601
|
Affiliation(s)
- C R Sanders
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106-4970, USA.
| | | |
Collapse
|
602
|
Prosser RS, Losonczi JA, Shiyanovskaya IV. Use of a Novel Aqueous Liquid Crystalline Medium for High-Resolution NMR of Macromolecules in Solution. J Am Chem Soc 1998. [DOI: 10.1021/ja982671r] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. Scott Prosser
- Department of Chemistry and the Liquid Crystal Institute Kent State University, Kent, Ohio 44242 Complex Carbohydrate Research Center University of Georgia, 220 Riverbend Rd. Athens, Georgia 30602-4712
| | - J. A. Losonczi
- Department of Chemistry and the Liquid Crystal Institute Kent State University, Kent, Ohio 44242 Complex Carbohydrate Research Center University of Georgia, 220 Riverbend Rd. Athens, Georgia 30602-4712
| | - I. V. Shiyanovskaya
- Department of Chemistry and the Liquid Crystal Institute Kent State University, Kent, Ohio 44242 Complex Carbohydrate Research Center University of Georgia, 220 Riverbend Rd. Athens, Georgia 30602-4712
| |
Collapse
|
603
|
Ottiger M, Bax A. Characterization of magnetically oriented phospholipid micelles for measurement of dipolar couplings in macromolecules. JOURNAL OF BIOMOLECULAR NMR 1998; 12:361-372. [PMID: 9835045 DOI: 10.1023/a:1008366116644] [Citation(s) in RCA: 152] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Weak alignment of solute molecules with the magnetic field can be achieved in a dilute liquid crystalline medium, consisting of an aqueous mixture of dimyristoyl-phosphatidylcholine (DMPC) and dihexanoyl-phosphatidylcholine (DHPC). For a certain range of molar ratios, DMPC and DHPC can form large, disc-shaped particles, commonly referred to as bicelles (Sanders and Schwonek, 1992), which cooperatively align in the magnetic field and induce a small degree of alignment on asymmetrically shaped solute molecules. As a result, dipolar couplings between pairs of 1H, 13C or 15N nuclei are no longer averaged to zero by rotational diffusion and they can be readily measured, providing valuable structural information. The stability of these liquid crystals and the degree of alignment of the solute molecules depend strongly on experimental variables such as the DMPC:DHPC ratio and concentration, the preparation protocol of the DMPC/DHPC mixtures, as well as salt, temperature, and pH. The lower temperature limit for which the liquid crystalline phase is stable can be reduced to 20 degrees C by using a ternary mixture of DHPC, DMPC, and 1-myristoyl-2-myristoleoyl-sn-glycero-3-phosphocholine, or a binary mixture of DHPC and ditridecanoyl-phosphatidylcholine. These issues are discussed, with an emphasis on the use of the medium for obtaining weak alignment of biological macromolecules.
Collapse
Affiliation(s)
- M Ottiger
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | | |
Collapse
|
604
|
Bertini I, Felli IC, Luchinat C. High magnetic field consequences on the NMR hyperfine shifts in solution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 134:360-364. [PMID: 9761711 DOI: 10.1006/jmre.1998.1507] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Pseudocontact shifts arise from the isotropic reorientational average of the dipolar coupling between unpaired electron and nuclei, in the presence of magnetic susceptibility anisotropy. The effect of residual orientation due to high magnetic fields on pseudocontact shifts is evaluated here. The effect is found to be smaller and of opposite sign with respect to another novel effect of high magnetic fields on hyperfine shifts due to saturation of the electron spin magnetic moment as described by the Brillouin equation. Copyright 1998 Academic Press.
Collapse
Affiliation(s)
- I Bertini
- Department of Chemistry, University of Florence, Florence, Italy
| | | | | |
Collapse
|
605
|
Abstract
New strategies have recently been developed for studying biological macromolecules of large size (beyond 100 kDa) in order to both improve the quality of the structures and make structure determination more efficient. This has been achieved by utilizing cross-correlation effects and novel labeling strategies, and developing novel NMR spectroscopy experiments.
Collapse
Affiliation(s)
- V Dötsch
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | | |
Collapse
|
606
|
Ottiger M, Delaglio F, Marquardt JL, Tjandra N, Bax A. Measurement of dipolar couplings for methylene and methyl sites in weakly oriented macromolecules and their use in structure determination. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 134:365-369. [PMID: 9761712 DOI: 10.1006/jmre.1998.1546] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A simple and effective method is described for simultaneously measuring dipolar couplings for methine, methylene, and methyl groups in weakly oriented macromolecules. The method is a J-modulated 3D version of the well-known [1H-13C] CT-HSQC experiment, from which the J and dipolar information are most accurately extracted by using time-domain fitting in the third, constant-time dimension. For CH2-sites, the method generally yields only the sum of the two individual 13C-1H couplings. Structure calculations are carried out by minimizing the deviation between the measured sum, and the sum predicted for each methylene on the basis of the structure. For rapidly spinning methyl groups the dipolar contribution to the splitting of the outer 13C quartet components can be used directly to constrain the orientation of the C-CH3 bond. Measured sidechain dipolar couplings are in good agreement with an ensemble of NMR structures calculated without use of these couplings.
Collapse
Affiliation(s)
- M Ottiger
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892-0520, USA
| | | | | | | | | |
Collapse
|
607
|
Kiddle GR, Homans SW. Residual dipolar couplings as new conformational restraints in isotropically 13C-enriched oligosaccharides. FEBS Lett 1998; 436:128-30. [PMID: 9771907 DOI: 10.1016/s0014-5793(98)01112-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the measurement of residual dipolar couplings for l3C-enriched NeuNAcalpha2-3Galbeta1-4Glc in a dilute liquid-crystalline medium. These couplings provide long-range conformational restraints that hitherto have not been available for oligosaccharides. We utilise these restraints in dynamical simulated annealing calculations, which support current models of the solution behaviour of the trisaccharide.
Collapse
Affiliation(s)
- G R Kiddle
- Centre for Biomolecular Sciences, University of St. Andrews, FIFE, UK
| | | |
Collapse
|
608
|
Bolon PJ, Prestegard JH. COSY Cross-Peaks from 1H−1H Dipolar Couplings in NMR Spectra of Field Oriented Oligosaccharides. J Am Chem Soc 1998. [DOI: 10.1021/ja982014z] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. J. Bolon
- Complex Carbohydrate Research Center University of Georgia, Athens, Georgia 30602
| | - J. H. Prestegard
- Complex Carbohydrate Research Center University of Georgia, Athens, Georgia 30602
| |
Collapse
|
609
|
Yang D, Tolman JR, Goto NK, Kay LE. An HNCO-based Pulse Scheme for the Measurement of 13Cα-1Hα One-bond Dipolar couplings in 15N, 13C Labeled Proteins. JOURNAL OF BIOMOLECULAR NMR 1998; 12:325-332. [PMID: 21136327 DOI: 10.1023/a:1008223017233] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A triple resonance pulse scheme is presented for recording 13Cα-1Hα one-bond dipolar couplings in 15N, 13C labeled proteins. HNCO correlation maps are generated where the carbonyl chemical shift is modulated by the 13Cα-1Hα coupling, with the two doublet components separated into individual data sets. The experiment makes use of recently described methodology whereby the protein of interest is dissolved in a dilute solution of bicelles which orient above a critical temperature, thus permitting measurement of significant couplings (Tjandra and Bax, 1997a). An application to the protein ubiquitin is described.
Collapse
Affiliation(s)
- D Yang
- The Protein Engineering Centers of Excellence and Departments of Medical Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8
| | | | | | | |
Collapse
|
610
|
Wang YX, Marquardt JL, Wingfield P, Stahl SJ, Lee-Huang S, Torchia D, Bax A. Simultaneous Measurement of 1H−15N, 1H−13C‘, and 15N−13C‘ Dipolar Couplings in a Perdeuterated 30 kDa Protein Dissolved in a Dilute Liquid Crystalline Phase. J Am Chem Soc 1998. [DOI: 10.1021/ja980862o] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yun-Xing Wang
- Molecular Structural Biology Unit, National Institute of Dental Research, Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 Department of Biochemistry, New York University School of Medicine, New York, New York 10016
| | - John L. Marquardt
- Molecular Structural Biology Unit, National Institute of Dental Research, Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 Department of Biochemistry, New York University School of Medicine, New York, New York 10016
| | - Paul Wingfield
- Molecular Structural Biology Unit, National Institute of Dental Research, Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 Department of Biochemistry, New York University School of Medicine, New York, New York 10016
| | - Stephen J. Stahl
- Molecular Structural Biology Unit, National Institute of Dental Research, Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 Department of Biochemistry, New York University School of Medicine, New York, New York 10016
| | - Sylvia Lee-Huang
- Molecular Structural Biology Unit, National Institute of Dental Research, Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 Department of Biochemistry, New York University School of Medicine, New York, New York 10016
| | - Dennis Torchia
- Molecular Structural Biology Unit, National Institute of Dental Research, Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 Department of Biochemistry, New York University School of Medicine, New York, New York 10016
| | - Ad Bax
- Molecular Structural Biology Unit, National Institute of Dental Research, Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 Department of Biochemistry, New York University School of Medicine, New York, New York 10016
| |
Collapse
|
611
|
Fischer MW, Zeng L, Majumdar A, Zuiderweg ER. Characterizing semilocal motions in proteins by NMR relaxation studies. Proc Natl Acad Sci U S A 1998; 95:8016-9. [PMID: 9653132 PMCID: PMC20921 DOI: 10.1073/pnas.95.14.8016] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The understanding of protein function is incomplete without the study of protein dynamics. NMR spectroscopy is valuable for probing nanosecond and picosecond dynamics via relaxation studies. The use of 15N relaxation to study backbone dynamics has become virtually standard. Here, we propose to measure the relaxation of additional nuclei on each peptide plane allowing for the observation of anisotropic local motions. This allows the nature of local motions to be characterized in proteins. As an example, semilocal rotational motion was detected for part of a helix of the protein Escherichia coli flavodoxin.
Collapse
Affiliation(s)
- M W Fischer
- Biophysics Research Division, The University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA
| | | | | | | |
Collapse
|
612
|
Gardner KH, Kay LE. The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:357-406. [PMID: 9646872 DOI: 10.1146/annurev.biophys.27.1.357] [Citation(s) in RCA: 510] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.
Collapse
Affiliation(s)
- K H Gardner
- Protein Engineering Network Centres of Excellence, University of Toronto, Ontario, Canada.
| | | |
Collapse
|
613
|
Clore GM, Gronenborn AM, Bax A. A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 133:216-221. [PMID: 9654491 DOI: 10.1006/jmre.1998.1419] [Citation(s) in RCA: 247] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
It has recently been shown that the degree of alignment of macromolecules in an aqueous dilute liquid crystalline medium of bicelles is sufficient to permit accurate values of residual 15N-1H, 13C-1H, and 13Calpha-C' dipolar couplings to be obtained on a routine basis, thereby providing potentially unique long-range structural information. To make use of this information in macromolecular structure determination, the magnitude of the axial and rhombic components of the molecular alignment tensor must be determined. This can be achieved by taking advantage of the fact that different, fixed-distance internuclear vector types are differently distributed relative to the alignment tensor. A histogram of the ensemble of normalized residual dipolar couplings for several such vector types approximates a powder pattern from which the magnitude of the axial and rhombic components are readily extracted in the absence of any prior structural information. The applicability of this method is demonstrated using synthetic data derived from four proteins representative of different sizes, topologies, and secondary structures, and experimental data measured on the small protein ubiquitin.
Collapse
Affiliation(s)
- G M Clore
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland, 20892-0520, USA
| | | | | |
Collapse
|
614
|
Prestegard JH. New techniques in structural NMR--anisotropic interactions. NATURE STRUCTURAL BIOLOGY 1998; 5 Suppl:517-22. [PMID: 9665182 DOI: 10.1038/756] [Citation(s) in RCA: 203] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structure determination of biomolecules by NMR has traditionally been based on nuclear Overhauser effects (NOEs). Now there are additional sources of information that can complement NOEs in cases where positioning of remote parts of molecules is important, and where extension to larger and more complex systems is desired.
Collapse
Affiliation(s)
- J H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens 30602-4712, USA.
| |
Collapse
|
615
|
Zwahlen C, Vincent SJF, Gardner KH, Kay LE. Significantly Improved Resolution for NOE Correlations from Valine and Isoleucine (Cγ2) Methyl Groups in 15N,13C- and 15N,13C,2H-Labeled Proteins. J Am Chem Soc 1998. [DOI: 10.1021/ja9742601] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Catherine Zwahlen
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Molecular and Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8, and Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Sébastien J. F. Vincent
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Molecular and Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8, and Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Kevin H. Gardner
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Molecular and Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8, and Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Lewis E. Kay
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Molecular and Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8, and Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| |
Collapse
|
616
|
Clore GM, Gronenborn AM, Tjandra N. Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 131:159-162. [PMID: 9533920 DOI: 10.1006/jmre.1997.1345] [Citation(s) in RCA: 203] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Residual dipolar couplings arising from small degrees of alignment of molecules in a magnetic field provide unique long-range structural information. The potential of this approach for structure refinement has recently been demonstrated for a protein-DNA complex in which the magnetic susceptibility tensor was axially symmetric. For most macromolecules and macromolecular complexes, however, axial symmetry cannot be assumed. Moreover, the presence of significant rhombicity will clearly affect the accuracy of the resulting coordinates. In this Communication we present a simple calculational strategy that makes use of simulated annealing refinement against the residual dipolar couplings in combination with a grid search, to simultaneously refine the structures and ascertain the magnitude of the axial and rhombic components of the tensor.
Collapse
Affiliation(s)
- G M Clore
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892-0520, USA
| | | | | |
Collapse
|
617
|
|
618
|
Bhattacharya S, Sukits SF, MacLaughlin KL, Lecomte JT. The tautomeric state of histidines in myoglobin. Biophys J 1997; 73:3230-40. [PMID: 9414234 PMCID: PMC1181225 DOI: 10.1016/s0006-3495(97)78348-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
1H-15N HMQC spectra were collected on 15N-labeled sperm whale myoglobin (Mb) to determine the tautomeric state of its histidines in the neutral form. By analyzing metaquoMb and metcyanoMb data sets collected at various pH values, cross-peaks were assigned to the imidazole rings and their patterns interpreted. Of the nine histidines not interacting with the heme in sperm whale myoglobin, it was found that seven (His-12, His-48, His-81, His-82, His-113, His-116, and His-119) are predominantly in the N epsilon2H form with varying degrees of contribution from the Ndelta1 H form. The eighth, His-24, is in the Ndelta1H state as expected from the solid state structure. 13C correlation spectra were collected to probe the state of the ninth residue (His-36). Tentative interpretation of the data through comparison with horse Mb suggested that this ring is predominantly in the Ndelta1H state. In addition, signals were observed from the histidines associated with the heme (His-64, His-93, and His-97) in the 1H-15N HMQC spectra of the metcyano form. In several cases, the tautomeric state of the imidazole ring could not be derived from inspection of the solid state structure. It was noted that hydrogen bonding of the ring was not unambiguously reflected in the nitrogen chemical shift. With the experimentally determined tautomeric state composition in solution, it will be possible to broaden the scope of other studies focused on the electrostatic contribution of histidines to the thermodynamic properties of myoglobin.
Collapse
Affiliation(s)
- S Bhattacharya
- Department of Chemistry and the Center for Biomolecular Structure and Function, The Pennsylvania State University, University Park 16802, USA
| | | | | | | |
Collapse
|
619
|
Tjandra N, Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 1997; 278:1111-4. [PMID: 9353189 DOI: 10.1126/science.278.5340.1111] [Citation(s) in RCA: 1203] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In isotropic solution, internuclear dipolar couplings average to zero as a result of rotational diffusion. By dissolving macromolecules in a dilute aqueous nematic discotic liquid-crystalline medium containing widely spaced magnetically oriented particles, a tunable degree of solute alignment with the magnetic field can be created while retaining the high resolution and sensitivity of the regular isotropic nuclear magnetic resonance (NMR) spectrum. Dipolar couplings between 1H-1H, 1H-13C, 1H-15N, and 13C-13C pairs in such an oriented macromolecule no longer average to zero, and are readily measured. Distances and angles derived from dipolar couplings in human ubiquitin are in excellent agreement with its crystal structure. The approach promises to improve the accuracy of structures determined by NMR, and extend the size limit.
Collapse
Affiliation(s)
- N Tjandra
- Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-0380, USA
| | | |
Collapse
|
620
|
Ottiger M, Tjandra N, Bax A. Magnetic Field Dependent Amide 15N Chemical Shifts in a Protein−DNA Complex Resulting from Magnetic Ordering in Solution. J Am Chem Soc 1997. [DOI: 10.1021/ja971639e] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcel Ottiger
- Contribution from the Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases and the Laboratory of Biophysical Chemistry, Building 3, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Nico Tjandra
- Contribution from the Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases and the Laboratory of Biophysical Chemistry, Building 3, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Ad Bax
- Contribution from the Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases and the Laboratory of Biophysical Chemistry, Building 3, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-0520
| |
Collapse
|
621
|
Ghose R, Prestegard JH. Electron spin-nuclear spin cross-correlation effects on multiplet splittings in paramagnetic proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1997; 128:138-143. [PMID: 9356268 DOI: 10.1006/jmre.1997.1227] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The effects of cross-correlation between Curie spin-nuclear dipole and nuclear dipole-nuclear dipole interactions on the linewidths and resonance frequencies of the individual lines of an AX multiplet in paramagnetic systems have been calculated. The implication of the relaxation-induced frequency shift of the lines (dynamic frequency shift) for the accurate measurement of residual dipolar couplings in field-oriented systems has been discussed. Our simulations indicate that these effects may play a role in the precise measurement of residual dipolar couplings in systems which belong to the small and intermediate tumbling regime, i.e., correlation times less than 5 ns.
Collapse
Affiliation(s)
- R Ghose
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | | |
Collapse
|
622
|
Abstract
Improvements in NMR instrumentation, higher magnetic field strengths, novel NMR experiments and new deuterium-labeling strategies have significantly increased the scope of structural problems that can now be addressed by solution NMR methods. To date, a number of structures of proteins of 30 kDa have been solved using multidimensional 15N,13C,2H NMR techniques, and this molecular weight limit will probably be surpassed in the near future.
Collapse
Affiliation(s)
- L E Kay
- Department of Medical Genetics, University of Toronto, Ontario, Canada.
| | | |
Collapse
|
623
|
Bax A, Tjandra N. High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium. JOURNAL OF BIOMOLECULAR NMR 1997; 10:289-292. [PMID: 9390407 DOI: 10.1023/a:1018308717741] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A mixture of dihexanoyl phosphatidylcholine and dimyristoyl phosphatidylcholine in water forms disc-shaped particles, often referred to as bicelles [Sanders and Schwonek (1992) Biochemistry, 31, 8898-8905]. These adopt an ordered, liquid crystalline phase, which can be maintained at very low concentrations of the bicelles (down to 3% w/v). At this concentration the spacing between individual bicelles, on average, exceeds 300 A. The bicelles are shown to have a negligible effect on the rotational diffusion of ubiquitin as judged by the 15N T1p values of the backbone amides relative to those in isotropic aqueous solution. The protein exhibits a residual degree of alignment which is proportional to the bicelle concentration, and approximately collinear with ubiquitin's rotational diffusion tensor. The degree of alignment obtained offers unique opportunities for studying the protein's structure and dynamics.
Collapse
Affiliation(s)
- A Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | | |
Collapse
|
624
|
Düx P, Whitehead B, Boelens R, Kaptein R, Vuister GW. Measurement of (15)N- (1)H coupling constants in uniformly (15)N-labeled proteins: Application to the photoactive yellow protein. JOURNAL OF BIOMOLECULAR NMR 1997; 10:301-6. [PMID: 20700833 DOI: 10.1023/a:1018393225804] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A modified HNHB experiment is presented that allows thedetermination of J(NH) coupling constants directly from the ratio ofcross-peak to diagonal-peak intensities. The experiment was applied to thephotoactive yellow protein (PYP) and yielded the magnitude of 117(3)J(NH(beta)) coupling constants. In addition, 29(3)J(NH(alpha(i-1))) coupling constantscould be measured, providing information about the backbone angle psi.These data, in conjunction with the magnitudes of the(3)J(H(N)H(alpha)) coupling constantsobtained from the HNHA spectrum, effectively discriminate the twopossibilities for the stereospecific assignment of theH(alpha) resonances in glycine residues. For all eight glycineresidues in PYP that were not subject to conformational averaging and hadnon-degenerate H(alpha) resonance frequencies, the J-couplingdata, together with limited NOE data, yielded the stereospecific assignmentof the H(alpha) resonances for these residues. In addition,reliable and precise phi,psi dihedral constraints were also derived forthese residues from the J-coupling data.
Collapse
Affiliation(s)
- P Düx
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | | | | | | | | |
Collapse
|
625
|
Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A. Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. NATURE STRUCTURAL BIOLOGY 1997; 4:732-8. [PMID: 9303001 DOI: 10.1038/nsb0997-732] [Citation(s) in RCA: 407] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Anisotropy of the molecular magnetic susceptibility gives rise to a small degree of alignment. The resulting residual dipolar couplings, which can now be measured with the advent of higher magnetic fields in NMR, contain information on the orientation of the internuclear vectors relative to the molecular magnetic susceptibility tensor, thereby providing information on long range order that is not accessible by any of the solution NMR parameters currently used in structure determination. Thus, the dipolar couplings constitute unique and powerful restraints in determining the structures of magnetically oriented macromolecules in solution. The method is demonstrated on a complex of the DNA-binding domain of the transcription factor GATA-1 with a 16 base pair oligodeoxyribonucleotide.
Collapse
Affiliation(s)
- N Tjandra
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | | | | | | | | |
Collapse
|
626
|
Alemany LB, Gonzalez A, Billups WE, Willcott MR, Ezell E, Gozansky E. Alignment Effects in High Field Proton NMR Spectra of the Hydrogenated Fullerenes C60H2 and C60H4: Evidence for Residual Anisotropic Dipole−Dipole Couplings. J Org Chem 1997. [DOI: 10.1021/jo961808y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - M. Robert Willcott
- Department of Radiology, The University of Texas Medical Branch, Galveston, Texas 77555-0793
| | | | | |
Collapse
|
627
|
Tjandra N, Garrett DS, Gronenborn AM, Bax A, Clore GM. Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. NATURE STRUCTURAL BIOLOGY 1997; 4:443-9. [PMID: 9187651 DOI: 10.1038/nsb0697-443] [Citation(s) in RCA: 156] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Structure determination by NMR presently relies on short range restraints between atoms in close spatial proximity, principally in the form of short (< 5 A) interproton distances. In the case of modular or multidomain proteins and linear nucleic acids, the density of short interproton distance contacts between structural elements far apart in the sequence may be insufficient to define their relative orientations. In this paper we show how the dependence of heteronuclear longitudinal and transverse relaxation times on the rotational diffusion anisotropy of non-spherical molecules can be readily used to directly provide restraints for simulated annealing structure refinement that characterize long range order a priori. The method is demonstrated using the N-terminal domain of Enzyme I,a protein of 259 residues comprising two distinct domains with a diffusion anisotropy(Dparallel/Dperpendicular)of approximately 2.
Collapse
Affiliation(s)
- N Tjandra
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | | | | | | | | |
Collapse
|
628
|
Abstract
Angles between two interatomic vectors are measured for structure elucidation in solution nuclear magnetic resonance (NMR). The angles can be determined directly by using the effects of dipole-dipole cross-correlated relaxation of double-quantum and zero-quantum coherences. The measured rates can be directly related to the angular geometry without need for calibration of a Karplus-type curve, as is the case for scalar coupling measurements, and depend only on the rotational correlation time of the molecule as an empirical parameter. This makes the determination of torsional angles independent from the measurement of coupling constants. The two interatomic vectors can in principle be arbitrarily far apart. The method was demonstrated on the measurement of the peptide backbone angle psi in the protein rhodniin, which is difficult to determine in solution by NMR spectroscopy.
Collapse
Affiliation(s)
- B Reif
- Institut für Organische Chemie, Marie-Curie-Strasse 11, Universität Frankfurt, D-60439 Frankfurt, Germany
| | | | | |
Collapse
|
629
|
Alemany LB, Gonzalez A, Luo W, Billups WE, Willcott MR, Ezell E, Gozansky E. Observation of Alignment Effects in High-Field Proton NMR Spectra of Hydrogenated Fullerenes: Evidence for Residual Anisotropic Dipole−Dipole Couplings. J Am Chem Soc 1997. [DOI: 10.1021/ja963493+] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
630
|
Gochin M. Nuclear Magnetic Resonance Studies of a Paramagnetic Metallo DNA Complex. J Am Chem Soc 1997. [DOI: 10.1021/ja9633169] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Miriam Gochin
- Department of Microbiology University of the Pacific School of Dentistry San Francisco, California 94115
| |
Collapse
|
631
|
Bax A, Tjandra N. Are proteins even floppier than we thought? NATURE STRUCTURAL BIOLOGY 1997; 4:254-6. [PMID: 9095188 DOI: 10.1038/nsb0497-254] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
632
|
Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH. NMR evidence for slow collective motions in cyanometmyoglobin. NATURE STRUCTURAL BIOLOGY 1997; 4:292-7. [PMID: 9095197 DOI: 10.1038/nsb0497-292] [Citation(s) in RCA: 217] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Residual dipolar couplings observed in NMR spectra at very high magnetic fields have been measured to a high degree of accuracy for the paramagnetic protein cyanometmyoglobin. Deviations of these measurements from predictions based on available crystallographic and solution structures are largely systematic and well correlated within a given helix of this highly alpha-helical protein. These observations can be explained by invoking collective motion and small displacements of representative helices from their reported average positions in the solid state. Thus, the measurements appear to be capable of providing important insights into slower, collective protein motions, which are likely to be important for function, and which have been difficult to study using established experimental techniques.
Collapse
Affiliation(s)
- J R Tolman
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
| | | | | | | |
Collapse
|
633
|
Tjandra N, Bax A. Measurement of dipolar contributions to 1JCH splittings from magnetic-field dependence of J modulation in two-dimensional NMR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1997; 124:512-5. [PMID: 9169226 DOI: 10.1006/jmre.1996.1088] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- N Tjandra
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | | |
Collapse
|
634
|
Ubbink M, Lian LY, Modi S, Evans PA, Bendall DS. Analysis of the 1H-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plastocyanin. Metal-dependent differences in the hydrogen-bond network around the copper site. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:132-47. [PMID: 8954163 DOI: 10.1111/j.1432-1033.1996.0132r.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
To compare cadmium-substituted plastocyanin with copper plastocyanin, the 1H-NMR spectra of CuI-, CuII- and Cd-plastocyanin from pea have been analyzed. Full assignments of the spectra of CuI- and Cd-plastocyanin indicate chemical shift differences up to 1 ppm. The affected protons are located in the four loops that surround the Cu site. The largest differences were found for protons in the hydrogen bond network which stabilizes this part of the protein. This suggests that the chemical shift differences are caused by very small but extensive structural changes in the network upon replacement of CuI by Cd. For CuII-plastocyanin the resonances of 72% of the protons observed in the CuI form have been identified. Protons within approximately 0.9 nm of the CuII were not observed due to fast paramagnetic relaxation. The protons between 0.9-1.7 nm from the CuII showed chemical shift differences up to 0.4 ppm compared to both CuI- and Cd-plastocyanin. These differences can be predicted assuming that they represent pseudocontact shifts. When corrected for the pseudocontact shift contribution, the CuII-plastocyanin chemical shifts were nearly all identical within error to those of the Cd form, but not of the CuI-plastocyanin, indicating that the CuII-plastocyanin structure, in as far as it can be observed, resembles Cd-rather than CuI-plastocyanin. In a single stretch of residues (64-69) chemical shift differences remained between all three forms after correction. The fact that pseudocontact shifts were observed for protons which were not broadened may be attributable to the weaker distance dependence of the pseudocontact shift effect compared to paramagnetic relaxation. This results in two shells around the Cu atom, an inner paramagnetic shell (0-0.9 nm), in which protons are not observed due to broadening, and an outer paramagnetic shell (0.9-1.7 nm), in which protons can be observed and show pseudocontact shifts. It is concluded that Cd-plastocyanin is a suitable redox-inactive substitute for Cu-plastocyanin.
Collapse
Affiliation(s)
- M Ubbink
- Department of Biochemistry, University of Cambridge, England.
| | | | | | | | | |
Collapse
|
635
|
Smith BO, Ito Y, Raine A, Teichmann S, Ben-Tovim L, Nietlispach D, Broadhurst RW, Terada T, Kelly M, Oschkinat H, Shibata T, Yokoyama S, Laue ED. An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. JOURNAL OF BIOMOLECULAR NMR 1996; 8:360-368. [PMID: 20686886 DOI: 10.1007/bf00410335] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/1996] [Accepted: 10/02/1996] [Indexed: 05/29/2023]
Abstract
A combination of calculation and experiment is used to demonstrate that the global fold of larger proteins can be rapidly determined using limited NMR data. The approach involves a combination of heteronuclear triple resonance NMR experiments with protonation of selected residue types in an otherwise completely deuterated protein. This method of labelling produces proteins with alpha-specific deuteration in the protonated residues, and the results suggest that this will improve the sensitivity of experiments involving correlation of side-chain ((1)H and (13)C) and backbone ((1)H and (15)N) amide resonances. It will allow the rapid assignment of backbone resonances with high sensitivity and the determination of a reasonable structural model of a protein based on limited NOE restraints, an application that is of increasing importance as data from the large number of genome sequencing projects accumulates. The method that we propose should also be of utility in extending the use of NMR spectroscopy to determine the structures of larger proteins.
Collapse
Affiliation(s)
- B O Smith
- Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QW, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
636
|
Tjandra N, Grzesiek S, Bax A. Magnetic Field Dependence of Nitrogen−Proton J Splittings in 15N-Enriched Human Ubiquitin Resulting from Relaxation Interference and Residual Dipolar Coupling. J Am Chem Soc 1996. [DOI: 10.1021/ja960106n] [Citation(s) in RCA: 216] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nico Tjandra
- Contribution from the Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Stephan Grzesiek
- Contribution from the Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Ad Bax
- Contribution from the Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| |
Collapse
|
637
|
Chapter 30. New NMR Methods for Structural Studies of Proteins to Aid in Drug Design. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1996. [DOI: 10.1016/s0065-7743(08)60469-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
|