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Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus. Molecules 2020; 25:molecules25245824. [PMID: 33321815 PMCID: PMC7763327 DOI: 10.3390/molecules25245824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 11/17/2022] Open
Abstract
In recent years, intrinsically disordered proteins (IDPs) and disordered domains have attracted great attention. Many of them contain linear motifs that mediate interactions with other factors during formation of multicomponent protein complexes. NMR spectrometry is a valuable tool for characterizing this type of interactions on both amino acid (aa) and atomic levels. Alphaviruses encode a nonstructural protein nsP3, which drives viral replication complex assembly. nsP3 proteins contain over 200-aa-long hypervariable domains (HVDs), which exhibits no homology between different alphavirus species, are predicted to be intrinsically disordered and appear to be critical for alphavirus adaptation to different cells. Previously, we have shown that nsP3 HVD of chikungunya virus (CHIKV) is completely disordered with low tendency to form secondary structures in free form. In this new study, we used novel NMR approaches to assign the spectra for the nsP3 HVD of Venezuelan equine encephalitis virus (VEEV). The HVDs of CHIKV and VEEV have no homology but are both involved in replication complex assembly and function. We have found that VEEV nsP3 HVD is also mostly disordered but contains a short stable α-helix in its C-terminal fragment, which mediates interaction with the members of cellular Fragile X syndrome protein family. Our NMR data also suggest that VEEV HVD has several regions with tendency to form secondary structures.
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Yoshimura Y, Mulder FAA. Sensitive and simplified: a combinatorial acquisition of five distinct 2D constant-time 13C- 1H NMR protein correlation spectra. JOURNAL OF BIOMOLECULAR NMR 2020; 74:695-706. [PMID: 32804297 DOI: 10.1007/s10858-020-00341-x] [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: 06/26/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
A procedure is presented for the substantial simplification of 2D constant-time 13C-1H heteronuclear single-quantum correlation (HSQC) spectra of 13C-enriched proteins. In this approach, a single pulse sequence simultaneously records eight sub-spectra wherein the phases of the NMR signals depend on spin topology. Signals from different chemical groups are then stratified into different sub-spectra through linear combination based on Hadamard encoding of 13CHn multiplicity (n = 1, 2, and 3) and the chemical nature of neighboring 13C nuclei (aliphatic, carbonyl/carboxyl, aromatic). This results in five sets of 2D NMR spectra containing mutually exclusive signals from: (i) 13Cβ-1Hβ correlations of asparagine and aspartic acid, 13Cγ-1Hγ correlations of glutamine and glutamic acid, and 13Cα-1Hα correlations of glycine, (ii) 13Cα-1Hα correlations of all residues but glycine, and (iii) 13Cβ-1Hβ correlations of phenylalanine, tyrosine, histidine, and tryptophan, and the remaining (iv) aliphatic 13CH2 and (v) aliphatic 13CH/13CH3 resonances. As HSQC is a common element of many NMR experiments, the spectral simplification proposed in this article can be straightforwardly implemented in experiments for resonance assignment and structure determination and should be of widespread utility.
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Affiliation(s)
- Yuichi Yoshimura
- Lifematics West-Japan Branch, Hirano-machi 4-6-16, Chuo-ku, Osaka, 541-0046, Japan
- Institute for Protein Research, Osaka University, Yamada-oka 3-2, Suita, Osaka, 565-0871, Japan
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
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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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Walinda E, Morimoto D, Shirakawa M, Sugase K. F 1 F 2-selective NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2017; 68:41-52. [PMID: 28474302 DOI: 10.1007/s10858-017-0113-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Fourier transform NMR spectroscopy has provided unprecedented insight into the structure, interaction and dynamic motion of proteins and nucleic acids. Conventional biomolecular NMR relies on the acquisition of three-dimensional and four-dimensional (4D) data matrices to establish correlations between chemical shifts in the frequency domains F 1, F 2, F 3 and F 1, F 2, F 3, F 4 respectively. While rich in information, these datasets require a substantial amount of acquisition time, are visually highly unintuitive, require expert knowledge to process, and sample dark and bright regions of the frequency domains equally. Here, we present an alternative approach to obtain multidimensional chemical shift correlations for biomolecules. This strategy focuses on one narrow frequency range, F 1 F 2, at a time and records the resulting F 3 F 4 correlation spectrum by two-dimensional NMR. As a result, only regions of the frequency domain that contain signals in F 1 F 2 ("bright regions") are sampled. F 1 F 2 selection is achieved by Hartmann-Hahn cross-polarization using weak radio frequency fields. This approach reveals information equivalent to that of a conventional 4D experiment, while the dimensional reduction may shorten the total acquisition time and simplifies spectral processing, interpretation and comparative analysis. Potential applicability of the F 1 F 2-selective approach is illustrated by de novo assignment, structural and dynamics studies of ubiquitin and fatty-acid binding protein 4 (FABP4). Further extension of this concept may spawn new selective NMR experiments to aid studies of site-specific structural dynamics, protein-protein interactions and allosteric modulation of protein structure.
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Affiliation(s)
- Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Sakyo-ku Yoshida Konoe-cho, Kyoto, 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku Kyoto-Daigaku Katsura, Kyoto, 615-8510, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku Kyoto-Daigaku Katsura, Kyoto, 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku Kyoto-Daigaku Katsura, Kyoto, 615-8510, Japan.
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Navarro R, Bornet O, Houot L, Lloubes R, Guerlesquin F, Nouailler M. (1)H, (15)N and (13)C resonance assignments of the C-terminal domain of Vibrio cholerae TolA protein. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:311-313. [PMID: 27436120 DOI: 10.1007/s12104-016-9690-y] [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: 03/22/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Vibrio cholerae is the bacterial causative agent of the human disease cholera. Non-pathogenic bacterium can be converted to pathogenic following infection by a filamentous phage, CTXΦ, that carries the cholera toxin encoding genes. A crucial step during phage infection requires a direct interaction between the CTXΦ minor coat protein (pIII(CTX)) and the C-terminal domain of V. cholerae TolA protein (TolAIIIvc). In order to get a better understanding of TolA function during the infection process, we have initiated a study of the V. cholerae TolAIII domain by 2D and 3D heteronuclear NMR. With the exception of the His-tag (H123-H128), 97 % of backbone (1)H, (15)N and (13)C resonances were assigned and the side chain assignments for 92 % of the protein were obtained (BMRB deposit with accession number 25689).
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Affiliation(s)
- Romain Navarro
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France
| | - Olivier Bornet
- Institut de Microbiologie de la Méditerranée, FR 3479, CNRS, Aix-Marseille Université, Marseille, France
| | - Laetitia Houot
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France
| | - Roland Lloubes
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France
| | - Françoise Guerlesquin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France
| | - Matthieu Nouailler
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS, Aix-Marseille Université, Marseille, France.
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6
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Dubey A, Mondal S, Chandra K, Atreya HS. Rapid identification of amino acid types in proteins using phase modulated 2D HN(CACB) and 2D HN(COCACB). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 267:22-29. [PMID: 27078090 DOI: 10.1016/j.jmr.2016.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/16/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
We present a simple approach to rapidly identify amino acid types in proteins from a 2D spectrum. The method is based on the fact that (13)C(β) chemical shifts of different amino acid types fall in distinct spectral regions. By evolving the (13)C chemical shifts in the conventional HNCACB or HN(CO)CACB type experiment for a single specified delay period, the phase of the cross peaks of different amino acid residues are modulated depending on their (13)C(β) shift values. Following this specified evolution period, the 2D HN projections of these experiments are acquired. The (13)C evolution period can be chosen such that all residues belonging to a given set of amino acid types have the same phase pattern (positive or negative) facilitating their identification. This approach does not require the preparation of any additional samples, involves the analysis of 2D [(15)N-(1)H] HSQC-type spectra obtained from the routinely used triple resonance experiments with minor modifications, and is applicable to deuterated proteins. The method will be useful for quick assignment of signals that shift during ligand binding or in combination with selective labeling/unlabeling approaches for identification of amino acid types to aid the sequential assignment process.
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Affiliation(s)
- Abhinav Dubey
- IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560012, India; NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Somnath Mondal
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India; Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kousik Chandra
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Hanudatta S Atreya
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India.
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7
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Piai A, Gonnelli L, Felli IC, Pierattelli R, Kazimierczuk K, Grudziąż K, Koźmiński W, Zawadzka-Kazimierczuk A. Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 64:239-53. [PMID: 26891900 PMCID: PMC4824835 DOI: 10.1007/s10858-016-0024-2] [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: 10/20/2015] [Accepted: 02/11/2016] [Indexed: 05/07/2023]
Abstract
Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using automatic strategies for their assignment is very attractive. In this article we present a new version of the automatic assignment program TSAR dedicated to intrinsically disordered proteins. In particular, we demonstrate how the automatic procedure can be improved by incorporating methods for amino acid recognition and information on chemical shifts in selected amino acids. The approach was tested in silico on 16 disordered proteins and experimentally on α-synuclein, with remarkably good results.
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Affiliation(s)
- Alessandro Piai
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Leonardo Gonnelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Isabella C Felli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | | | - Katarzyna Grudziąż
- 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
| | - Anna Zawadzka-Kazimierczuk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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8
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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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9
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Felli IC, Pierattelli R. Novel methods based on (13)C detection to study intrinsically disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:115-25. [PMID: 24656084 DOI: 10.1016/j.jmr.2013.10.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 05/23/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by highly flexible solvent exposed backbones and can sample many different conformations. These properties confer them functional advantages, complementary to those of folded proteins, which need to be characterized to expand our view of how protein structural and dynamic features affect function beyond the static picture of a single well defined 3D structure that has influenced so much our way of thinking. NMR spectroscopy provides a unique tool for the atomic resolution characterization of highly flexible macromolecules in general and of IDPs in particular. The peculiar properties of IDPs however have profound effects on spectroscopic parameters. It is thus worth thinking about these aspects to make the best use of the great potential of NMR spectroscopy to contribute to this fascinating field of research. In particular, after many years of dealing with exclusively heteronuclear NMR experiments based on (13)C direct detection, we would like here to address their relevance when studying IDPs.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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Pantoja-Uceda D, Santoro J. A suite of amino acid residue type classification pulse sequences for 13C-detected NMR of proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:190-196. [PMID: 23892405 DOI: 10.1016/j.jmr.2013.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 06/24/2013] [Accepted: 06/28/2013] [Indexed: 06/02/2023]
Abstract
A suite of (13)C-detected NMR pulse sequences to edit the correlation peaks of the CACO and CON spectra according to the amino acid residue type is presented. The pulse sequences exploit the topology of the C(β) carbon and led to the sorting of the CACO or CON signals into several classes depending on the nature of the generating residue. A set of four or eight correlation spectra is recorded where the sign of the cross peaks changes from one spectrum to another according to the amino acid type of the corresponding residue in the protein sequence. Linear combination of these spectra produces subspectra showing signals from residues having similar C(β) topology. The presence of weak breakthrough peaks does not prevent the proper classification, since this is obtained from the subspectrum in which the correlation peak is more intense. The experiments were tested on a globular protonated protein ((13)C, (15)N labeled Ubiquitin), on a globular deuterated protein ((2)H, (13)C, (15)N labeled Ubiquitin), and on an intrinsically disordered protein ((13)C, (15)N labeled Nupr1).
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Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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Jaipuria G, Krishnarjuna B, Mondal S, Dubey A, Atreya HS. Amino acid selective labeling and unlabeling for protein resonance assignments. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 992:95-118. [PMID: 23076581 DOI: 10.1007/978-94-007-4954-2_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Structural characterization of proteins by NMR spectroscopy begins with the process of sequence specific resonance assignments in which the (1)H, (13)C and (15)N chemical shifts of all backbone and side-chain nuclei in the polypeptide are assigned. This process requires different isotope labeled forms of the protein together with specific experiments for establishing the sequential connectivity between the neighboring amino acid residues. In the case of spectral overlap, it is useful to identify spin systems corresponding to the different amino acid types selectively. With isotope labeling this can be achieved in two ways: (i) amino acid selective labeling or (ii) amino acid selective 'unlabeling'. This chapter describes both these methods with more emphasis on selective unlabeling describing the various practical aspects. The recent developments involving combinatorial selective labeling and unlabeling are also discussed.
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Affiliation(s)
- Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore, India
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12
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Bermel W, Bertini I, Chill J, Felli IC, Haba N, Kumar M. V. V, Pierattelli R. Exclusively Heteronuclear13C-Detected Amino-Acid-Selective NMR Experiments for the Study of Intrinsically Disordered Proteins (IDPs). Chembiochem 2012; 13:2425-32. [DOI: 10.1002/cbic.201200447] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Indexed: 12/20/2022]
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Pantoja-Uceda D, Santoro J. New amino acid residue type identification experiments valid for protonated and deuterated proteins. JOURNAL OF BIOMOLECULAR NMR 2012; 54:145-53. [PMID: 22945427 DOI: 10.1007/s10858-012-9665-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/04/2012] [Indexed: 05/23/2023]
Abstract
Two experiments are presented that yield amino acid type identification of individual residues in a protein by editing the (1)H-(15)N correlations into four different 2D subspectra, each corresponding to a different amino acid type class, and that can be applied to deuterated proteins. One experiment provides information on the amino acid type of the residue preceding the detected amide (1)H-(15)N correlation, while the other gives information on the type of its own residue. Versions for protonated proteins are also presented, and in this case it is possible to classify the residues into six different classes. Both sequential and intraresidue experiments provide highly complementary information, greatly facilitating the assignment of protein resonances. The experiments will also assist in transferring the assignment of a protein to the spectra obtained under different experimental conditions (e.g. temperature, pH, presence of ligands, cofactors, etc.).
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Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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14
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Rasia RM, Brutscher B, Plevin MJ. Selective Isotopic Unlabeling of Proteins Using Metabolic Precursors: Application to NMR Assignment of Intrinsically Disordered Proteins. Chembiochem 2012; 13:732-9. [DOI: 10.1002/cbic.201100678] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Indexed: 11/11/2022]
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15
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Krishnarjuna B, Jaipuria G, Thakur A, D’Silva P, Atreya HS. Amino acid selective unlabeling for sequence specific resonance assignments in proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 49:39-51. [PMID: 21153044 PMCID: PMC3020294 DOI: 10.1007/s10858-010-9459-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 11/16/2010] [Indexed: 05/14/2023]
Abstract
Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective 'unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly (13)C/(15)N labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {(12)CO( i )-(15)N( i+1)}-filtered HSQC, which aids in linking the (1)H(N)/(15)N resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to (2)H labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of (14)N at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.
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Affiliation(s)
- B. Krishnarjuna
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
| | - Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012 India
| | - Anushikha Thakur
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012 India
- Chemical Biology Programme, Indian Institute of Science, Bangalore, 560012 India
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | - Patrick D’Silva
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
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Pantoja-Uceda D, Santoro J. Amino acid type identification in NMR spectra of proteins via beta- and gamma-carbon edited experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 195:187-95. [PMID: 18829356 DOI: 10.1016/j.jmr.2008.09.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 09/08/2008] [Accepted: 09/11/2008] [Indexed: 05/23/2023]
Abstract
In this work, we introduce a set of pulse sequences that provide amino acid type identification of the NH correlation signals of proteins. The first pulse sequence is a modification of the CBCA(CO)NH experiment that exploits spin-coupling topologies to differentiate between amino acid types. A set of eight 2D (1)H-(15)N correlation spectra is recorded where the sign of the cross-peaks change from one spectrum to another according to the amino acid type of the preceding residue in the protein sequence. Linear combination of these eight data sets produces four subspectra. Taking also into account the sign of the correlation signals, this method allows the classification of the NH signals into six different groups, depending on the character of the preceding residue. This sequence is complemented with a (CGCBCACO)NH experiment that allows the subdivision of the largest of these groups into two smaller ones. Finally, a modification of the CBCANH experiment led to a similar classification of NH signals into six different groups, but now depending on the type of its own amino acid. The set of pulse sequences is demonstrated with two proteins of small to moderate size.
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Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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Sánchez R, Pantoja-Uceda D, Torres D, Prieto J, Campos-Olivas R, Blanco FJ. NMR assignment and secondary structure of human growth arrest and DNA damage alpha protein (Gadd45 alpha). BIOMOLECULAR NMR ASSIGNMENTS 2008; 2:139-142. [PMID: 19636889 DOI: 10.1007/s12104-008-9105-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 07/28/2008] [Indexed: 05/28/2023]
Abstract
Gadd45 alpha is a predominantly nuclear protein encoded by a DNA-damage-inducible gene which is transcriptionally regulated by the tumor suppressor p53. The interactions of Gadd45 alpha with several other proteins play a central role in DNA repair, cell cycle control and apoptosis. The NMR assignments of human Gadd45 alpha protein reported here provide the basis for further characterization of these interactions.
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Affiliation(s)
- Ricardo Sánchez
- Structural Biology Unit, CIC Biogune, Parque Tecnológico de Bizkaia, Ed. 800, Derio, 48160, Spain
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Wu PSC, Ozawa K, Jergic S, Su XC, Dixon NE, Otting G. Amino-acid type identification in 15N-HSQC spectra by combinatorial selective 15N-labelling. JOURNAL OF BIOMOLECULAR NMR 2006; 34:13-21. [PMID: 16505960 DOI: 10.1007/s10858-005-5021-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 11/02/2005] [Indexed: 05/06/2023]
Abstract
The efficiency of cell-free protein synthesis combined with combinatorial selective 15N-labelling provides a method for the rapid assignment of 15N-HSQC cross-peaks to the 19 different non-proline amino-acid types from five 15N-HSQC spectra. This strategy was explored with two different constructs of the C-terminal domain V of the tau subunit of the Escherichia coli DNA polymerase III holoenzyme, tauC16 and tauC14. Since each of the five 15N-HSQC spectra contained only about one third of the cross-peaks present in uniformly labelled samples, spectral overlap was much reduced. All 15N-HSQC cross-peaks of the backbone amides could be assigned to the correct amino-acid type. Availability of the residue-type information greatly assisted the evaluation of the changes in chemical shifts observed for corresponding residues in tauC16 vs. those in tauC14, and the analysis of the structure and mobility of the C-terminal residues present in tauC16 but not in tauC14.
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Affiliation(s)
- Peter S C Wu
- Research School of Chemistry, Australian National University, Canberra, ACT, 0200, Australia
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