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Hansen MR, Hanson P, Pardi A. Pf1 filamentous phage as an alignment tool for generating local and global structural information in nucleic acids. J Biomol Struct Dyn 2016; 17 Suppl 1:365-9. [PMID: 22607445 DOI: 10.1080/07391102.2000.10506642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Pf1 filamentous phage represent a simple versatile method for generating partially ordered macromolecules in solution. The phage allow tunable degrees of alignment of macromolecules under a wide range of temperature and solvent conditions. The negatively charged phage are ideal for aligning negatively charged nucleic acids and these phage-nucleic acid solutions are stable indefinitely. We have used Pf1 phage to align various DNA and RNA molecules in solution for measurement of dipolar coupling interactions. These dipolar couplings can be used to improve the local structure of nucleic acids. More importantly they also contain information on the global structure, such as DNA bending, which presently cannot be obtained by standard NMR methods. The principles involved in using Pf1 phage to generate solutions of partially order macromolecules will be discussed. The use of (1)H-(1)H, (1)H-(13)C and (1)H-(15)N dipolar couplings for generating angle constraints for structure refinement of nucleic acids will also be discussed.
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Affiliation(s)
- M R Hansen
- a Department of Chemistry and Biochemistry , University of Colorado at Boulder , Boulder , CO , 80309-0215
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2
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Thiagarajan-Rosenkranz P, Draney AW, Smrt ST, Lorieau JL. A Positively Charged Liquid Crystalline Medium for Measuring Residual Dipolar Couplings in Membrane Proteins by NMR. J Am Chem Soc 2015; 137:11932-4. [PMID: 26348133 DOI: 10.1021/jacs.5b07515] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pallavi Thiagarajan-Rosenkranz
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Adrian W. Draney
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Sean T. Smrt
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Justin L. Lorieau
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
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3
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Mai-Prochnow A, Hui JGK, Kjelleberg S, Rakonjac J, McDougald D, Rice SA. 'Big things in small packages: the genetics of filamentous phage and effects on fitness of their host'. FEMS Microbiol Rev 2015; 39:465-87. [PMID: 25670735 DOI: 10.1093/femsre/fuu007] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 12/17/2014] [Indexed: 01/01/2023] Open
Abstract
This review synthesizes recent and past observations on filamentous phages and describes how these phages contribute to host phentoypes. For example, the CTXφ phage of Vibrio cholerae encodes the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the emergence of new pathogenic strains. Other effects of filamentous phage include horizontal gene transfer, biofilm development, motility, metal resistance and the formation of host morphotypic variants, important for the biofilm stress resistance. These phages infect a wide range of Gram-negative bacteria, including deep-sea, pressure-adapted bacteria. Many filamentous phages integrate into the host genome as prophage. In some cases, filamentous phages encode their own integrase genes to facilitate this process, while others rely on host-encoded genes. These differences are mediated by different sets of 'core' and 'accessory' genes, with the latter group accounting for some of the mechanisms that alter the host behaviours in unique ways. It is increasingly clear that despite their relatively small genomes, these phages exert signficant influence on their hosts and ultimately alter the fitness and other behaviours of their hosts.
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Affiliation(s)
- Anne Mai-Prochnow
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia
| | - Janice Gee Kay Hui
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia
| | - Staffan Kjelleberg
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Diane McDougald
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Scott A Rice
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
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4
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Arbogast L, Majumdar A, Tolman JR. Unraveling long range residual dipolar coupling networks in strongly aligned proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 235:26-31. [PMID: 23917309 DOI: 10.1016/j.jmr.2013.06.024] [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: 05/22/2013] [Revised: 06/26/2013] [Accepted: 06/28/2013] [Indexed: 06/02/2023]
Abstract
Long-range residual dipolar couplings (lrRDCs) have the potential to serve as powerful structural restraints in protein NMR spectroscopy as they can provide both distance and orientation information about nuclei separate in sequence but close in space. Current nonselective methods for their measurement are limited to moderate alignment strengths due to the sheer abundance of active couplings at stronger alignment. This limits the overall magnitude and therefore distance across which couplings can be measured. We have developed a double resonance technique for the inversion of individual coupled spin pairs, called Selective Inversion by Single Transition Cross Polarization (SIST-CP). This technique enables the selective recoupling of lrRDCs, thus allowing the complex multiplets occurring in strongly aligned systems to be disentangled. This technique is demonstrated in the context of an application to the measurement of (13)C'-(1)H(N) lrRDCs in strongly aligned proteins.
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Affiliation(s)
- Luke Arbogast
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
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5
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Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy. Molecules 2013; 18:11904-37. [PMID: 24077173 PMCID: PMC6270068 DOI: 10.3390/molecules181011904] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/28/2013] [Accepted: 09/17/2013] [Indexed: 11/16/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-tc window (defined as τ(c) < supra-τ(c) < 40 μs; in which tc is the overall tumbling time of a molecule) from the perspective of local inter-nuclear vector dynamics extracted from residual dipolar couplings (RDCs) and from the perspective of conformational exchange captured by relaxation dispersion measurements (RD). The goal of the first section is to present a detailed analysis of how to extract protein dynamics encoded in RDCs and how to relate this information to protein functionality within the previously inaccessible supra-τ(c) window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τ(c) scale by up to a factor of two (motion up to 25 μs). From the data obtained with these techniques and methodology, the importance of the supra-τ(c) scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τ(c) scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.
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6
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Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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7
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Latham MP, Pardi A. Measurement of imino 1H-1H residual dipolar couplings in RNA. JOURNAL OF BIOMOLECULAR NMR 2009; 43:121-129. [PMID: 19067179 PMCID: PMC2846714 DOI: 10.1007/s10858-008-9293-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 11/12/2008] [Accepted: 11/13/2008] [Indexed: 05/27/2023]
Abstract
Imino (1)H-(15)N residual dipolar couplings (RDCs) provide additional structural information that complements standard (1)H-(1)H NOEs leading to improvements in both the local and global structure of RNAs. Here, we report measurement of imino (1)H-(1)H RDCs for the Iron Responsive Element (IRE) RNA and native E. coli tRNA(Val) using a BEST-Jcomp-HMQC2 experiment. (1)H-(1)H RDCs are observed between the imino protons in G-U wobble base pairs and between imino protons on neighboring base pairs in both RNAs. These imino (1)H-(1)H RDCs complement standard (1)H-(15)N RDCs because the (1)H-(1)H vectors generally point along the helical axis, roughly perpendicular to (1)H-(15)N RDCs. The use of longitudinal relaxation enhancement increased the signal-to-noise of the spectra by ~3.5-fold over the standard experiment. The ability to measure imino (1)H-(1)H RDCs offers a new restraint, which can be used in NMR domain orientation and structural studies of RNAs.
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8
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Hennig M, Williamson JR, Brodsky AS, Battiste JL. Recent advances in RNA structure determination by NMR. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.7. [PMID: 18428875 DOI: 10.1002/0471142700.nc0707s02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Despite recent advances in the solution of NMR structures of RNA and RNA-ligand complexes, the rate limiting step remains the gathering of a large number of NOE and torsion restraints. Additional sources of information for structure determination of larger RNA molecules have recently become available, and it is possible to supplement NOE and J-coupling data with the measurement of dipolar couplings and cross-correlated relaxation rates in high-resolution NMR spectroscopy.
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Affiliation(s)
- M Hennig
- The Scripps Research Institute, La Jolla, California, USA
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9
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Parella T, Espinosa JF. Long-range 1H-1H NMR correlation: extending connectivities to remote bonds via an intermediate heterospin. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:464-470. [PMID: 18288678 DOI: 10.1002/mrc.2200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
An out-and-stay 2D proton-proton NMR correlation experiment is proposed to detect long-range proton-proton connectivities up to six and seven bonds away. The magnetization flow pathway is based on a consecutive, dual-step J(CH)-transfer mechanism and it allows one to trace out (1)H-(1)H connectivities between protons belonging to different spin systems. This novel experimental scheme will be particularly useful in cases when carbon resonances overlap, providing connectivity information that could not be obtained in a HMBC experiment. The success of the experiment is demonstrated in the structural studies of a wide variety of chemical compounds.
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Affiliation(s)
- Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193-Bellaterra, Barcelona, Spain.
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10
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Vögeli B, Yao L, Bax A. Protein backbone motions viewed by intraresidue and sequential HN-Halpha residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2008; 41:17-28. [PMID: 18458825 PMCID: PMC2587141 DOI: 10.1007/s10858-008-9237-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 04/07/2008] [Indexed: 05/26/2023]
Abstract
Triple resonance E.COSY-based techniques were used to measure intra-residue and sequential H(N)-H(alpha) residual dipolar couplings (RDCs) for the third IgG-binding domain of protein G (GB3), aligned in Pf1 medium. Measurements closely correlate with values predicted on the basis of an NMR structure, previously determined on the basis of a large number of one-bond backbone RDCs measured in five alignment media. However, in particular the sequential H(N)-H(alpha) RDCs are smaller than predicted for a static structure, suggesting a degree of motion for these internuclear vectors that exceeds that of the backbone amide N-H vectors. Of all experimentally determined GB3 structures available, the best correlation between experimental (1)H-(1)H couplings is observed for a GB3 ensemble, previously derived to generate a realistic picture of the conformational space sampled by GB3 (Clore and Schwieters, J Mol Biol 355:879-886, 2006). However, for both NMR and X-ray-derived structures the (1)H-(1)H couplings are found to be systematically smaller than expected on the basis of alignment tensors derived from (15)N-(1)H amide RDCs, assuming librationally corrected N-H bond lengths of 1.041 A.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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11
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Kummerlöwe G, Knör S, Frank AO, Paululat T, Kessler H, Luy B. Deuterated polymer gels for measuring anisotropic NMR parameters with strongly reduced artefacts. Chem Commun (Camb) 2008:5722-4. [DOI: 10.1039/b812905c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Klages J, Kessler H, Glaser SJ, Luy B. J-ONLY-TOCSY: efficient suppression of RDC-induced transfer in homonuclear TOCSY experiments using JESTER-1-derived multiple pulse sequences. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 189:217-227. [PMID: 17936049 DOI: 10.1016/j.jmr.2007.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Revised: 09/14/2007] [Accepted: 09/14/2007] [Indexed: 05/25/2023]
Abstract
The main purpose of homonuclear Hartmann-Hahn or TOCSY experiments is the assignment of spin systems based on efficient coherence transfer via scalar couplings. In partially aligned samples, however, magnetization is also transferred via residual dipolar couplings (RDCs) and therefore through space correlations can be observed in COSY and TOCSY experiments that make the unambiguous assignment of covalently bound spins impossible. In this article, we show that the JESTER-1 multiple pulse sequence, originally designed for broadband heteronuclear isotropic Hartmann-Hahn transfer, efficiently suppresses the homonuclear dipolar coupling Hamiltonian. This suppression can be enhanced even further by variation of the supercycling scheme. The application of the resulting element in homonuclear TOCSY periods results in coherence transfer via J-couplings only. As a consequence, the assignment of scalar coupled spin systems is also possible in partially aligned samples. The bandwidth of coherence transfer for the JESTER-1-derived sequences is comparable to existing TOCSY multiple pulse sequences. Results are demonstrated in theory and experiment.
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Affiliation(s)
- Jochen Klages
- Department Chemie, Organische Chemie II, Technische Universität München, Lichtenbergstrasse 4, D-85747, Garching, Germany
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13
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Thaning J, Högberg CJ, Stevensson B, Lyubartsev AP, Maliniak A. Molecular Conformations in a Phospholipid Bilayer Extracted from Dipolar Couplings: A Computer Simulation Study. J Phys Chem B 2007; 111:13638-44. [DOI: 10.1021/jp075278t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan Thaning
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Carl-Johan Högberg
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Baltzar Stevensson
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Arnold Maliniak
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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14
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Shahkhatuni AA, Shahkhatuni AG, Panosyan HA, Sahakyan AB, Byeon IJL, Gronenborn AM. Assessment of solvent effects: do weak alignment media affect the structure of the solute? MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45:557-63. [PMID: 17534883 DOI: 10.1002/mrc.2004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Alignment media used for measuring residual dipolar couplings, such as solutions of filamentous phages, phospholipid mixtures, polyacrylamide gels and various lyotropic liquid crystalline systems were investigated with respect to solvent effects on molecular structure. Structural parameters of the small rigid model compound 13C-acetonitrile were calculated from dipolar couplings and variations from expectation values were used for assessment of solvent effects. Only minor solvent effects were observed for most of the media employed and the measured structural data are in good agreement with microwave data and theoretical predictions.
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Affiliation(s)
- Astghik A Shahkhatuni
- Molecule Structure Research Center of National Academy of Sciences, Yerevan, 0014, Armenia
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15
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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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16
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Latham MP, Brown DJ, McCallum SA, Pardi A. NMR methods for studying the structure and dynamics of RNA. Chembiochem 2006; 6:1492-505. [PMID: 16138301 DOI: 10.1002/cbic.200500123] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Proper functioning of RNAs requires the formation of complex three-dimensional structures combined with the ability to rapidly interconvert between multiple functional states. This review covers recent advances in isotope-labeling strategies and NMR experimental approaches that have promise for facilitating solution structure determinations and dynamics studies of biologically active RNAs. Improved methods for the production of isotopically labeled RNAs combined with new multidimensional heteronuclear NMR experiments make it possible to dramatically reduce spectral crowding and simplify resonance assignments for RNAs. Several novel applications of experiments that directly detect hydrogen-bonding interactions are discussed. These studies demonstrate how NMR spectroscopy can be used to distinguish between possible secondary structures and identify mechanisms of ligand binding in RNAs. A variety of recently developed methods for measuring base and sugar residual dipolar couplings are described. NMR residual dipolar coupling techniques provide valuable data for determining the long-range structure and orientation of helical regions in RNAs. A number of studies are also presented where residual dipolar coupling constraints are used to determine the global structure and dynamics of RNAs. NMR relaxation data can be used to probe the dynamics of macromolecules in solution. The power dependence of transverse rotating-frame relaxation rates was used here to study dynamics in the minimal hammerhead ribozyme. Improved methods for isotopically labeling RNAs combined with new types of structural data obtained from a growing repertoire of NMR experiments are facilitating structural and dynamic studies of larger RNAs.
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Affiliation(s)
- Michael P Latham
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, CO 80309-0215, USA
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17
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Thaning J, Stevensson B, Maliniak A. Molecular structure extracted from residual dipolar couplings: Diphenylmethane dissolved in a nematic liquid crystal. J Chem Phys 2005; 123:044507. [PMID: 16095369 DOI: 10.1063/1.1950629] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper describes an analysis of 1H-1H residual dipolar couplings (RDCs) in diphenylmethane (DPM) dissolved in a nematic liquid crystal, reported by Celebre et al. [J. Chem. Phys. 118, 6417 (2003)]. In that article, the conformational distribution function for DPM was extracted from the RDCs, using the additive potential (AP) model which is based on the molecular-field theory. The AP approach is a powerful, and frequently used, tool for analysis of the nuclear-magnetic-resonance (NMR) parameters in liquid crystals. It requires, however, a priori knowledge of the functional form of the torsional potential, which may even for a simple molecule, such as DPM, be complicated to determine. Here, we analyze the same set of the RDCs using our APME procedure, which is a hybrid model based on the AP approach and maximum entropy (ME) theory. The APME procedure does not require any assumptions about the functional form of the torsional potential and, in contrast with the ME method, is applicable to weakly ordered systems. In the investigation reported in the present study, the results from the APME analysis are in good agreement with the AP interpretation, whereas the ME approach essentially fails in the extraction of the conformational distribution function for DPM.
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Affiliation(s)
- Johan Thaning
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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18
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Meiler J, Baker D. The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 173:310-316. [PMID: 15780923 DOI: 10.1016/j.jmr.2004.11.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Revised: 11/24/2004] [Indexed: 05/24/2023]
Abstract
We illustrate how moderate resolution protein structures can be rapidly obtained by interlinking computational prediction methodologies with un- or partially assigned NMR data. To facilitate the application of our recently described method of ranking and subsequent refining alternative structural models using unassigned NMR data [Proc. Natl. Acad. Sci. USA 100 (2003) 15404] for such "structural genomics"-type experiments it is combined with protein models from several prediction techniques, enhanced to utilize partial assignments, and applied on a protein with an unknown structure and fold. From the original NMR spectra obtained for the 140 residue fumarate sensor DcuS, 1100 1H, 13C, and 15N chemical shift signals, 3000 1H-1H NOESY cross peak intensities, and 209 backbone residual dipolar couplings were extracted and used to rank models produced by de novo structure prediction and comparative modeling methods. The ranking proceeds in two steps: first, an optimal assignment of the NMR peaks to atoms is found for each model independently, and second, the models are ranked based on the consistency between the NMR data and the model assuming these optimal assignments. The low-resolution model selected using this ranking procedure had the correct overall fold and a global backbone RMSD of 6.0 angstrom, and was subsequently refined to 3.7 angstrom RMSD. With the incorporation of a small number of NOE and residual dipolar coupling constraints available very early in the traditional spectral assignment process, a model with an RMSD of 2.8 angstrom could rapidly be built. The ability to generate moderate resolution models within days of NMR data collection should facilitate large scale NMR structure determination efforts.
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Affiliation(s)
- Jens Meiler
- Department of Biochemistry, University of Washington, BOX 357350, Seattle, WA 98195, USA.
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19
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Abstract
NMR spectroscopy is a powerful tool for studying proteins and nucleic acids in solution. This is illustrated by the fact that nearly half of all current RNA structures were determined by using NMR techniques. Information about the structure, dynamics, and interactions with other RNA molecules, proteins, ions, and small ligands can be obtained for RNA molecules up to 100 nucleotides. This review provides insight into the resonance assignment methods that are the first and crucial step of all NMR studies, into the determination of base-pair geometry, into the examination of local and global RNA conformation, and into the detection of interaction sites of RNA. Examples of NMR investigations of RNA are given by using several different RNA molecules to illustrate the information content obtainable by NMR spectroscopy and the applicability of NMR techniques to a wide range of biologically interesting RNA molecules.
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Affiliation(s)
- Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
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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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21
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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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22
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Vögeli B, Kovacs H, Pervushin K. Measurements of side-chain 13C-13C residual dipolar couplings in uniformly deuterated proteins. J Am Chem Soc 2004; 126:2414-20. [PMID: 14982448 DOI: 10.1021/ja0381813] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
13C-only spectroscopy was used to measure multiple residual (13)C-(13)C dipolar couplings (RDCs) in uniformly deuterated and (13)C-labeled proteins. We demonstrate that (13)C-start and (13)C-observe spectra can be routinely used to measure an extensive set of the side-chain residual (13)C-(13)C dipolar couplings upon partial alignment of human ubiquitin in the presence of bacteriophages Pf1. We establish that, among different broadband polarization transfer schemes, the FLOPSY family can be used to exchange magnetization between a J coupled network of spins while largely decoupling dipolar interactions between these spins. An excellent correlation between measured RDCs and the 3D structure of the protein was observed, indicating a potential use of the (13)C-(13)C RDCs in the structure determination of perdeuterated proteins.
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Affiliation(s)
- Beat Vögeli
- Laboratorium für Physikalische Chemie, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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23
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Pappalardo L, Janausch IG, Vijayan V, Zientz E, Junker J, Peti W, Zweckstetter M, Unden G, Griesinger C. The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli. J Biol Chem 2003; 278:39185-8. [PMID: 12907689 DOI: 10.1074/jbc.c300344200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of the water-soluble, periplasmic domain of the fumarate sensor DcuS (DcuS-pd) has been determined by NMR spectroscopy in solution. DcuS is a prototype for a sensory histidine kinase with transmembrane signal transfer. DcuS belongs to the CitA family of sensors that are specific for sensing di- and tricarboxylates. The periplasmic domain is folded autonomously and shows helices at the N and the C terminus, suggesting direct linking or connection to helices in the two transmembrane regions. The structure constitutes a novel fold. The nearest structural neighbor is the Per-Arnt-Sim domain of the photoactive yellow protein that binds small molecules covalently. Residues Arg107, His110, and Arg147 are essential for fumarate sensing and are found clustered together. The structure constitutes the first periplasmic domain of a two component sensory system and is distinctly different from the aspartate sensory domain of the Tar chemotaxis sensor.
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Affiliation(s)
- Lucia Pappalardo
- Max Planck Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany
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24
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Stevensson B, Sandström D, Maliniak A. Conformational distribution functions extracted from residual dipolar couplings: A hybrid model based on maximum entropy and molecular field theory. J Chem Phys 2003. [DOI: 10.1063/1.1586914] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Cai M, Williams DC, Wang G, Lee BR, Peterkofsky A, Clore GM. Solution structure of the phosphoryl transfer complex between the signal-transducing protein IIAGlucose and the cytoplasmic domain of the glucose transporter IICBGlucose of the Escherichia coli glucose phosphotransferase system. J Biol Chem 2003; 278:25191-206. [PMID: 12716891 DOI: 10.1074/jbc.m302677200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The solution structure of the final phosphoryl transfer complex in the glucose-specific arm of the Escherichia coli phosphotransferase system, between enzyme IIAGlucose (IIAGlc) and the cytoplasmic B domain (IIBGlc) of the glucose transporter IICBGlc, has been solved by NMR. The interface (approximately 1200-A2 buried surface) is formed by the interaction of a concave depression on IIAGlc with a convex protrusion on IIBGlc. The phosphoryl donor and acceptor residues, His-90 of IIAGlc and Cys-35 of IIBGlc (residues of IIBGlc are denoted in italics) are in close proximity and buried at the center of the interface. Cys-35 is primed for nucleophilic attack on the phosphorus atom by stabilization of the thiolate anion (pKa approximately 6.5) through intramolecular hydrogen bonding interactions with several adjacent backbone amide groups. Hydrophobic intermolecular contacts are supplemented by peripheral electrostatic interactions involving an alternating distribution of positively and negatively charged residues on the interaction surfaces of both proteins. Salt bridges between the Asp-38/Asp-94 pair of IIAGlc and the Arg-38/Arg-40 pair of IIBGlc neutralize the accumulation of negative charge in the vicinity of both the Sgamma atom of Cys-35 and the phosphoryl group in the complex. A pentacoordinate phosphoryl transition state is readily accommodated without any change in backbone conformation, and the structure of the complex accounts for the preferred directionality of phosphoryl transfer between IIAGlc and IIBGlc. The structures of IIAGlc.IIBGlc and the two upstream complexes of the glucose phosphotransferase system (EI.HPr and IIAGlc.HPr) reveal a cascade in which highly overlapping binding sites on HPr and IIAGlc recognize structurally diverse proteins.
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Affiliation(s)
- Mengli Cai
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Bendiak B. Sensitive through-space dipolar correlations between nuclei of small organic molecules by partial alignment in a deuterated liquid solvent. J Am Chem Soc 2002; 124:14862-3. [PMID: 12475324 DOI: 10.1021/ja028412q] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Through-space residual dipolar correlations in NMR spectra can be measured between nuclei of small organic molecules by partially aligning them with respect to the magnetic field in a pure deuterated liquid solvent, 4-pentyl-4'-cyanobiphenyl. A simple temperature change of this liquid phase enables spectra to be compared between samples under isotropic tumbling conditions and weakly oriented anisotropic states. This should provide access of a number of small nonpolar molecules to more sensitive through-space nuclear correlations than possible through NOE experiments, depending on the net orientation of specific nuclear pairs with respect to the magnetic field and the specific coherence transfers employed.
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Affiliation(s)
- Brad Bendiak
- Department of Cellular and Structural Biology, University of Colorado Health Sciences Center, Campus Box B111, 4200 East Ninth Avenue, Denver, CO 80262, USA.
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27
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Koenig BW, Kontaxis G, Mitchell DC, Louis JM, Litman BJ, Bax A. Structure and orientation of a G protein fragment in the receptor bound state from residual dipolar couplings. J Mol Biol 2002; 322:441-61. [PMID: 12217702 DOI: 10.1016/s0022-2836(02)00745-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Residual dipolar couplings for a ligand that is in fast exchange between a free state and a state where it is bound to a macroscopically ordered membrane protein carry precise information on the structure and orientation of the bound ligand. The couplings originate in the bound state but can be detected on the free ligand using standard high resolution NMR. This approach is used to study an analog of the C-terminal undecapeptide of the alpha-subunit of the heterotrimeric G protein transducin when bound to photo-activated rhodopsin. Rhodopsin is the major constituent of disk-shaped membrane vesicles from rod outer segments of bovine retinas, which align spontaneously in the NMR magnet. Photo-activation of rhodopsin triggers transient binding of the peptide, resulting in measurable dipolar contributions to 1J(NH) and 1J(CH) splittings. These dipolar couplings report on the time-averaged orientation of bond vectors in the bound peptide relative to the magnetic field, i.e. relative to the membrane normal. Approximate distance restraints of the bound conformation were derived from transferred NOEs, as measured from the difference of NOESY spectra recorded prior to and after photo-activation. The N-terminal eight residues of the bound undecapeptide adopt a near-ideal alpha-helical conformation. The helix is terminated by an alpha(L) type C-cap, with Gly9 at the C' position in the center of the reverse turn. The angle between the helix axis and the membrane normal is 40 degrees (+/-4) degrees. Peptide protons that make close contact with the receptor are identified by analysis of the NOESY cross-relaxation pattern and include the hydrophobic C terminus of the peptide.
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Affiliation(s)
- Bernd W Koenig
- Structural Biology Institute, IBI-2, Research Center Jülich, D-52425 Jülich, Germany.
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28
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Abstract
DNA oligonucleotides that have repetitive tracts of guanine bases can form G-quadruplex structures that display an amazing polymorphism. Structures of several new G-quadruplexes have been solved recently that greatly expand the known structural motifs observed in nucleic acid quadruplexes. Base triads, base hexads, and quartets that contain cytosine have recently been identified stacked over the familiar G-quartets. The current status of the diverse array of structural features in quadruplexes is described and used to provide insight into the polymorphism and folding pathways. This review also summarizes recent progress in the techniques used to probe the structures of G-quadruplexes and discusses the role of ion binding in quadruplex formation. Several of the quadruplex structures featured in this review can be accessed in the online version of this review as CHIME representations.
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Affiliation(s)
- M A Keniry
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia.
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29
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Kramer F, Glaser SJ. Efficiency of homonuclear Hartmann-Hahn and COSY-type mixing sequences in the presence of scalar and residual dipolar couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 155:83-91. [PMID: 11945036 DOI: 10.1006/jmre.2002.2511] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the presence of scalar (J) and residual dipolar (D) couplings, the transfer efficiency of homonuclear Hartmann-Hahn and COSY-type mixing depends on the ratio D/J and on the mixing sequence. This dependence is analyzed theoretically and the results are confirmed experimentally. At least two different mixing sequences are required to yield good transfer efficiencies for all ratios D/J. In contrast to COSY-type experiments, homonuclear Hartmann-Hahn sequences can provide efficient transfer even if the sum of D and J is zero, i.e., if the coupling vanishes in the weak coupling limit.
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Affiliation(s)
- Frank Kramer
- Institut für Organische Chemie und Biochemie II, Technische Universität München, Garching, Germany
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30
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Naito A, Nagao T, Obata M, Shindo Y, Okamoto M, Yokoyama S, Tuzi S, Saitô H. Dynorphin induced magnetic ordering in lipid bilayers as studied by (31)P NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1558:34-44. [PMID: 11750262 DOI: 10.1016/s0005-2736(01)00420-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipid bilayers of dimyristoyl phosphatidylcholine (DMPC) containing opioid peptide dynorphin A(1-17) are found to be spontaneously aligned to the applied magnetic field near at the phase transition temperature between the gel and liquid crystalline states (T(m)=24 degrees C), as examined by 31P NMR spectroscopy. The specific interaction between the peptide and lipid bilayer leading to this property was also examined by optical microscopy, light scattering, and potassium ion-selective electrode, together with a comparative study on dynorphin A(1-13). A substantial change in the light scattering intensity was noted for DMPC containing dynorphin A(1-17) near at T(m) but not for the system containing A(1-13). Besides, reversible change in morphology of bilayer, from small lipid particles to large vesicles, was observed by optical microscope at T(m). These results indicate that lysis and fusion of the lipid bilayers are induced by the presence of dynorphin A(1-17). It turned out that the bilayers are spontaneously aligned to the magnetic field above T(m) in parallel with the bilayer surface, because a single 31P NMR signal appeared at the perpendicular position of the 31P chemical shift tensor. In contrast, no such magnetic ordering was noted for DMPC bilayers containing dynorphin A(1-13). It was proved that DMPC bilayer in the presence of dynorphin A(1-17) forms vesicles above T(m), because leakage of potassium ion from the lipid bilayers was observed by potassium ion-selective electrode after adding Triton X-100. It is concluded that DMPC bilayer consists of elongated vesicles with the long axis parallel to the magnetic field, together with the data of microscopic observation of cylindrical shape of the vesicles. Further, the long axis is found to be at least five times longer than the short axis of the elongated vesicles in view of simulated 31P NMR lineshape.
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Affiliation(s)
- Akira Naito
- Department of Life Science, Himeji Institute of Technology, 3-2-1 Kouto, Kamigori, 678-1297, Hyogo, Japan.
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31
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Tian F, Valafar H, Prestegard JH. A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. J Am Chem Soc 2001; 123:11791-6. [PMID: 11716736 DOI: 10.1021/ja011806h] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new approach for simultaneous protein backbone resonance assignment and structure determination by NMR is introduced. This approach relies on recent advances in high-resolution NMR spectroscopy that allow observation of anisotropic interactions, such as dipolar couplings, from proteins partially aligned in field ordered media. Residual dipolar couplings are used for both geometric information and a filter in the assembly of residues in a sequential manner. Experimental data were collected in less than one week on a small redox protein, rubredoxin, that was 15N enriched but not enriched above 1% natural abundance in 13C. Given the acceleration possible with partial 13C enrichment, the protocol described should provide a very rapid route to protein structure determination. This is critical for the structural genomics initiative where protein expression and structural determination in a high-throughput manner will be needed.
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Affiliation(s)
- F Tian
- Southeast Collaboratory for Structural Genomics, University of Georgia, Athens, Georgia 30602-4712, USA
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32
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Luy B, Barchi JJ, Marino JP. S(3)E-E.COSY methods for the measurement of (19)F associated scalar and dipolar coupling constants. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 152:179-184. [PMID: 11531377 DOI: 10.1006/jmre.2001.2386] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A (1)H-(19)F spin state selective excitation (S(3)E) pulse sequence element has been applied in combination with (1)H homonuclear mixing to create E.COSY-type experiments designed to measure scalar J(HF2') and J(HH2') and residual dipolar D(HF2') and D(HH2') couplings in 2'-deoxy-2'-fluoro-sugars. The (1)H-(19)F S(3)E pulse sequence element, which resembles a simple INEPT sequence, achieves spin-state-selective correlation between geminal (1)H-(19)F spin pairs by linear combination of in-phase (19)F magnetization and anti-phase magnetization evolved from (1)H. Since the S(3)E sequence converts both (19)F and (1)H steady-state polarization into observable coherences, an approximately twofold signal increase is observed for fully relaxed (1)H-(19)F spin pairs with respect to a standard (1)H coupled (19)F 1D experiment. The improved sensitivity and resolution afforded by the use of (1)H-(19)F S(3)E E.COSY-type experiments for measuring couplings is demonstrated on the nucleoside 9-(2',3'-dideoxy-2'-fluoro-beta-D-threo-pentofuranosyl)adenine (beta-FddA) and on a selectively 2'-fluorine labeled 21mer RNA oligonucleotide.
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Affiliation(s)
- B Luy
- Center for Advanced Research in Biotechnology, University of Maryland and the National Institute for Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
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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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Affiliation(s)
- I Bertini
- Magnetic Resonance Center (CERM), University of Florence, Florence 50019, Italy
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35
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36
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Meiler J, Prompers JJ, Peti W, Griesinger C, Brüschweiler R. Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J Am Chem Soc 2001; 123:6098-107. [PMID: 11414844 DOI: 10.1021/ja010002z] [Citation(s) in RCA: 241] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of internal motions on residual dipolar NMR couplings of proteins partially aligned in a liquid-crystalline environment are analyzed using a 10 ns molecular dynamics (MD) computer simulation of ubiquitin. For a set of alignment tensors with different orientations and rhombicities, MD-averaged dipolar couplings are determined and subsequently interpreted for different scenarios in terms of effective alignment tensors, average orientations of dipolar vectors, and intramolecular reorientational vector distributions. Analytical relationships are derived that reflect similarities and differences between motional scaling of dipolar couplings and scaling of dipolar relaxation data (NMR order parameters). Application of the self-consistent procedure presented here to dipolar coupling measurements of biomolecules aligned in different liquid-crystalline media should allow one to extract in a "model-free" way average orientations of dipolar vectors and specific aspects of their motions.
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Affiliation(s)
- J Meiler
- Institut für Organische Chemie, Universität Frankfurt, Marie-Curie-Strasse 11, D-60439 Frankfurt am Main, Germany
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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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38
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Krishna NR, Agrawal PK. Molecular structure of the carbohydrate-protein linkage region fragments from connective-tissue proteoglycans. Adv Carbohydr Chem Biochem 2001; 56:201-34. [PMID: 11039112 DOI: 10.1016/s0065-2318(01)56005-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- N R Krishna
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham 35294-2041, USA
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39
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Al-Hashimi HM, Majumdar A, Gorin A, Kettani A, Skripkin E, Patel DJ. Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation. J Am Chem Soc 2001; 123:633-40. [PMID: 11456575 DOI: 10.1021/ja003379y] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a new NMR procedure for determining the three-dimensional fold of C2-symmetric nucleic acid homodimers that relies on long-range orientational constraints derived from the measurement of two independent sets of residual dipolar couplings under two alignment conditions. The application is demonstrated on an (15)N/(13)C-enriched deoxyoligonucleotide sequence, d(G-G-G-T-T-C-A-G-G), shown previously to dimerize into a quadruplex in solution and form a pair of G.(C-A) triads and G-G-G-G tetrads (G-tetrad) motifs. One-bond (1)H-(15)N ((1)D(NH)) and (1)H-(13)C ((1)D(CH)) residual dipolar couplings have been measured between nuclei in the bases of these motifs using bacteriophage as an ordering medium, and under direct magnetic field alignment (800 MHz). By combining the two dipolar data sets in an order matrix analysis, the orientation of the G.(C-A) triad relative to the G-tetrad within a contiguous monomeric unit can directly be determined, even in the presence of interstrand/intrastrand NOE ambiguity. We further demonstrate that the orientation of the C2-axis of molecular symmetry in the homodimer relative to the G.(C-A) triad and G-tetrad motifs can unambiguously be determined using the two sets of independent dipolar coupling measurements. The three-dimensional fold of the homodimer determined using this procedure is very regular and in excellent agreement with a previously determined high-resolution NOE-based NMR structure, where interstrand/intrastrand NOEs were treated as ambiguous and where noncrystallographic symmetry constraints were implicitly imposed during the structure calculation.
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Affiliation(s)
- H M Al-Hashimi
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
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40
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Desvaux H, Gabriel JCP, Berthault P, Camerel F. First Use of a Mineral Liquid Crystal for Measurement of Residual Dipolar Couplings of a Nonlabeled Biomolecule. Angew Chem Int Ed Engl 2001; 40:373-376. [DOI: 10.1002/1521-3773(20010119)40:2<373::aid-anie373>3.0.co;2-r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2000] [Indexed: 11/10/2022]
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41
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Erstmalige Verwendung eines anorganischen Flüssigkristalls für die Messung der Rest-Dipol-Dipol-Kopplung eines nichtmarkierten Biomoleküls. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010119)113:2<387::aid-ange387>3.0.co;2-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Luy B, Glaser SJ. Superposition of scalar and residual dipolar couplings: analytical transfer functions for three spins 1/2 under cylindrical mixing conditions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 148:169-181. [PMID: 11133291 DOI: 10.1006/jmre.2000.2194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The superposition of scalar and residual dipolar couplings gives rise to so-called cylindrical mixing Hamiltonians in dipolar coupling spectroscopy. General analytical polarization and coherence transfer functions are presented for three cylindrically coupled spins 12 under energy-matched conditions. In addition, the transfer efficiency is analyzed as a function of the relative coupling constants for characteristic special cases.
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Affiliation(s)
- B Luy
- Center of Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
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43
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44
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Veglia G, Opella SJ. Lanthanide Ion Binding to Adventitious Sites Aligns Membrane Proteins in Micelles for Solution NMR Spectroscopy. J Am Chem Soc 2000. [DOI: 10.1021/ja002119d] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gianluigi Veglia
- Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104
| | - Stanley J. Opella
- Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104
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45
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Bertini I, Castellani F, Luchinat C, Martini G, Parigi G, Ristori S. Partial Orientation of Cytochrome c in a Lyotropic Liquid Crystal: Residual H−H Dipolar Coupling. J Phys Chem B 2000. [DOI: 10.1021/jp0009608] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivano Bertini
- CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, and Department of Chemistry, University of Florence, Via G. Capponi 9, 50121 Florence, Italy
| | - Federica Castellani
- CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, and Department of Chemistry, University of Florence, Via G. Capponi 9, 50121 Florence, Italy
| | - Claudio Luchinat
- CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, and Department of Chemistry, University of Florence, Via G. Capponi 9, 50121 Florence, Italy
| | - Giacomo Martini
- CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, and Department of Chemistry, University of Florence, Via G. Capponi 9, 50121 Florence, Italy
| | - Giacomo Parigi
- CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, and Department of Chemistry, University of Florence, Via G. Capponi 9, 50121 Florence, Italy
| | - Sandra Ristori
- CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, and Department of Chemistry, University of Florence, Via G. Capponi 9, 50121 Florence, Italy
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46
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Vermeulen A, Zhou H, Pardi A. Determining DNA Global Structure and DNA Bending by Application of NMR Residual Dipolar Couplings. J Am Chem Soc 2000. [DOI: 10.1021/ja001919l] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annaleen Vermeulen
- Contribution from the Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215
| | - Hongjun Zhou
- Contribution from the Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215
| | - Arthur Pardi
- Contribution from the Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215
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47
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Hansen MR, Hanson P, Pardi A. Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions. Methods Enzymol 2000; 317:220-40. [PMID: 10829283 DOI: 10.1016/s0076-6879(00)17017-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- M R Hansen
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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Tjandra N, Tate SI, Ono A, Kainosho M, Bax A. The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase. J Am Chem Soc 2000. [DOI: 10.1021/ja000324n] [Citation(s) in RCA: 157] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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McCallum SA, Hitchens TK, Torborg C, Rule GS. Ligand-induced changes in the structure and dynamics of a human class Mu glutathione S-transferase. Biochemistry 2000; 39:7343-56. [PMID: 10858281 DOI: 10.1021/bi992767d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glutathione transferases are detoxification enzymes that catalyze the addition of glutathione (GSH) to a wide variety of hydrophobic compounds. Although this group of enzymes has been extensively characterized by crystallographic studies, little is known about their dynamic properties. This study investigates the role of protein dynamics in the mechanism of a human class mu enzyme (GSTM2-2) by characterizing the motional properties of the unliganded enzyme, the enzyme-substrate (GSH) complex, an enzyme-product complex [S-(2,4-dinitrobenzyl)glutathione, GSDNB], and an enzyme-inhibitor complex (S-1-hexylglutathione, GSHEX). The kinetic on- and off-rates for these ligands are 10-20-fold lower than the diffusion limit, suggesting dynamic conformational heterogeneity of the active site. The off-rate of GSDNB is similar to the turnover number for its enzymatic formation, suggesting that product release is rate-limiting when 1-chloro-2,4-dinitrobenzene is the substrate. The dynamic properties of GSTM2-2 were investigated over a wide range of time scales using (15)N nuclear spin relaxation, residual dipolar couplings, and amide hydrogen-deuterium exchange rates. These data show that the majority of the protein backbone is rigid on the nanosecond to picosecond time scale for all forms of the enzyme. The presence of motion on the millisecond to microsecond time scale was detected for a small number of residues within the active site. These motions are likely to play a role in facilitating substrate binding and product release. The residual dipolar couplings also show that the conformation of the active site region is more open in solution than in the crystalline environment, further enhancing ligand accessibility to the active site. Amide hydrogen-deuterium exchange rates indicate a reduction in the dynamic properties of several residues near the active site due to the binding of ligand. GSH binding reduces the exchange rate of a number of residues in proximity to its binding site, while GSHEX causes a reduction in amide-exchange rates throughout the entire active site region. The location of the dinitrobenzene (DNB) ring in the GSDNB-GSTM2-2 complex was modeled using chemical shift changes that occur when GSDNB binds to the enzyme. The DNB ring makes a number of contacts with hydrophobic residues in the active site, including Met108. Replacement of Met108 with Ala increases the turnover number of the enzyme by a factor of 1.7.
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Affiliation(s)
- S A McCallum
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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50
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Brunner E, Ogle J, Wenzler M, Kalbitzer HR. Molecular alignment of proteins in bicellar solutions: quantitative evaluation of effects induced in 2D COSY spectra. Biochem Biophys Res Commun 2000; 272:694-8. [PMID: 10860817 DOI: 10.1006/bbrc.2000.2815] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Partial molecular alignment leads to an incomplete averaging of anisotropic magnetic interactions such as magnetic dipole interaction or chemical shift anisotropy. In the present contribution we quantitatively describe and evaluate the effects induced by the addition of magnetically oriented lipid bicelles in homonuclear two-dimensional (2D) NMR correlation (COSY) spectra of proteins. It is shown that 2D COSY experiments allow the measurement of H(N)-H(alpha) residual dipole couplings of positive sign which can be used for structure refinement. In contrast to the double- and triple-resonance experiments previously proposed, these measurements can be carried out even on nonisotope-enriched samples.
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Affiliation(s)
- E Brunner
- Universität Regensburg, Institut für Biophysik und Physikalische Biochemie, Germany
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