1
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Walder BJ, Fritzsching KJ. Weighted A nX multiplets. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 347:107353. [PMID: 36571906 DOI: 10.1016/j.jmr.2022.107353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 06/18/2023]
Abstract
That the NMR transition of a spin-1/2 nucleus is split into n evenly spaced lines by indirect dipole-dipole (J) coupling to n magnetically equivalent nuclei, whose successive amplitudes follow the nth row of Pascal's triangle, is an elementary result in NMR. Described here are a family of less well known multiplet structures with different amplitudes for the evenly spaced lines. The amplitudes can be derived from the nth row of Pascal's triangle by weighting the corresponding value of the row by z or z2, where z is related to the summed magnetic quantum number of the magnetically equivalent spins. z1-multiplets have been described in INEPT experiments. A z2-multiplet can be indirectly observed in HSQC experiments when the decoupling pulse during t1 is removed, i.e., an F1-coupled HSQC. While not difficult to generate and despite some reported usefulness, to the best of our knowledge, z2-multiplets have not been rigorously described in previous literature.
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Affiliation(s)
- Brennan J Walder
- Sandia National Laboratories, 1611 Innovation Pkwy SE, 87123 Albuquerque, NM, USA.
| | - Keith J Fritzsching
- Sandia National Laboratories, 1611 Innovation Pkwy SE, 87123 Albuquerque, NM, USA.
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2
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Becker J, Koos MRM, Schulze-Sünninghausen D, Luy B. ASAP-HSQC-TOCSY for fast spin system identification and extraction of long-range couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 300:76-83. [PMID: 30711785 DOI: 10.1016/j.jmr.2018.12.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Based on Ernst-angle-type excitation and Acceleration by Sharing Adjacent Polarization (ASAP), a fast HSQC-TOCSY experiment is introduced. In the approach, the DIPSI-2 isotropic mixing period of the ASAP-HSQC is simply shifted, which provides a TOCSY period without additional application of rf-energy. The ASAP-HSQC-TOCSY allows the acquisition of a conventional 2D in about 30 s. Alternatively, it allows the acquisition of highly carbon-resolved spectra (several Hz digital resolution) on the order of minutes. An ASAP-HSQC-TOCSY-IPAP variant, finally, allows the sign-sensitive extraction of heteronuclear long-range coupling constants from a pair of highly resolved spectra in less than an hour. Pulse sequences, several example spectra, and a discussion of results are given.
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Affiliation(s)
- Johanna Becker
- Institut für Organische Chemie and Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Martin R M Koos
- Institut für Organische Chemie and Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - David Schulze-Sünninghausen
- Institut für Organische Chemie and Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Burkhard Luy
- Institut für Organische Chemie and Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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3
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Marcó N, Nolis P, Gil RR, Parella T. 2J HH-resolved HSQC: Exclusive determination of geminal proton-proton coupling constants. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 282:18-26. [PMID: 28686954 DOI: 10.1016/j.jmr.2017.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 06/07/2023]
Abstract
The measurement of two-bond proton-proton coupling constants (2JHH) in prochiral CH2 groups from the F2 dimension of 2D spectra is not easy due to the usual presence of complex multiplet J patterns, line broadening effects and strong coupling artifacts. These drawbacks are particularly pronounced and frequent in AB spin systems, as those normally exhibited by the pair of diastereotopic CH2 protons. Here, a novel 2JHH-resolved HSQC experiment for the exclusive and accurate determination of the magnitude of 2JHH from the doublet displayed along the highly-resolved indirect F1 dimension is described. A pragmatic 2JHH NMR profile affords a fast overview of the full range of existing 2JHH values. In addition, a 2JHH/δ(13C)-scaled version proves to be an efficient solution when severe signal overlapping complicate a rigorous analysis. The performance of the method is compared with other current techniques and illustrated by the determination of challenging residual dipolar 2DHH coupling constants of small molecules dissolved in weakly orienting media.
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Affiliation(s)
- Núria Marcó
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Pau Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Catalonia, Spain.
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4
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Marcó N, Gil RR, Parella T. Structural discrimination from in situ measurement of 1 D CH and 2 D HH residual dipolar coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:540-545. [PMID: 28043096 DOI: 10.1002/mrc.4575] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 06/06/2023]
Abstract
A fast residual dipolar coupling constant-assisted strategy involving the simultaneous determination of scalar and total coupling constants from a single 1 JCH /2 JHH -resolved NMR spectrum is reported. It is shown that the concerted use of the directly measured 1 DCH (for all CHn multiplicities) and 2 DHH residual dipolar couplings allows an on-the-fly assignment of diastereotopic CH2 protons, as well as of an efficient discrimination between diastereoisomeric structures of strychnine which contains six stereocenters. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Núria Marcó
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
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5
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Augustyniak R, Stanek J, Colaux H, Bodenhausen G, Koźmiński W, Herrmann T, Ferrage F. Nuclear overhauser spectroscopy of chiral CHD methylene groups. JOURNAL OF BIOMOLECULAR NMR 2016; 64:27-37. [PMID: 26614488 DOI: 10.1007/s10858-015-0002-0] [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: 06/23/2015] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure.
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Affiliation(s)
- Rafal Augustyniak
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Henri Colaux
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
| | - Geoffrey Bodenhausen
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
- Ecole Polytechnique Fédérale de Lausanne, Institut des Sciences et Ingénierie Chimiques, BCH, 1015, Lausanne, Switzerland
| | - Wiktor Koźmiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, Université de Lyon/UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Fabien Ferrage
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France.
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France.
- UMR 7203 LBM, CNRS, 75005, Paris, France.
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6
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Castañar L, Sistaré E, Virgili A, Williamson RT, Parella T. Suppression of phase and amplitude J(HH) modulations in HSQC experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:115-119. [PMID: 25279825 DOI: 10.1002/mrc.4149] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/11/2014] [Accepted: 08/25/2014] [Indexed: 06/03/2023]
Abstract
The amplitude and the phase of cross peaks in conventional 2D HSQC experiments are modulated by both proton-proton, J(HH), and proton-carbon, (1)J(CH), coupling constants. It is shown by spectral simulation and experimentally that J(HH) interferences are suppressed in a novel perfect-HSQC pulse scheme that incorporates perfect-echo INEPT periods. The improved 2D spectra afford pure in-phase cross peaks with respect to (1)J(CH) and J(HH), irrespective of the experiment delay optimization. In addition, peak volumes are not attenuated by the influence of J(HH), rendering practical issues such as phase correction, multiplet analysis, and signal integration more appropriate.
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Affiliation(s)
- Laura Castañar
- Servei de Ressonància Magnètica Nuclear, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Catalonia, Spain; Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Catalonia, Spain
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7
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Saurí J, Castañar L, Nolis P, Virgili A, Parella T. Straightforward measurement of individual (1)J(CH) and (2)J(HH) in diastereotopic CH(2) groups. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 242:33-40. [PMID: 24602927 DOI: 10.1016/j.jmr.2014.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/31/2014] [Accepted: 02/02/2014] [Indexed: 06/03/2023]
Abstract
The C-H(A) cross-peak corresponding to a diastereotopic CHAHB methylene spin system exhibits a characteristic 1:0:1 multiplet pattern along the indirect dimension of a ω1-coupled HSQC spectrum. It is shown here that the use of the initial (13)C Boltzmann polarization instead of the regular INEPT-based (1)H Boltzmann polarization makes visible the central lines of this multiplet pattern. A spin-state-selective method is proposed for the efficient measurement of both (1)J(CHA) and (1)J(CHB) along the indirect dimension of a 2D spectrum as well as to the magnitude and the sign of the geminal (2)J(HAHB) coupling constant from the straightforward analysis of a single four-component E.COSY cross-peak. Additionally, the extraction of (1)J(CH) values for CH and CH3 multiplicities can be also performed from the same spectrum. The success of the method is also illustrated for the determination of residual dipolar (1)D(CH) and (2)D(HH) coupling constants in a small molecule weakly aligned in a PMMA swollen gel.
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Affiliation(s)
- Josep Saurí
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Laura Castañar
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Pau Nolis
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Albert Virgili
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain.
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8
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Lupulescu A, Olsen GL, Frydman L. Toward single-shot pure-shift solution 1H NMR by trains of BIRD-based homonuclear decoupling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 218:141-146. [PMID: 22446507 DOI: 10.1016/j.jmr.2012.02.018] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/22/2012] [Accepted: 02/23/2012] [Indexed: 05/31/2023]
Abstract
Achieving homonuclear 1H decoupling remains one of the key challenges in liquid-state NMR. Such spectra would endow a variety of organic and analytical applications with an increased resolution, and would ideally do so even in a one-dimensional format. A number of parallel efforts aimed at achieving this goal using two-dimensional acquisitions have been proposed; approaches demonstrated over recent years include, among others, new modes for achieving purely-absorptive J spectroscopy, the use of spatially-selective manipulations, and exploiting the natural spin dilution afforded by heteronuclei. The present study relies on the latter approach, and explores the use of BIRD pulses distinguishing between protons bonded to (13)C from those bonded to (12)C, to achieve homonuclear decoupling in a continuous 1D scan. Studies on several representative compounds demonstrate that this goal can be implemented in a robust format, provided that suitable care is also taken to suppress unwanted coherences, of making all manipulations sufficiently broad-banded, and to provide adequate heteronuclear decoupling of the targeted protons. Dependable homonuclear decoupling performance can then be achieved, with minimal line width, fine-tuning, and sensitivity penalties.
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Affiliation(s)
- Adonis Lupulescu
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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9
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Carlomagno T. NMR in natural products: understanding conformation, configuration and receptor interactions. Nat Prod Rep 2012; 29:536-54. [PMID: 22456471 DOI: 10.1039/c2np00098a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.
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Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg
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10
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Thiele CM, Bermel W. Speeding up the measurement of one-bond scalar (1J) and residual dipolar couplings (1D) by using non-uniform sampling (NUS). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:134-43. [PMID: 22342269 DOI: 10.1016/j.jmr.2012.01.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/12/2012] [Accepted: 01/22/2012] [Indexed: 05/16/2023]
Abstract
The accurate and precise measurement of one-bond scalar and residual dipolar coupling (RDC) constants is of prime importance to be able to use RDCs for structure determination. If coupling constants are to be extracted from the indirect dimension of HSQC spectra a significant saving of measurement time can be achieved by non-uniform sampling (NUS). Coupling constants can either be obtained with the same precision as in traditionally acquired spectra in a fraction of the measurement time or the precision can be significantly improved if the same amount of measurement time as for traditionally acquired spectra is invested. The application of NUS for the measurement of (1)J (scalar coupling constants) and (1)T (total couplings constants) from different kinds of ω(1)-coupled spectra (including also J-scaled ones) is examined in detail and the possible gains in time or resolution are discussed. When using the newly proposed compressed sensing (CS) algorithm for processing, the quality of the spectra is comparable to the traditionally sampled ones.
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Affiliation(s)
- Christina M Thiele
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Petersenstr. 22, 64287 Darmstadt, Germany.
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11
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Kummerlöwe G, Luy B. Residual dipolar couplings as a tool in determining the structure of organic molecules. Trends Analyt Chem 2009. [DOI: 10.1016/j.trac.2008.11.016] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Affiliation(s)
- Christina M. Thiele
- Technische Universität Darmstadt, Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Petersenstr. 22, 64287 Darmstadt, Germany, Fax: +49‐6151‐165531
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13
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Cramer N, Helbig S, Baro A, Laschat S, Diestel R, Sasse F, Mathieu D, Richter C, Kummerlöwe G, Luy B, Schwalbe H. Synthesis and Biological Properties of Cylindramide Derivatives: Evidence for Calcium-Dependent Cytotoxicity of Tetramic Acid Lactams. Chembiochem 2008; 9:2474-86. [DOI: 10.1002/cbic.200800284] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Guichard G, Violette A, Chassaing G, Miclet E. Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:918-924. [PMID: 18720449 DOI: 10.1002/mrc.2271] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Ability of N,N'-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent (3)J(HH) constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual (1)J(CH) couplings within each methylene group revealed uniform values throughout the oligourea sequence, with (1)J(CH) systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at (13)C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons.
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Affiliation(s)
- Gilles Guichard
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Immunologie et Chimie Thérapeutique, 15, Rue Descartes, Strasbourg F-67084, France
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15
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Luy B, Frank A, Kessler H. Conformational Analysis of Drugs by Nuclear Magnetic Resonance Spectroscopy. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/9783527621286.ch9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Tzvetkova P, Simova S, Luy B. P.E.HSQC: a simple experiment for simultaneous and sign-sensitive measurement of (1JCH+DCH) and (2JHH+DHH) couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 186:193-200. [PMID: 17347001 DOI: 10.1016/j.jmr.2007.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 02/09/2007] [Accepted: 02/12/2007] [Indexed: 05/14/2023]
Abstract
The angular information content of residual dipolar couplings between nuclei of fixed distance makes the accurate and sign-sensitive measurement of (1JCH+DCH) and (2JHH+DHH) couplings highly desirable. Experiments published so far are typically highly specialized for the effective measurement of a subset of couplings. The P.E.HSQC presented here, is an E.COSY based experiment which allows the simultaneous measurement of all heteronuclear and homonuclear couplings within CH, CH2, and CH3 groups in a single spectrum with the necessary precision and sign information. The simplicity of the approach and the absence of artefacts like phase distortions due to antiphase evolution make it ideally suited for coupling determination of organic molecules at natural abundance.
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Affiliation(s)
- Pavleta Tzvetkova
- Department Chemie, Organische Chemie II, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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17
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Kobzar K, Luy B. Analyses, extensions and comparison of three experimental schemes for measuring ((n)J(CH)+D(CH))-couplings at natural abundance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 186:131-41. [PMID: 17336556 DOI: 10.1016/j.jmr.2007.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 02/05/2007] [Accepted: 02/05/2007] [Indexed: 05/14/2023]
Abstract
Three types of experiments for measuring (n)J(CH) heteronuclear long-range coupling constants are examined and extended with state-of-the-art pulse sequence building-blocks: The use of a HMBC with corresponding reference-HSQC for accurate coupling determination is combined with the constant time technique and the conversion of antiphase magnetization into ZQ/DQ-coherences; CPMG-based LR-CAHSQC and BIRD(r,X)-HSQMBC experiments are examined in detail with respect to their coherence transfer properties; finally, the HSQC-TOCSY-IPAP experiment is introduced, a sequence derived from previously published alpha and beta selective HSQC-TOCSYs using a different spin state selection technique and a recently developed ZQ-suppression method. The experiments are characterized with their advantages and disadvantages and compared using strychnine and menthol as standard molecules.
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Affiliation(s)
- Kyryl Kobzar
- Department Chemie, Organische Chemie II, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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18
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Nolis P, Parella T. Simultaneous alpha/beta spin-state selection for (13)C and (15)N from a time-shared HSQC-IPAP experiment. JOURNAL OF BIOMOLECULAR NMR 2007; 37:65-77. [PMID: 17160627 DOI: 10.1007/s10858-006-9104-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Accepted: 10/19/2006] [Indexed: 05/12/2023]
Abstract
Two novel HSQC-IPAP approaches are proposed to achieve alpha/beta spin-state editing simultaneously for (13)C and (15)N in a single NMR experiment. The pulse schemes are based on a time-shared (TS) 2D (1)H,(13)C/(1)H,(15)N-HSQC correlation experiment that combines concatenated echo elements for simultaneous J(CH) and J(NH) coupling constants evolution, TS evolution of (13)C and (15)N chemical shifts in the indirect dimension and heteronuclear alpha/beta-spin-state selection by means of the IPAP principle. Heteronuclear alpha/beta-editing for all CH( n ) (n = 1-3) and NH( n ) (1-2) multiplicities can be achieved in the detected F2 dimension of a single TS-HSQC-F2-IPAP experiment. On the other hand, an alternative TS-HSQC-F1-IPAP experiment is also proposed to achieve alpha/beta-editing in the indirect F1 dimension. Experimental and simulated data is provided to evaluate these principles in terms of sensitivity and performance simultaneously on backbone and side-chain CH, CH(2), CH(3), NH, and NH(2) spin systems in uniformly (13)C/(15)N-labeled proteins and in small natural-abundance peptides.
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Affiliation(s)
- Pau Nolis
- Servei de Ressonància Magnètica Nuclear, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
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19
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Residual Dipolar Couplings Report on the Active Conformation of Rhodopsin-Bound Protein Fragments. Top Curr Chem (Cham) 2006. [DOI: 10.1007/128_2006_088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Nolis P, Espinosa JF, Parella T. Optimum spin-state selection for all multiplicities in the acquisition dimension of the HSQC experiment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 180:39-50. [PMID: 16448830 DOI: 10.1016/j.jmr.2006.01.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Revised: 12/29/2005] [Accepted: 01/04/2006] [Indexed: 05/06/2023]
Abstract
Most conventional heteronuclear spin-state-selective (S(3)) NMR experiments only work for a specific multiplicity, typically IS spin systems. Here, we introduce a general and efficient IPAP strategy to achieve S(3) editing simultaneously for all multiplicities in the acquisition dimension of the HSQC experiment. Complementary in-phase (HSQC-IP) and anti-phase (HSQC-AP) data are separately recorded with a simple phase exchange of two 90 degrees proton pulses involved in the mixing process of the F2-coupled sensitivity-improved HSQC pulse sequence. Additive and subtractive linear combination of these IP/AP data generates simplified F2-alpha/beta-spin-edited HSQC subspectra for all IS, I(2)S, and I(3)S spin systems and combines enhanced and optimized sensitivity with excellent tolerance to unwanted cross-talk contributions over a considerable range of coupling constants. Practical aspects such as pulse phase settings, transfer efficiency dependence, inter-pulse delay optimization, and percentage of cross-talk are theoretically analyzed and discussed as a function of each I(n)S multiplicity. Particular emphasis on the features associated to spin-editing in diastereotopic I(2)S spin systems and application to the measurement of long-range proton-carbon coupling constants are also provided.
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Affiliation(s)
- Pau Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
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21
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de Alba E, Tjandra N. Interference between cross-correlated relaxation and the measurement of scalar and dipolar couplings by Quantitative J. JOURNAL OF BIOMOLECULAR NMR 2006; 35:1-16. [PMID: 16791736 DOI: 10.1007/s10858-006-0028-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 02/27/2006] [Indexed: 05/10/2023]
Abstract
The effects of cross-correlated relaxation in Quantitative J methods are analyzed. One-bond 1H-13C scalar and dipolar couplings of protein methine and methylene sites are obtained by monitoring proton and carbon magnetization in Quantitative J experiments. We find that scalar and dipolar couplings of the same pair of nuclei vary depending on the type of magnetization involved. These discrepancies can be as large as several Hz for methylene moieties. The contribution of dynamic frequency shifts, which are known to affect J couplings, is too small to explain the observed differences. We show that processes of magnetization transfer originated by cross-correlated relaxation are largely responsible for these discrepancies. We estimate the error transferred to methylene J values by cross-correlation interference, and show that is close to the experimentally observed one. Furthermore, this analysis indicates that cross-correlated relaxation effects under isotropic and anisotropic media differ, indicating that errors are not cancelled in residual dipolar coupling measurements.
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Affiliation(s)
- Eva de Alba
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, Maryland, 20892, USA.
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22
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Pristovsek P, Franzoni L. Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data. J Comput Chem 2006; 27:791-7. [PMID: 16526035 DOI: 10.1002/jcc.20389] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In many cases of protein structure determination by NMR a high-quality structure is required. An important contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists. Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and used on NMR data of alpha-helical and beta-sheet proteins using homology models and/or X-ray structures. The program produced no erroneous stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar coupling information is available.
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Affiliation(s)
- Primoz Pristovsek
- National Institute of Chemistry, Laboratory of Biotechnology, P.O. Box 660, Hajdrihova 19, S-1001 Ljubljana, Slovenia
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23
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Miclet E, Boisbouvier J, Bax A. Measurement of eight scalar and dipolar couplings for methine-methylene pairs in proteins and nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2005; 31:201-216. [PMID: 15803394 DOI: 10.1007/s10858-005-0175-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Accepted: 12/20/2004] [Indexed: 05/24/2023]
Abstract
A new 3D, spin-state-selective coherence transfer NMR experiment is described that yields accurate measurements for eight scalar or dipolar couplings within a spin system composed of a methylene adjacent to a methine group. Implementations of the experiment have been optimized for proteins and for nucleic acids. The experiments are demonstrated for Cbeta-Calpha moieties of the third IgG-binding domain from Streptococcal Protein G (GB3) and for C5'-C4' groups in a 24-nt RNA oligomer. Chemical shifts of Calpha, Cbeta and Hbeta (respectively C4', C5' and H5') are dispersed in the three orthogonal dimensions, and the absence of heteronuclear decoupling leads to distinct and well-resolved E.COSY multiplet patterns. In an isotropic sample, the E.COSY displacements correspond to 1J(CalphaHalpha), 2J(CalphaHbeta2)+2J(CalphaHbeta3), 2J(CbetaHalpha), 1J(CbetaHbeta2)+1J(CbetaHbeta3), 1J(CbetaHbeta2)-2J(Hbeta2Hbeta3), 1J(CbetaHbeta3)-2J(Hbeta2Hbeta3), 3J(HalphaHbeta2) and 3J(HalphaHbeta3) for proteins, and 1J(C4'H4'), 2J(C4'H5')+2J(C4'H5"), 2J(C5'H4'), 1J(C5'H5')+1J(C5'H5"), 1J(C5'H5')-2J(H5'H5"), 1J(C5'H5")-2J(H5'H5"), 3J(H4'H5') and 3J(H4'H5") in nucleic acids. The experiment, based on relaxation-optimized spectroscopy, yields best results when applied to residues where the methine-methylene group corresponds to a reasonably isolated spin system, as applies for C, F, Y, W, D, N and H residues in proteins, or the C5'-C4' groups in nucleic acids. Splittings can be measured under either isotropic or weakly aligned conditions, yielding valuable structural information both through the 3J couplings and the one-, two- and three-bond dipolar interactions. Dipolar couplings for 10 out of 13 sidechains in GB3 are found to be in excellent agreement with its X-ray structure, whereas one residue adopts a different backbone geometry, and two residues are subject to extensive chi1 rotamer averaging. The abundance of dipolar couplings can also yield stereospecific assignments of the non-equivalent methylene protons. For the RNA oligomer, dipolar data yielded stereospecific assignments for six out of the eight C5'H2 groups in the loop region of the oligomer, in all cases confirmed by 1J(C5'H5')>1J(C5'H5"), and H5' resonating downfield of H5".
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Affiliation(s)
- Emeric Miclet
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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Miclet E, Williams DC, Clore GM, Bryce DL, Boisbouvier J, Bax A. Relaxation-optimized NMR spectroscopy of methylene groups in proteins and nucleic acids. J Am Chem Soc 2004; 126:10560-70. [PMID: 15327312 DOI: 10.1021/ja047904v] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A large fraction of hydrogens in proteins and nucleic acids is of the methylene type. Their detailed study, however, in terms of structure and dynamics by NMR spectroscopy is hampered by their fast relaxation properties, which give rise to low sensitivity and resolution. It is demonstrated that six different relaxation interference processes, involving 1H-13C and 1H-1H dipolar interactions and 1H and 13C chemical shift anisotropy, can be used simultaneously to mitigate these problems effectively. The approach is applicable to the majority of NMR experiments commonly used to study side chain and backbone conformation. For proteins, its efficiency is evaluated quantitatively for two samples: the third IgG-binding domain from Streptococcal Protein G and the protein calmodulin complexed with a 26-residue target peptide. Gains in both resolution and sensitivity by up to factors of 3.2 and 2.0, respectively, are observed for Gly residues at high magnetic field strengths, but even at much lower fields gains remain substantial. The resolution enhancement obtained for methylene groups makes possible a detailed analysis of spectral regions commonly considered inaccessible due to spectral crowding. For DNA, the high resolution now obtainable for C5' sites permits an H5'/H5''-based sequential NOE assignment procedure, complementary to the conventional base-H1'/H2'/H2'' pathway.
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Affiliation(s)
- Emeric Miclet
- Contribution from the Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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25
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Parella T, Gairí M. Simultaneous Recording of Spin-State-Selective NMR Spectra for Different InS Spin Systems. J Am Chem Soc 2004; 126:9821-6. [PMID: 15291586 DOI: 10.1021/ja0495866] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heteronuclear magnetization transfer occurring during heteronuclear cross-polarization mixing processes in liquid-state NMR experiments can be easily monitored as a function of the involved in-phase, antiphase, and multiple-quantum magnetization components. The theoretical background on the simultaneous detection of E.COSY-type, TROSY-type, or spin-edited multiplet patterns for different IS and I(2)S spin systems in the same solution-state NMR spectrum is described. The proposed pulse scheme preserves high sensitivity levels and shows good tolerance to the presence of undesired cross-talk artifacts for both NH and NH(2) multiplicities providing an interesting NMR tool for biomolecular applications.
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Affiliation(s)
- Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autonoma de Barcelona, E-08193, Bellaterra, Spain.
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26
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Prestegard JH, Bougault CM, Kishore AI. Residual Dipolar Couplings in Structure Determination of Biomolecules. Chem Rev 2004; 104:3519-40. [PMID: 15303825 DOI: 10.1021/cr030419i] [Citation(s) in RCA: 340] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
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27
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Kramer F, Jung A, Brunner E, Glaser SJ. Determining the relative sign and size of scalar and residual dipolar couplings in homonuclear two-spin systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 169:49-59. [PMID: 15183356 DOI: 10.1016/j.jmr.2004.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Revised: 03/31/2004] [Indexed: 05/24/2023]
Abstract
Based on the sign and amplitude of TOCSY transfer functions, it is possible to determine the relative sign and size of scalar and residual dipolar couplings in homonuclear spin systems consisting of two spins 1/2. The efficiency of different mixing sequences and different transfer functions is examined both theoretically and experimentally.
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Affiliation(s)
- Frank Kramer
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
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28
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Kövér KE, Fehér K. Measurement of one-bond heteronuclear dipolar coupling contributions for amine and diastereotopic methylene protons. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 168:307-313. [PMID: 15140442 DOI: 10.1016/j.jmr.2004.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2003] [Revised: 03/03/2004] [Indexed: 05/24/2023]
Abstract
One-bond heteronuclear and two-bond homonuclear residual dipolar couplings measured at methylene or amine sites can be utilized as long-range constraints in structure determination of molecules as well as to facilitate characterization of local conformation by stereospecific assignment of diastereotopic protons. We present two J-modulated HMQC type experiments to measure the one-bond heteronuclear dipolar coupling contributions of geminal protons individually. In addition two-bond homonuclear residual dipolar couplings between the diastereotopic protons are also obtained.
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Affiliation(s)
- Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, P.O. Box 21, H-4010 Debrecen, Hungary.
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29
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Thiele CM. Simultaneous Assignment of All Diastereotopic Protons in Strychnine Using RDCs: PELG as Alignment Medium for Organic Molecules. J Org Chem 2004; 69:7403-13. [PMID: 15497963 DOI: 10.1021/jo049867w] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The concept of using residual dipolar couplings (RDCs) for the structure determination of organic molecules is applied to the simultaneous assignment of all diastereotopic protons in strychnine. To use this important NMR parameter the molecule has to be aligned in the magnetic field. Here we present a new alignment medium for organic substrates. The optimization of the alignment properties of mixtures of poly-gamma-ethyl-L-glutamate (PELG) and CDCl(3) are described and the alignment properties of PELG at different concentrations are evaluated. A comparison of PELG with poly-gamma-benzyl-L-glutamate (PBLG) shows considerable differences in the magnitude of alignment for strychnine in the two alignment media. PELG induces a lower degree of order and makes the measurement of residual dipolar couplings (RDCs) in strychnine possible. All one-bond C-H RDCs of strychnine in PELG were determined by using 2D heteronuclear single quantum coherence (HSQC) spectroscopy. The strategy for the extraction of RDCs for methylene groups is described in detail. The RDCs and order parameters are used to assign pairs of diastereotopic protons. This methodology can distinguish not only one pair of diastereotopic protons but it can be used to assign all pairs of diastereotopic protons simultaneously. Two different calculation approaches to achieve this task are described in detail.
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Affiliation(s)
- Christina M Thiele
- Institut für Analytische Chemie, Universität Leipzig, Johannisallee 29, D-04103 Leipzig, Germany.
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30
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Miclet E, O'Neil-Cabello E, Nikonowicz EP, Live D, Bax A. 1H-1H dipolar couplings provide a unique probe of RNA backbone structure. J Am Chem Soc 2004; 125:15740-1. [PMID: 14677953 DOI: 10.1021/ja0388212] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A NMR method is described that permits simultaneous measurement of the geminal 2JH1H2 + 2DH1H2 splitting and the sum of the 1JCH1 + 1DCH1 + 1JCH2 + 1DCH2 couplings for methylene groups, where 2DH1H2 and 1DCH are residual dipolar couplings, occurring when molecules are weakly oriented relative to the magnetic field. By suppressing either the upfield or downfield half of the 1H-1H geminal doublet, the experiment yields improved resolution relative to regular two-dimensional 1H-13C correlation spectra, making it applicable to systems of considerable complexity. The method is demonstrated for measurement of all 2DH5'H5'' couplings in a 24-nucleotide 13C-enriched RNA stem loop structure, weakly aligned in liquid crystalline Pf1. The method is equally applicable to methylene groups in 13C-labeled proteins and to natural abundance samples of smaller molecules.
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Affiliation(s)
- Emeric Miclet
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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31
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Luy B, Marino JP. JE-TROSY: combined J- and TROSY-spectroscopy for the measurement of one-bond couplings in macromolecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 163:92-98. [PMID: 12852911 DOI: 10.1016/s1090-7807(03)00105-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
With the application of RDCs in high-resolution NMR studies of macromolecules, there has been an interest in the development of accurate, sensitive methods for measuring 15N-1H and 13C-1H one-bond coupling constants. Most methods for determining these couplings are based on the measurement of the displacement between cross-peak components in J-coupled spectra. However, for large macromolecules and macromolecular complexes, these methods are often unreliable since differential relaxation can significantly broaden one of the multiplet components (i.e., the anti-TROSY component) and thereby make accurate determination of its position difficult. To overcome this problem, a J-evolved transverse relaxation optimized (JE-TROSY) method is presented for the determination of one-bond couplings that involves J-evolution of the sharpest cross-peak multiplet component selected in a TROSY experiment. Couplings are measured from the displacement of the TROSY component in the additional J-evolution dimension relative to a zero frequency origin. The JE-TROSY method is demonstrated on uniformly labeled 15N, 13C-labeled RNA and peptide samples, as well as with an RNA-protein complex, in which the protein is uniformly 15N, 13C-labeled. In all cases, resolved, sensitive spectra are obtained from which heteronuclear one-bond J-couplings could be accurately and easily measured.
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Affiliation(s)
- Burkhard Luy
- Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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32
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Permi P. Two simple NMR experiments for measuring dipolar couplings in asparagine and glutamine side chains. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 153:267-272. [PMID: 11740905 DOI: 10.1006/jmre.2001.2449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Residual dipolar couplings are now widely used for structure determination of biological macromolecules. Until recently, the main focus has been on measurement of dipolar couplings in the protein main chain. However, with the aim of more complete protein structure, it is also essential to have information on the orientation of protein side chains. In addition, residual dipolar couplings can potentially be employed to study molecular dynamics. In this Communication, two simple NH(2) and spin-state edited experiments are presented for rapid and convenient determination of five residual dipolar couplings from (15)N, (1)H correlation spectrum in asparagine and glutamine side chains. The pulse sequences are demonstrated on two proteins, 30.4-kDa Cel6A in diluted liquid crystal phase and 18-kDa human cardiac troponin C in water.
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Affiliation(s)
- P Permi
- Institute of Biotechnology, University of Helsinki, Helsinki, FIN-00014, Finland.
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33
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Affiliation(s)
- A Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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34
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Wu Z, Bax A. Measurement of homonuclear proton couplings based on cross-peak nulling in CT-COSY. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 151:242-252. [PMID: 11531346 DOI: 10.1006/jmre.2001.2358] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A method in which 1H-1H scalar and dipolar couplings are obtained from the cross-peak nulling condition in a series of constant-time (CT) COSY spectra, as a function of the duration of the CT period, is described. The method is best suited for measurement of 1H-1H couplings in the range 5-20 Hz. It is shown, however, that results can be sensitive to cross-correlated relaxation effects. Also, artifactual resonances, resulting from strong coupling, can be quite pronounced in CT-COSY spectra, even when /J(AB)/(deltaA-deltaB)/<0.1. The experiments are demonstrated for the DNA dodecamer d(CGCGAATTCGCG)2, both in isotropic solution and in a liquid crystalline phase.
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Affiliation(s)
- Z Wu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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35
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Mittermaier A, Kay LE. Chi1 torsion angle dynamics in proteins from dipolar couplings. J Am Chem Soc 2001; 123:6892-903. [PMID: 11448195 DOI: 10.1021/ja010595d] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experiments are presented for the measurement of one-bond carbon-proton dipolar coupling values at CH and CH2 ositions in 13C-labeled, approximately 50% fractionally deuterated proteins. 13Cbeta-1Hbeta dipolar couplings have been measured for 38 of 49 possible residues in the 63-amino-acid B1 domain of peptostreptococcal protein L in two aligning media and interpreted in the context of side-chain chi1 torsion angle dynamics. The beta protons for 18 of the 25 beta-methylene-containing amino acids for which dipolar data are available can be unambiguously stereoassigned, and for those residues which are best fit to a single rotamer model the chi(1) angles obtained deviate from crystal structure values by only 5.2 degrees (rmsd). The results for 11 other residues are significantly better fit by a model that assumes jumps between the three canonical (chi1 approximately -60 degrees, 60 degrees, 180 degrees ) rotamers. Relative populations of the rotamers are determined to within +/-6% uncertainty on average and correlate with dihedral angles observed for the three molecules in the crystal asymmetric unit. Entropic penalties for quenching chi1 jumps are considered for six mobile residues thought to be involved in binding to human immunoglobulins. This study demonstrates that dipolar couplings may be used to characterize both the conformation of static residues and side-chain motion with high precision.
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Affiliation(s)
- A Mittermaier
- Protein Engineering Centers of Excellence and the Department of Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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36
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37
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Hennig M, Carlomagno T, Williamson JR. Residual dipolar coupling TOCSY for direct through space correlations of base protons and phosphorus nuclei in RNA. J Am Chem Soc 2001; 123:3395-6. [PMID: 11457087 DOI: 10.1021/ja005835o] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M Hennig
- Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, MB 33 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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