application of automated projection spectroscopy for a micro-crystalline protein in the solid state.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Center for Integrated Protein Science (CiPSM), Munich, Germany
| | - Suresh K Vasa
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Center for Integrated Protein Science (CiPSM), Munich, Germany
| | - Rasmus Linser
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
- Center for Integrated Protein Science (CiPSM), Munich, Germany.
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany.
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3
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Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra. Nat Commun 2018; 9:384. [PMID: 29374165 PMCID: PMC5786013 DOI: 10.1038/s41467-017-02592-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 12/12/2017] [Indexed: 12/22/2022] Open
Abstract
Automated methods for NMR structure determination of proteins are continuously becoming more robust. However, current methods addressing larger, more complex targets rely on analyzing 6-10 complementary spectra, suggesting the need for alternative approaches. Here, we describe 4D-CHAINS/autoNOE-Rosetta, a complete pipeline for NOE-driven structure determination of medium- to larger-sized proteins. The 4D-CHAINS algorithm analyzes two 4D spectra recorded using a single, fully protonated protein sample in an iterative ansatz where common NOEs between different spin systems supplement conventional through-bond connectivities to establish assignments of sidechain and backbone resonances at high levels of completeness and with a minimum error rate. The 4D-CHAINS assignments are then used to guide automated assignment of long-range NOEs and structure refinement in autoNOE-Rosetta. Our results on four targets ranging in size from 15.5 to 27.3 kDa illustrate that the structures of proteins can be determined accurately and in an unsupervised manner in a matter of days.
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4
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Żerko S, Byrski P, Włodarczyk-Pruszyński P, Górka M, Ledolter K, Masliah E, Konrat R, Koźmiński W. Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein. JOURNAL OF BIOMOLECULAR NMR 2016; 65:193-203. [PMID: 27430223 PMCID: PMC4983291 DOI: 10.1007/s10858-016-0048-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/09/2016] [Indexed: 05/04/2023]
Abstract
New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.
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Affiliation(s)
- Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
| | - Piotr Byrski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
| | | | - Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
- Section of Biophysics, Faculty of Physics, University of Warsaw, 02093, Warsaw, Poland
| | - Karin Ledolter
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Eliezer Masliah
- Departments of Neuroscience and Pathology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Konrat
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland.
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5
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Flamm AG, Żerko S, Zawadzka-Kazimierczuk A, Koźmiński W, Konrat R, Coudevylle N. 1H, 15N, 13C resonance assignment of human GAP-43. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:171-174. [PMID: 26748655 PMCID: PMC4788685 DOI: 10.1007/s12104-015-9660-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/28/2015] [Indexed: 05/31/2023]
Abstract
GAP-43 is a 25 kDa neuronal intrinsically disordered protein, highly abundant in the neuronal growth cone during development and regeneration. The exact molecular function(s) of GAP-43 remains unclear but it appears to be involved in growth cone guidance and actin cytoskeleton organization. Therefore, GAP-43 seems to play an important role in neurotransmitter vesicle fusion and recycling, long-term potentiation, spatial memory formation and learning. Here we report the nearly complete assignment of recombinant human GAP-43.
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Affiliation(s)
- Andrea Gabriele Flamm
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Anna Zawadzka-Kazimierczuk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Robert Konrat
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Nicolas Coudevylle
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria.
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6
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Nowakowski M, Saxena S, Stanek J, Żerko S, Koźmiński W. Applications of high dimensionality experiments to biomolecular NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 90-91:49-73. [PMID: 26592945 DOI: 10.1016/j.pnmrs.2015.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/03/2015] [Accepted: 07/03/2015] [Indexed: 05/23/2023]
Abstract
High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable time. In this review we present and compare some significant applications of NMR experiments of dimensionality higher than three in the field of biomolecular studies in solution.
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Affiliation(s)
- Michał Nowakowski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Saurabh Saxena
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Jan Stanek
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Szymon Żerko
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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7
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Platzer G, Żerko S, Saxena S, Koźmiński W, Konrat R. (1)H, (15)N, (13)C resonance assignment of human osteopontin. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:289-292. [PMID: 25616494 PMCID: PMC4568010 DOI: 10.1007/s12104-014-9594-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/03/2014] [Indexed: 06/04/2023]
Abstract
Osteopontin (OPN) is a 33.7 kDa intrinsically disordered protein and a member of the SIBLING family of proteins. OPN is bearing a signal peptide for secretion into the extracellular space, where it exerts its main physiological function, the control of calcium biomineralization. It is often involved in tumorigenic processes influencing proliferation, migration and survival, as well as the adhesive properties of cancer cells via CD44 and integrin signaling pathways. Here we report the nearly complete NMR chemical shift assignment of recombinant human osteopontin.
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Affiliation(s)
- Gerald Platzer
- Max F. Perutz Laboratories, Department of Computational and Structural Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria.
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Saurabh Saxena
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Robert Konrat
- Max F. Perutz Laboratories, Department of Computational and Structural Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria.
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8
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Ueda T, Yoshiura C, Matsumoto M, Kofuku Y, Okude J, Kondo K, Shiraishi Y, Takeuchi K, Shimada I. Development of a method for reconstruction of crowded NMR spectra from undersampled time-domain data. JOURNAL OF BIOMOLECULAR NMR 2015; 62:31-41. [PMID: 25677224 PMCID: PMC4432090 DOI: 10.1007/s10858-015-9908-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/07/2015] [Indexed: 05/27/2023]
Abstract
NMR is a unique methodology for obtaining information about the conformational dynamics of proteins in heterogeneous biomolecular systems. In various NMR methods, such as transferred cross-saturation, relaxation dispersion, and paramagnetic relaxation enhancement experiments, fast determination of the signal intensity ratios in the NMR spectra with high accuracy is required for analyses of targets with low yields and stabilities. However, conventional methods for the reconstruction of spectra from undersampled time-domain data, such as linear prediction, spectroscopy with integration of frequency and time domain, and analysis of Fourier, and compressed sensing were not effective for the accurate determination of the signal intensity ratios of the crowded two-dimensional spectra of proteins. Here, we developed an NMR spectra reconstruction method, "conservation of experimental data in analysis of Fourier" (Co-ANAFOR), to reconstruct the crowded spectra from the undersampled time-domain data. The number of sampling points required for the transferred cross-saturation experiments between membrane proteins, photosystem I and cytochrome b 6 f, and their ligand, plastocyanin, with Co-ANAFOR was half of that needed for linear prediction, and the peak height reduction ratios of the spectra reconstructed from truncated time-domain data by Co-ANAFOR were more accurate than those reconstructed from non-uniformly sampled data by compressed sensing.
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Affiliation(s)
- Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0075 Japan
| | - Chie Yoshiura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masahiko Matsumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Japan Biological Informatics Consortium, Aomi, Koto-ku, Tokyo, 135-8073 Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Koh Takeuchi
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0075 Japan
- Molecular Profiling Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo, 135-0064 Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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9
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Brutscher B, Felli IC, Gil-Caballero S, Hošek T, Kümmerle R, Piai A, Pierattelli R, Sólyom Z. NMR Methods for the Study of Instrinsically Disordered Proteins Structure, Dynamics, and Interactions: General Overview and Practical Guidelines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:49-122. [PMID: 26387100 DOI: 10.1007/978-3-319-20164-1_3] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thanks to recent improvements in NMR instrumentation, pulse sequence design, and sample preparation, a panoply of new NMR tools has become available for atomic resolution characterization of intrinsically disordered proteins (IDPs) that are optimized for the particular chemical and spectroscopic properties of these molecules. A wide range of NMR observables can now be measured on increasingly complex IDPs that report on their structural and dynamic properties in isolation, as part of a larger complex, or even inside an entire living cell. Herein we present basic NMR concepts, as well as optimised tools available for the study of IDPs in solution. In particular, the following sections are discussed hereafter: a short introduction to NMR spectroscopy and instrumentation (Sect. 3.1), the effect of order and disorder on NMR observables (Sect. 3.2), particular challenges and bottlenecks for NMR studies of IDPs (Sect. 3.3), 2D HN and CON NMR experiments: the fingerprint of an IDP (Sect. 3.4), tools for overcoming major bottlenecks of IDP NMR studies (Sect. 3.5), 13C detected experiments (Sect. 3.6), from 2D to 3D: from simple snapshots to site-resolved characterization of IDPs (Sect. 3.7), sequential NMR assignment: 3D experiments (Sect. 3.8), high-dimensional NMR experiments (nD, with n>3) (Sect. 3.9) and conclusions and perspectives (Sect. 3.10).
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Affiliation(s)
- Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France.
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | | | - Tomáš Hošek
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Rainer Kümmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Alessandro Piai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | - Zsófia Sólyom
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France
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10
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Krähenbühl B, Lukavsky P, Wider G. Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10. JOURNAL OF BIOMOLECULAR NMR 2014; 59:231-40. [PMID: 24899400 DOI: 10.1007/s10858-014-9841-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/27/2014] [Indexed: 05/15/2023]
Abstract
A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [(13)C, (15)N]-labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3 mM sample of an RNA stem-loop with 48 nucleotides, K10, which is responsible for dynein-mediated localization of Drosophila fs(1)K10 mRNA transcripts. The automated analysis of the APSY data led to highly accurate and precise 3- to 4-dimensional peak lists. They provided a reliable basis for the subsequent sequence-specific resonance assignment with the algorithm FLYA and resulted in the fully automated resonance assignment of more than 80 % of the resonances of the (13)C-(1)H moieties at the 1', 2', 5, 6, and 8 positions in the nucleotides. The procedure was robust with respect to numerous impurity peaks, low concentration of this for NMR comparably large RNA, and structural features such as a loop, single-nucleotide bulges and a non-Watson-Crick wobble base pairs. Currently, there is no precise chemical shift statistics (as used by FLYA) for RNA regions which deviate from the regular A-form helical structure. Reliable and precise peak lists are thus required for automated sequence-specific assignment, as provided by APSY.
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Affiliation(s)
- Barbara Krähenbühl
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
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11
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Kovacs H, Gossert A. Improved NMR experiments with ¹³C-isotropic mixing for assignment of aromatic and aliphatic side chains in labeled proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 58:101-112. [PMID: 24390406 DOI: 10.1007/s10858-013-9808-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/20/2013] [Indexed: 06/03/2023]
Abstract
Three improved ¹³C-spinlock experiments for side chain assignments of isotope labelled proteins in liquid state are presented. These are based on wide bandwidth spinlock techniques that have become possible with contemporary cryogenic probes. The first application, the H(C(ali)C(aro))H-TOCSY, is an HCCH-TOCSY in which all CHn moieties of a protein are detected in a single experiment, including the aromatic ones. This enables unambiguous assignment of aromatic and aliphatic amino acids in a single, highly sensitive experiment. In the second application, the ¹³C-detected C(all)-TOCSY, magnetization transfer comprises all carbons--aliphatic, aromatic as well as the carbonyl carbons--making the complete carbon assignment possible using one spectrum only. Thirdly, the frequently used HC(CCO)NH experiment was redesigned by replacing the long C-carbonyl refocused INEPT transfer step by direct ¹³C-¹³C-TOCSY magnetization transfer from side chain carbons to the backbone carbonyls. The resulting HC(CCO)NH experiment minimizes relaxation losses because it is shorter and represents a more sensitive alternative particularly for larger proteins. The performance of the experiments is demonstrated on isotope labeled proteins up to the size of 43 kDa.
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Affiliation(s)
- Helena Kovacs
- Bruker BioSpin AG, Industriestrasse 26, 8117, Fällanden, Switzerland,
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12
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Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Koźmiński W. High-Dimensional NMR Spectra for Structural Studies of Biomolecules. Chemphyschem 2013; 14:3015-25. [DOI: 10.1002/cphc.201300277] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 11/06/2022]
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13
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Krähenbühl B, Boudet J, Wider G. 4D experiments measured with APSY for automated backbone resonance assignments of large proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 56:149-154. [PMID: 23625454 DOI: 10.1007/s10858-013-9731-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/16/2013] [Indexed: 06/02/2023]
Abstract
Detailed structural and functional characterization of proteins by solution NMR requires sequence-specific resonance assignment. We present a set of transverse relaxation optimization (TROSY) based four-dimensional automated projection spectroscopy (APSY) experiments which are designed for resonance assignments of proteins with a size up to 40 kDa, namely HNCACO, HNCOCA, HNCACB and HN(CO)CACB. These higher-dimensional experiments include several sensitivity-optimizing features such as multiple quantum parallel evolution in a 'just-in-time' manner, aliased off-resonance evolution, evolution-time optimized APSY acquisition, selective water-handling and TROSY. The experiments were acquired within the concept of APSY, but they can also be used within the framework of sparsely sampled experiments. The multidimensional peak lists derived with APSY provided chemical shifts with an approximately 20 times higher precision than conventional methods usually do, and allowed the assignment of 90 % of the backbone resonances of the perdeuterated primase-polymerase ORF904, which contains 331 amino acid residues and has a molecular weight of 38.4 kDa.
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Affiliation(s)
- Barbara Krähenbühl
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
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14
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Krähenbühl B, Hofmann D, Maris C, Wider G. Sugar-to-base correlation in nucleic acids with a 5D APSY-HCNCH or two 3D APSY-HCN experiments. JOURNAL OF BIOMOLECULAR NMR 2012; 52:141-150. [PMID: 22143941 DOI: 10.1007/s10858-011-9588-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/16/2011] [Indexed: 05/31/2023]
Abstract
A five-dimensional (5D) APSY (automated projection spectroscopy) HCNCH experiment is presented, which allows unambiguous correlation of sugar to base nuclei in nucleic acids. The pulse sequence uses multiple quantum (MQ) evolution which enables long constant-time evolution periods in all dimensions, an improvement that can also benefit non-APSY applications. Applied with an RNA with 23 nucleotides the 5D APSY-HCNCH experiment produced a complete and highly precise 5D chemical shift list within 1.5 h. Alternatively, and for molecules where the out-and-stay 5D experiment sensitivity is not sufficient, a set of out-and-back 3D APSY-HCN experiments is proposed: an intra-base (3D APSY-b-HCN) experiment in an MQ or in a TROSY version, and an MQ sugar-to-base (3D APSY-s-HCN) experiment. The two 3D peak lists require subsequent matching via the N1/9 chemical shift values to one 5D peak list. Optimization of the 3D APSY experiments for maximal precision in the N1/9 dimension allowed matching of all (15)N chemical shift values contained in both 3D peak lists. The precise 5D chemical shift correlation lists resulting from the 5D experiment or a pair of 3D experiments also provide a valuable basis for subsequent connection to chemical shifts derived with other experiments.
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Affiliation(s)
- Barbara Krähenbühl
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
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15
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Stanek J, Augustyniak R, Koźmiński W. Suppression of sampling artefacts in high-resolution four-dimensional NMR spectra using signal separation algorithm. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 214:91-102. [PMID: 22070970 DOI: 10.1016/j.jmr.2011.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/10/2011] [Accepted: 10/17/2011] [Indexed: 05/04/2023]
Abstract
The development of non-uniform sampling (NUS) strategies permits to obtain high-dimensional spectra with increased resolution in significantly reduced experimental time. We extended a previously proposed signal separation algorithm (SSA) to process sparse four-dimensional NMR data. It is employed for two experiments carried out for a partially unstructured 114-residue construct of chicken Engrailed 2 protein, namely 4D HCCH-TOCSY and 4D C,N-edited NOESY. The SSA allowed us to obtain high-quality spectra using only as little as 0.16% of the available samples, with low sampling artefacts approaching the thermal noise level in most spectral regions. It is demonstrated that NUS 4D HCCH-TOCSY is dominated by sampling noise and requires efficient artefact suppression. On the other hand, 4D C,N-edited NOESY is a particularly attractive experiment for NUS, as the absence of diagonal peaks renders the problem of artefacts less critical. We also present a transverse-relaxation optimized sequence for HMQC that is especially designed for longer evolution periods in the indirectly detected proton dimension in high-dimensional pulse sequences. In conjunction with novel sampling strategies and efficient processing methods, this improvement enabled us to obtain unique structural information about aliphatic-amide contacts.
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Affiliation(s)
- Jan Stanek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02093 Warsaw, Poland
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Kupče Ē, Freeman R. Parallel receivers and sparse sampling in multidimensional NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:1-13. [PMID: 21924931 DOI: 10.1016/j.jmr.2011.08.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 08/19/2011] [Accepted: 08/21/2011] [Indexed: 05/31/2023]
Abstract
The recent introduction of NMR spectrometers with multiple receivers permits spectra from several different nuclear species to be recorded in parallel, and several standard pulse sequences to be combined into a single entity. It is shown how these improvements in the flow and quality of spectral information can be significantly augmented by compressive sensing techniques--controlled aliasing, Hadamard spectroscopy, single-point evaluation of evolution space (SPEED), random sampling, projection-reconstruction, and hyperdimensional NMR. Future developments of these techniques are confidently expected to mitigate one of the most serious limitations in multidimensional NMR--the excessive duration of the measurements.
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Affiliation(s)
- Ēriks Kupče
- Agilent Technologies, 6 Mead Road, Yarnton, Oxford OX5 1QU, UK.
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Krähenbühl B, Hiller S, Wider G. 4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 51:313-318. [PMID: 21947871 DOI: 10.1007/s10858-011-9572-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 08/06/2011] [Indexed: 05/31/2023]
Abstract
A four-dimensional (4D) APSY (automated projection spectroscopy)-HBCB(CG)CDHD experiment is presented. This 4D experiment correlates aromatic with aliphatic carbon and proton resonances from the same amino acid side chain of proteins in aqueous solution. It thus allows unambiguous sequence-specific assignment of aromatic amino acid ring signals based on backbone assignments. Compared to conventional 2D approaches, the inclusion of evolution periods on (1)H(β) and (13)C(δ) efficiently removes overlaps, and provides two additional frequencies for consequent automated or manual matching. The experiment was successfully applied to three proteins with molecular weights from 6 to 13 kDa. For the complementation of the assignment of the aromatic resonances, TOCSY- or COSY-based versions of a 4D APSY-HCCH(aro) sequence are proposed.
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Affiliation(s)
- Barbara Krähenbühl
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
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Abstract
This chapter presents the NMR technique APSY (automated projection spectroscopy) and its applications for sequence-specific resonance assignments of proteins. The result of an APSY experiment is a list of chemical shift correlations for an N-dimensional NMR spectrum (N≥3). This list is obtained in a fully automated way by the dedicated algorithm GAPRO (geometric analysis of projections) from a geometric analysis of experimentally recorded, low-dimensional projections. Because the positions of corresponding peaks in multiple projections are correlated, thermal noise and other uncorrelated artifacts are efficiently suppressed. We describe the theoretical background of the APSY method and discuss technical aspects that guide its optimal use. Further, applications of APSY-NMR spectroscopy for fully automated sequence-specific backbone and side chain assignments of proteins are described. We discuss the choice of suitable experiments for this purpose and show several examples. APSY is of particular interest for the assignment of soluble unfolded proteins, which is a time-consuming task by conventional means. With this class of proteins, APSY-NMR experiments with up to seven dimensions have been recorded. Sequence-specific assignments of protein side chains in turn are obtained from a 5D TOCSY-APSY-NMR experiment.
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Affiliation(s)
- Sebastian Hiller
- Biozentrum, Universität Basel, Klingelbergstr. 70, 4056, Basel, Switzerland.
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Gossert AD, Hiller S, Fernández C. Automated NMR Resonance Assignment of Large Proteins for Protein−Ligand Interaction Studies. J Am Chem Soc 2010; 133:210-3. [DOI: 10.1021/ja108383x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alvar D. Gossert
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland, and Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland, and Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - César Fernández
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland, and Biozentrum, University of Basel, 4056 Basel, Switzerland
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Solution structure and activation mechanism of ubiquitin-like small archaeal modifier proteins. J Mol Biol 2010; 405:1040-55. [PMID: 21112336 DOI: 10.1016/j.jmb.2010.11.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 11/18/2010] [Accepted: 11/19/2010] [Indexed: 11/23/2022]
Abstract
In archaea, two ubiquitin-like small archaeal modifier protein (SAMPs) were recently shown to be conjugated to proteins in vivo. SAMPs display homology to bacterial MoaD sulfur transfer proteins and eukaryotic ubiquitin-like proteins, and they share with them the conserved C-terminal glycine-glycine motif. Here, we report the solution structure of SAMP1 from Methanosarcina acetivorans and the activation of SAMPs by an archaeal protein with homology to eukaryotic E1 enzymes. Our results show that SAMP1 possesses a β-grasp fold and that its hydrophobic and electrostatic surface features are similar to those of MoaD. M. acetivorans SAMP1 exhibits an extensive flexible surface loop between helix-2 and the third strand of the β-sheet, which contributes to an elongated surface groove that is not observed in bacterial ubiquitin homologues and many other SAMPs. We provide in vitro biochemical evidence that SAMPs are activated in an ATP-dependent manner by an E1-like enzyme that we have termed E1-like SAMP activator (ELSA). We show that activation occurs by formation of a mixed anhydride (adenylate) at the SAMP C-terminus and is detectable by SDS-PAGE and electrospray ionization mass spectrometry.
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Coggins BE, Venters RA, Zhou P. Radial sampling for fast NMR: Concepts and practices over three decades. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:381-419. [PMID: 20920757 PMCID: PMC2951763 DOI: 10.1016/j.pnmrs.2010.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/16/2010] [Indexed: 05/04/2023]
Affiliation(s)
- Brian E. Coggins
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | - Ronald A. Venters
- Duke University NMR Center, Duke University Medical Center, Durham, NC 27710
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
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Marion D. Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and fast pulsing methods for unfolded proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 206:81-87. [PMID: 20594882 DOI: 10.1016/j.jmr.2010.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 05/31/2010] [Accepted: 06/06/2010] [Indexed: 05/29/2023]
Abstract
Resonance assignment of intrinsically disordered proteins is made difficult by the extensive spectral overlaps. High-resolution 3D and 4D spectra are thus essential for this purpose. We have adapted the series of 3D BEST-experiments proposed by Lescop et al. [E. Lescop, P. Schanda, B. Brutscher, A set of BEST triple-resonance experiments for time-optimized protein resonance assignment, J. Magn. Reson. 187 (2007) 163-169] to the case of unfolded proteins. Longer acquisitions in the indirect dimensions are obtained by implementing semi-constant time evolution and sparse sampling. Using maximum entropy reconstruction for the indirect dimensions, the artifact intensity due to sparse sampling can be reduced to a level similar to the other sources of noise. The reduction of the sampled increments and the shorter duration of individual transients makes it possible to record a 4D experiment with reasonable resolution in less than 60 h.
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Affiliation(s)
- Dominique Marion
- Laboratoire de RMN, Institut de Biologie Structurale Jean-Pierre Ebel, UMR5075 CNRS-CEA-UJF, 41, Rue Jules Horowitz, 38027 Grenoble Cedex, France.
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Mobli M, Stern AS, Bermel W, King GF, Hoch JC. A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 204:160-4. [PMID: 20299257 PMCID: PMC2859963 DOI: 10.1016/j.jmr.2010.02.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 01/27/2010] [Accepted: 02/15/2010] [Indexed: 05/11/2023]
Abstract
One of the stiffest challenges in structural studies of proteins using NMR is the assignment of sidechain resonances. Typically, a panel of lengthy 3D experiments are acquired in order to establish connectivities and resolve ambiguities due to overlap. We demonstrate that these experiments can be replaced by a single 4D experiment that is time-efficient, yields excellent resolution, and captures unique carbon-proton connectivity information. The approach is made practical by the use of non-uniform sampling in the three indirect time dimensions and maximum entropy reconstruction of the corresponding 3D frequency spectrum. This 4D method will facilitate automated resonance assignment procedures and it should be particularly beneficial for increasing throughput in NMR-based structural genomics initiatives.
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Affiliation(s)
- Mehdi Mobli
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, 4072 QLD, Australia.
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Kazimierczuk K, Zawadzka A, Koźmiński W. Narrow peaks and high dimensionalities: exploiting the advantages of random sampling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 197:219-28. [PMID: 19185522 DOI: 10.1016/j.jmr.2009.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 12/17/2008] [Accepted: 01/04/2009] [Indexed: 05/04/2023]
Abstract
Level of artifacts in spectra obtained by Multidimensional Fourier Transform has been studied, considering randomly sampled signals of high dimensionality and long evolution times. It has been shown theoretically and experimentally, that this level is dependent on the number of time domain samples, but not on its relation to the number of points required in appropriate conventional experiment. Independence of the evolution time domain size (in the terms of both: dimensionality and evolution time reached), suggests that random sampling should be used rather to design new techniques with large time domain than to accelerate standard experiments. 5D HC(CC-TOCSY)CONH has been presented as the example of such approach. The feature of Multidimensional Fourier Transform, namely the possibility of calculating spectral values at arbitrary chosen frequency points, allowed easy examination of resulting spectrum. We present the example of such approach, referred to as Sparse Multidimensional Fourier Transform.
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