1
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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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2
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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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3
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Löhr F, Tumulka F, Bock C, Abele R, Dötsch V. An extended combinatorial 15N, 13Cα, and 13C' labeling approach to protein backbone resonance assignment. JOURNAL OF BIOMOLECULAR NMR 2015; 62:263-79. [PMID: 25953311 DOI: 10.1007/s10858-015-9941-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/28/2015] [Indexed: 05/07/2023]
Abstract
Solution NMR studies of α-helical membrane proteins are often complicated by severe spectral crowding. In addition, hydrophobic environments like detergent micelles, isotropic bicelles or nanodiscs lead to considerably reduced molecular tumbling rates which translates into line-broadening and low sensitivity. Both difficulties can be addressed by selective isotope labeling methods. In this publication, we propose a combinatorial protocol that utilizes four different classes of labeled amino acids, in which the three backbone heteronuclei (amide nitrogen, α-carbon and carbonyl carbon) are enriched in (15)N or (13)C isotopes individually as well as simultaneously. This results in eight different combinations of dipeptides giving rise to cross peaks in (1)H-(15)N correlated spectra. Their differentiation is achieved by recording a series of HN-detected 2D triple-resonance spectra. The utility of this new scheme is demonstrated with a homodimeric 142-residue membrane protein in DHPC micelles. Restricting the number of selectively labeled samples to three allowed the identification of the amino-acid type for 77 % and provided sequential information for 47 % of its residues. This enabled us to complete the backbone resonance assignment of the uniformly labeled protein merely with the help of a 3D HNCA spectrum, which can be collected with reasonable sensitivity even for relatively large, non-deuterated proteins.
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Affiliation(s)
- Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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4
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Tossavainen H, Seppälä J, Sethi R, Pihlajamaa T, Permi P. H(N), N(H), C (α), C (β), and methyl group assignments of filamin multidomain fragments IgFLNc4-5 and IgFLNa3-5. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:47-50. [PMID: 24414222 DOI: 10.1007/s12104-014-9542-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/04/2014] [Indexed: 06/03/2023]
Abstract
Filamins regulate the actin cytoskeleton by cross-linking actin filaments, linking the cytoskeleton to the cell membrane, and through interaction with numerous binding partners such as intracellular signalling molecules, ion channels, receptors, enzymes and transcription factors. The rod region of filamins consists of 24 immunoglubulin (Ig)-like repeats, for some of which the functional unit is a domain pair. Our aim is to study filamin Ig domain-domain interactions and quaternary arrangement as well as to locate peptide binding sites on domain assemblies. We report here the H(N), N(H), C(α), C(β), and methyl group assignments of filamin A three-domain fragment IgFLNa3-5 and filamin C two-domain fragment IgFLNc4-5.
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Affiliation(s)
- Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland
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5
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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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6
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Hellman M, Piirainen H, Jaakola VP, Permi P. Bridge over troubled proline: assignment of intrinsically disordered proteins using (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H experiments concomitantly with HNCO and i(HCA)CO(CA)NH. JOURNAL OF BIOMOLECULAR NMR 2014; 58:49-60. [PMID: 24346685 DOI: 10.1007/s10858-013-9804-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/09/2013] [Indexed: 05/21/2023]
Abstract
NMR spectroscopy is by far the most versatile and information rich technique to study intrinsically disordered proteins (IDPs). While NMR is able to offer residue level information on structure and dynamics, assignment of chemical shift resonances in IDPs is not a straightforward process. Consequently, numerous pulse sequences and assignment protocols have been developed during past several years, targeted especially for the assignment of IDPs, including experiments that employ H(N), H(α) or (13)C detection combined with two to six indirectly detected dimensions. Here we propose two new HN-detection based pulse sequences, (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H, that provide correlations with (1)H(N)(i - 1), (13)C'(i - 1) and (15)N(i), and (1)H(N)(i + 1), (13)C'(i) and (15)N(i) frequencies, respectively. Most importantly, they offer sequential links across the proline bridges and enable filling the single proline gaps during the assignment. We show that the novel experiments can efficiently complement the information available from existing HNCO and intraresidual i(HCA)CO(CA)NH pulse sequences and their concomitant usage enabled >95 % assignment of backbone resonances in cytoplasmic tail of adenosine receptor A2A in comparison to 73 % complete assignment using the HNCO/i(HCA)CO(CA)NH data alone.
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Affiliation(s)
- Maarit Hellman
- Program in Structural Biology and Biophysics, Institute of Biotechnology/NMR Laboratory, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland
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7
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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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8
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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: 16] [Impact Index Per Article: 1.3] [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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9
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Greenfield NJ, Kotlyanskaya L, Hitchcock-DeGregori SE. Structure of the N terminus of a nonmuscle alpha-tropomyosin in complex with the C terminus: implications for actin binding. Biochemistry 2009; 48:1272-83. [PMID: 19170537 PMCID: PMC4410877 DOI: 10.1021/bi801861k] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Tropomyosin is a coiled-coil actin binding protein that stabilizes the filament, protects it from severing, and cooperatively regulates actin's interaction with myosin. Depending on the first coding exon, tropomyosins are low molecular weight (LMW), found in the cytoskeleton and predominant in transformed cells, or high molecular weight (HMW), found in muscle and nonmuscle cells. The N- and C-terminal ends form a complex that allows tropomyosin to associate N terminus-to-C terminus along the actin filament. We determined the structure of a LMW tropomyosin N-terminal model peptide complexed with a smooth/nonmuscle tropomyosin C-terminal peptide. Using NMR and circular dichroism we showed that both ends become more helical upon complex formation but that the C-terminal peptide is partially unfolded at 20 degrees C. The first five residues of the N terminus that are disordered in the free peptide are more helical and are part of the overlap complex. NMR data indicate residues 2-17 bind to the C terminus in the complex. The data support a model for the LMW overlap complex that is homologous to the striated muscle tropomyosin complex in which the ends are oriented in parallel N terminus-to-C terminus with the plane of the N-terminal coiled coil perpendicular to the plane of the C terminus. The main difference is that the overlap spans 16 residues in the LMW tropomyosin complex compared to 11 residues in the HMW striated muscle overlap complex. We discuss the relevance of a stable but dynamic intermolecular junction for high-affinity binding to actin.
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Affiliation(s)
- Norma J. Greenfield
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Piscataway, NJ 08854
| | - Lucy Kotlyanskaya
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Piscataway, NJ 08854
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10
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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: 29] [Impact Index Per Article: 1.8] [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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11
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Lescop E, Rasia R, Brutscher B. Hadamard amino-acid-type edited NMR experiment for fast protein resonance assignment. J Am Chem Soc 2008; 130:5014-5. [PMID: 18345629 DOI: 10.1021/ja800914h] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An original Hadamard-encoding scheme allows discrimination among seven amino acid types in a single two-dimensional NMR experiment. Combined with hyperdimensional NMR techniques, this presents a promising new method for fast, automated backbone resonance assignment of proteins in only a few hours time.
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Affiliation(s)
- Ewen Lescop
- IBS, Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, F-38027 Grenoble, France
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12
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Greenfield NJ, Kostyukova AS, Hitchcock-DeGregori SE. Structure and tropomyosin binding properties of the N-terminal capping domain of tropomodulin 1. Biophys J 2004; 88:372-83. [PMID: 15475586 PMCID: PMC1305014 DOI: 10.1529/biophysj.104.051128] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two families of actin regulatory proteins are the tropomodulins and tropomyosins. Tropomodulin binds to tropomyosin (TM) and to the pointed end of actin filaments and "caps" the pointed end (i.e., inhibits its polymerization and depolymerization). Tropomodulin 1 has two distinct actin-capping regions: a folded C-terminal domain (residues 160-359), which does not bind to TM, and a conserved, N-terminal region, within residues 1-92 that binds TM and requires TM for capping activity. NMR and circular dichroism were used to determine the structure of a peptide containing residues 1-92 of tropomodulin (Tmod1(1-92)) and to define its TM binding site. Tmod1(1-92) is mainly disordered with only one helical region, residues 24-35. This helix forms part of the TM binding domain, residues 1-35, which become more ordered upon binding a peptide containing the N-terminus of an alpha-TM. Mutation of L27 to E or G in the Tmod helix reduces TM affinity. Residues 49-92 are required for capping but do not bind TM. Of these, residues 67-75 have the sequence of an amphipathic helix, but are not helical. Residues 55-62 and 76-92 display negative 1H-15N heteronuclear Overhauser enhancements showing they are flexible. The conformational dynamics of these residues may be important for actin capping activity.
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Affiliation(s)
- Norma J Greenfield
- Department of Neuroscience and Cell Biology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635, USA.
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13
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Monleón D, Colson K, Moseley HNB, Anklin C, Oswald R, Szyperski T, Montelione GT. Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2003; 2:93-101. [PMID: 12836666 DOI: 10.1023/a:1020499629298] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.
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Affiliation(s)
- Daniel Monleón
- Center for Advanced Biotechnology, and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA
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14
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Greenfield NJ, Palm T, Hitchcock-DeGregori SE. Structure and interactions of the carboxyl terminus of striated muscle alpha-tropomyosin: it is important to be flexible. Biophys J 2002; 83:2754-66. [PMID: 12414708 PMCID: PMC1302360 DOI: 10.1016/s0006-3495(02)75285-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Tropomyosin (TM) binds to and regulates the actin filament. We used circular dichroism and heteronuclear NMR to investigate the secondary structure and interactions of the C terminus of striated muscle alpha-TM, a major functional determinant, using a model peptide, TM9a(251-284). The (1)H(alpha) and (13)C(alpha) chemical shift displacements show that residues 252 to 277 are alpha-helical but residues 278 to 284 are nonhelical and mobile. The (1)H(N) and (13)C' displacements suggest that residues 257 to 269 form a coiled coil. Formation of an "overlap" binary complex with a 33-residue N-terminal chimeric peptide containing residues 1 to 14 of alpha-TM perturbs the (1)H(N) and (15)N resonances of residues 274 to 284. Addition of a fragment of troponin T, TnT(70-170), to the binary complex perturbs most of the (1)H(N)-(15)N cross-peaks. In addition, there are many new cross-peaks, showing that the binding is asymmetric. Q263, in a proposed troponin T binding site, shows two sets of side-chain (15)N-(1)H cross-peaks, indicating conformational flexibility. The conformational equilibrium of the side chain changes upon formation of the binary and ternary complexes. Replacing Q263 with leucine greatly increases the stability of TM9a(251-284) and reduces its ability to form the binary and ternary complexes, showing that conformational flexibility is crucial for the binding functions of the C terminus.
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Affiliation(s)
- Norma J Greenfield
- University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854-5635, USA.
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15
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Greenfield NJ, Huang YJ, Palm T, Swapna GV, Monleon D, Montelione GT, Hitchcock-DeGregori SE. Solution NMR structure and folding dynamics of the N terminus of a rat non-muscle alpha-tropomyosin in an engineered chimeric protein. J Mol Biol 2001; 312:833-47. [PMID: 11575936 DOI: 10.1006/jmbi.2001.4982] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tropomyosin is an alpha-helical coiled-coil protein that aligns head-to-tail along the length of the actin filament and regulates its function. The solution structure of the functionally important N terminus of a short 247-residue non-muscle tropomyosin was determined in an engineered chimeric protein, GlyTM1bZip, consisting of the first 19 residues of rat short alpha-tropomyosin and the last 18 residues of the GCN4 leucine zipper. A gene encoding GlyTM1bZip was synthesized, cloned and expressed in Escherichia coli. Triple resonance NMR spectra were analyzed with the program AutoAssign to assign its backbone resonances. Multidimensional nuclear Overhauser effect spectra, X-filtered spectra and (3)J(H(N)-H(alpha)) scalar coupling were analyzed using AutoStructure. This is the first application of this new program to determine the three-dimensional structure of a symmetric homodimer and a structure not previously reported. Residues 7-35 in GlyTM1bZip form a coiled coil, but neither end is helical. Heteronuclear (15)N-(1)H nuclear Overhauser effect data showed that the non-helical N-terminal residues are flexible. The (13)C' chemical shifts of the coiled-coil backbone carbonyl groups in GlyTM1bZip showed a previously unreported periodicity, where resonances arising from residues at the coiled-coil interface in a and d positions of the heptad repeat were displaced relatively upfield and those arising from residues in c positions were displaced relatively downfield. Heteronuclear single quantum coherence spectra, collected as a function of temperature, showed that cross-peaks arising from the alpha-helical backbone and side-chains at the coiled-coil interface broadened or shifted with T(M) values approximately 20 degrees C lower than the loss of alpha-helix measured by circular dichroism, suggesting the presence of a folding intermediate. The side-chain of Ile14, a residue essential for binding interactions, exhibited multiple conformations. The conformational flexibility of the N termini of short tropomyosins may be important for their binding specificity.
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Affiliation(s)
- N J Greenfield
- Department of Neuroscience and Cell Biology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, NJ 08854-5635, USA.
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Moseley HN, Monleon D, Montelione GT. Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol 2001; 339:91-108. [PMID: 11462827 DOI: 10.1016/s0076-6879(01)39311-4] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- H N Moseley
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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Schubert M, Oschkinat H, Schmieder P. MUSIC, selective pulses, and tuned delays: amino acid type-selective (1)H-(15)N correlations, II. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 148:61-72. [PMID: 11133277 DOI: 10.1006/jmre.2000.2222] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Amino acid type-selective experiments help to remove ambiguities in either manual or automated assignment procedures. Here we present modified triple-resonance experiments that yield amino acid type-selective (1)H-(15)N correlations. They are based on the MUSIC coherence transfer scheme which replaces the initial INEPT transfer and is selective for XH(2) or XH(3) (where X is either (15)N or (13)C). Signals of the desired amino acid types are thus selected based on the topology of the side chain. MUSIC is combined with selective pulses and carefully tuned delays to create experiments for Ser (S-HSQC); Val, Ile, and Ala (VIA-HSQC); Leu and Ala (LA-HSQC); Asp, Asn, and Gly (DNG-HSQC), as well as Glu, Gln, and Gly (EQG-HSQC). The new experiments are recorded as two-dimensional spectra and their performance is demonstrated by their application to two protein domains of 83 and 115 residues.
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Affiliation(s)
- M Schubert
- Forschungsinstitut fŭr Molekulare Pharmakologie, Robert-Roessle-Str. 10, Berlin, D-13125, Germany
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Schubert M, Smalla M, Schmieder P, Oschkinat H. MUSIC in triple-resonance experiments: amino acid type-selective (1)H-(15)N correlations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 141:34-43. [PMID: 10527741 DOI: 10.1006/jmre.1999.1881] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Amino acid type-selective triple-resonance experiments can be of great help for the assignment of protein spectra, since they help to remove ambiguities in either manual or automated assignment procedures. Here, modified triple-resonance experiments that yield amino acid type-selective (1)H-(15)N correlations are presented. They are based on novel coherence transfer schemes, the MUSIC pulse sequence elements, that replace the initial INEPT transfer and are selective for XH(2) or XH(3) (X can be (15)N or (13)C). The desired amino acid type is thereby selected based on the topology of the side chain. Experiments for Gly (G-HSQC); Ala (A-HSQC); Thr, Val, Ile, and Ala (TAVI-HSQC); Thr and Ala (TA-HSQC), as well as Asn and Gln (N-HSQC and QN-HSQC), are described. The new experiments are recorded as two-dimensional experiments and therefore need only small amounts of spectrometer time. The performance of the experiments is demonstrated with the application to two protein domains. Copyright 1999 Academic Press.
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Affiliation(s)
- M Schubert
- Forschungsinstitut fur Molekulare Pharmakologie, Alfred-Kowalke-Strasse 4, Berlin, D-10315, Germany
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Abstract
Recent developments in protein NMR technology have provided spectral data that are highly amenable to analysis by advanced computer software systems. Specific data collection strategies, coupled with these computer programs, allow automated analysis of extensive backbone and sidechain resonance assignments and three-dimensional structures for proteins of 50 to 200 amino acids.
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Affiliation(s)
- H N Moseley
- Center for Advanced Biotechnology and Medicine Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, 08854-5638, USA.
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Swapna GV, Montelione GT. Sensitivity-enhanced sim-CT HMQC PFG-HBHA(CO)NH and PFG-CBCA(CO)NH triple-resonance experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 137:437-442. [PMID: 10089179 DOI: 10.1006/jmre.1998.1699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Short transverse relaxation times of Calpha and Cbeta single-quantum coherences reduce the sensitivity of triple-resonance experiments involving transfers of Calpha/Cbeta or Halpha/Hbeta coherences. Multiple-quantum line-narrowing techniques improve the relaxation properties of 13C coherences, thereby increasing the sensitivity of the experiment. In the present work, we describe PFG-CBCA(CO)NH and PFG-HBHA(CO)NH experiments that utilize heteronuclear multiple-quantum coherences in a simultaneous constant-time period to obtain completely decoupled spectra with improved sensitivity. Results indicate that approximately 30% of cross peaks show an average enhancement of approximately 15% in the CBCA(CO)NH experiment. In the related HBHA(CO)NH experiment, approximately 97% of the cross peaks show an average enhancement of approximately 40%.
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Affiliation(s)
- G V Swapna
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, 08854-5638, USA.
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Schmieder P, Leidert M, Kelly M, Oschkinat H. Multiplicity-Selective Coherence Transfer Steps for the Design of Amino Acid-Selective Experiments-A Triple-Resonance Experiment Selective for Asn and Gln. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 131:199-202. [PMID: 9571093 DOI: 10.1006/jmre.1997.1348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A multiplicity-selective coherence transfer step is discussed, that can replace the normal INEPT transfer in triple-resonance experiments. Depending on the pulse sequence in which they are implemented, amino acid-selective experiments will be created. Two experiments selective for Asn and Gln are proposed. Copyright 1998 Academic Press.
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Affiliation(s)
- P Schmieder
- Forschungsinstitut für Molekulare Pharmakologie, Alfred-Kowalke-Strasse 4, Berlin, D-10315, Germany
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Tashiro M, Tejero R, Zimmerman DE, Celda B, Nilsson B, Montelione GT. High-resolution solution NMR structure of the Z domain of staphylococcal protein A. J Mol Biol 1997; 272:573-90. [PMID: 9325113 DOI: 10.1006/jmbi.1997.1265] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor from the bacterium Staphylococcus aureus. Because of their small size and immunoglobulin (IgG)-binding activities, domains of protein A are targets for protein engineering efforts and for the development of computational approaches for de novo protein folding. The NMR solution structure of an engineered IgG-binding domain of SpA, the Z domain (an analog of the B domain of SpA), has been determined by simulated annealing with restrained molecular dynamics on the basis of 671 conformational constraints. The Z domain contains three well-defined alpha-helices corresponding to polypeptide segments Lys7 to Leu17 (helix 1), Glu24 to Asp36 (helix 2), and Ser41 to Ala54 (helix 3). A family of ten conformers representing the solution structure of the Z domain was computed by simulated annealing of restrained molecular dynamics using the program CONGEN. The average of the root-mean-square deviations (r.m. s.d.) of the individual NMR conformers, relative to the mean coordinates, for the backbone atoms N, Calpha and C' of residues Phe5 through Ala56 is 0.69 A; the corresponding backbone r.m.s.d. for the three-helical core is 0.44 A. Helices 1, 2 and 3 are antiparallel in orientation (Omega12=-170(+/-4) degrees , Omega13=+16(+/-3) degrees , Omega23=+173(+/-7) degrees ). A comparison of backbone amide hydrogen/deuterium exchange rates in free and IgG-bound Z domains demonstrates that the amide protons of helices 1, 2 and 3 are protected from rapid exchange in both states, indicating that all three helices are also intact in the IgG-bound state. These solution NMR results differ from the previously determined X-ray structure of the similar SpA B domain in complex with the Fc fragment of a human IgG antibody, where helix 3 is not observed in the electron density map and from the solution NMR structure of the B domain, where helix 3 is observed but helix 1 is tilted by approximately 30 degrees with respect to helices 2 and 3. Hydrogen-bonded N-cap and C-cap formation is observed for all three helices of the Z domain; these capping interactions appear to be highly conserved in the five homologous domains of SpA.
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Affiliation(s)
- M Tashiro
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854-5638, USA
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