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Hussain A, Paukovich N, Henen MA, Vögeli B. Advances in the exact nuclear Overhauser effect 2018-2022. Methods 2022; 206:87-98. [PMID: 35985641 PMCID: PMC9596134 DOI: 10.1016/j.ymeth.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
The introduction of the exact nuclear Overhauser enhancement (eNOE) methodology to solution-state nuclear magnetic resonance (NMR) spectroscopy results in tighter distance restraints from NOEs than in convention analysis. These improved restraints allow for higher resolution in structure calculation and even the disentanglement of different conformations of macromolecules. While initial work primarily focused on technical development of the eNOE, structural studies aimed at the elucidation of spatial sampling in proteins and nucleic acids were published in parallel prior to 2018. The period of 2018-2022 saw a continued series of technical innovation, but also major applications addressing biological questions. Here, we review both aspects, covering topics from the implementation of non-uniform sampling of NOESY buildups, novel pulse sequences, adaption of the eNOE to solid-state NMR, advances in eNOE data analysis, and innovations in structural ensemble calculation, to applications to protein, RNA, and DNA structure elucidation.
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Affiliation(s)
- Alya Hussain
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17(th) Avenue, Aurora, CO 80045, USA
| | - Natasia Paukovich
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17(th) Avenue, Aurora, CO 80045, USA
| | - Morkos A Henen
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17(th) Avenue, Aurora, CO 80045, USA; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Beat Vögeli
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17(th) Avenue, Aurora, CO 80045, USA.
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2
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Nichols PJ, Born A, Henen MA, Strotz D, Jones DN, Delaglio F, Vögeli B. Reducing the measurement time of exact NOEs by non-uniform sampling. JOURNAL OF BIOMOLECULAR NMR 2020; 74:717-739. [PMID: 32880802 PMCID: PMC9204832 DOI: 10.1007/s10858-020-00344-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/23/2020] [Indexed: 05/13/2023]
Abstract
We have previously reported on the measurement of exact NOEs (eNOEs), which yield a wealth of additional information in comparison to conventional NOEs. We have used these eNOEs in a variety of applications, including calculating high-resolution structures of proteins and RNA molecules. The collection of eNOEs is challenging, however, due to the need to measure a NOESY buildup series consisting of typically four NOESY spectra with varying mixing times in a single measurement session. While the 2D version can be completed in a few days, a fully sampled 3D-NOESY buildup series can take 10 days or more to acquire. This can be both expensive as well as problematic in the case of samples that are not stable over such a long period of time. One potential method to significantly decrease the required measurement time of eNOEs is to use non-uniform sampling (NUS) to decrease the number of points measured in the indirect dimensions. The effect of NUS on the extremely tight distance restraints extracted from eNOEs may be very pronounced. Therefore, we investigated the fidelity of eNOEs measured from three test cases at decreasing NUS densities: the 18.4 kDa protein human Pin1, the 4.1 kDa WW domain of Pin1 (both in 3D), and a 4.6 kDa 14mer RNA UUCG tetraloop (2D). Our results show that NUS imparted negligible error on the eNOE distances derived from good quality data down to 10% sampling for all three cases, but there is a noticeable decrease in the eNOE yield that is dependent upon the underlying sparsity, and thus complexity, of the sample. For Pin1, this transition occurred at roughly 40% while for the WW domain and the UUCG tetraloop it occurred at lower NUS densities of 20% and 10%, respectively. We rationalized these numbers through reconstruction simulations under various conditions. The extent of this loss depends upon the number of scans taken as well as the number of peaks to be reconstructed. Based on these findings, we have created guidelines for choosing an optimal NUS density depending on the number of peaks needed to be reconstructed in the densest region of a 2D or 3D NOESY spectrum.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, 8093, Zürich, Switzerland
| | - David N Jones
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, ML, 20850, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA.
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3
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Petrović D, Wang X, Strodel B. How accurately do force fields represent protein side chain ensembles? Proteins 2018; 86:935-944. [DOI: 10.1002/prot.25525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/02/2018] [Accepted: 05/14/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Dušan Petrović
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Department of Cell and Molecular Biology; Uppsala University, BMC Box 596; Uppsala, 751 24 Sweden
| | - Xue Wang
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf, Universitätsstraße 1; Düsseldorf, 40225 Germany
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf, Universitätsstraße 1; Düsseldorf, 40225 Germany
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4
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Born A, Henen MA, Nichols P, Wang J, Jones DN, Vögeli B. Efficient Stereospecific H β2/3 NMR Assignment Strategy for Mid-Size Proteins. MAGNETOCHEMISTRY 2018; 4. [PMID: 31093488 PMCID: PMC6513325 DOI: 10.3390/magnetochemistry4020025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We present a strategy for stereospecific NMR assignment of Hβ2 and Hβ3 protons in mid-size proteins (~150 residues). For such proteins, resonance overlap in standard experiments is severe, thereby preventing unambiguous assignment of a large fraction of β-methylenes. To alleviate this limitation, assignment experiments may be run in high static fields, where higher decoupling power is required. Three-bond Hα–Hβ J-couplings (3JHα–Hβ) are critical for stereospecific assignments of β-methylene protons, and for determining rotameric χ1 states. Therefore, we modified a pulse sequence designed to measure accurate 3JHα–Hβ couplings such that probe heating was reduced, while the decoupling performance was improved. To further increase the resolution, we applied non-uniform sampling (NUS) schemes in the indirect 1H and 13C dimensions. The approach was applied to two medium-sized proteins, odorant binding protein 22 (OBP22; 14.4 kDa) and Pin1 (18.2 kDa), at 900 MHz polarizing fields. The coupling values obtained from NUS and linear sampling were extremely well correlated. However, NUS decreased the overlap of Hβ2/3 protons, thus supplying a higher yield of extracted 3JHα-Hβ coupling values when compared with linear sampling. A similar effect could be achieved with linear prediction applied to the linearly sampled data prior to the Fourier transformation. Finally, we used 3JHα–Hβ couplings from Pin1 in combination with either conventional or exact nuclear Overhauser enhancement (eNOE) restraints to determine the stereospecific assignments of β-methylene protons. The use of eNOEs further increased the fraction of unambiguously assigned resonances when compared with procedures using conventional NOEs.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.); (P.N.)
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.); (P.N.)
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Parker Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.); (P.N.)
| | - Jing Wang
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (J.W.); (D.N.J.)
| | - David N Jones
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (J.W.); (D.N.J.)
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.); (P.N.)
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Strotz D, Orts J, Chi CN, Riek R, Vögeli B. eNORA2 Exact NOE Analysis Program. J Chem Theory Comput 2017; 13:4336-4346. [PMID: 28727914 DOI: 10.1021/acs.jctc.7b00436] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have recently developed an NMR protocol to extract exact distances between nuclei in proteins from an exact interpretation of NOESY buildup intensities (eNOEs). This enabled us to calculate multistate structural ensembles that exhibit realistic spatial sampling and long-range correlations. Our initial studies were laborious and required a deep understanding of the underlying spin dynamics. Here, we present a MatLab package that integrates all data processing steps required to convert intensities of assigned peaks in NOESY series into upper and lower distance limits for structure calculation. Those steps include organization of the data in object format, extraction of autorelaxation and cross-relaxation rate constants by fitting of diagonal peak decays and cross peak buildups, validation of the data, correction for spin diffusion, graphical display of the results, and generation of distance limits in CYANA compatible format. The analysis may be carried out using a full relaxation matrix or a simplified "divide and conquer" approach that allows for partial deuteration of protons. As the program does not require expertise beyond that of standard resonance assignment/structure calculation, it is suitable for experts and nonexperts alike.
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Affiliation(s)
- Dean Strotz
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Julien Orts
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Celestine N Chi
- Institute of Medical Biochemistry and Microbiology, Uppsala Biomedical Center, Uppsala University , 751 23 Uppsala, Sweden
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver , 12801 East 17th Avenue, Aurora, Colorado 80045, United States
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The Exact Nuclear Overhauser Enhancement: Recent Advances. Molecules 2017; 22:molecules22071176. [PMID: 28708092 PMCID: PMC6152122 DOI: 10.3390/molecules22071176] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 02/04/2023] Open
Abstract
Although often depicted as rigid structures, proteins are highly dynamic systems, whose motions are essential to their functions. Despite this, it is difficult to investigate protein dynamics due to the rapid timescale at which they sample their conformational space, leading most NMR-determined structures to represent only an averaged snapshot of the dynamic picture. While NMR relaxation measurements can help to determine local dynamics, it is difficult to detect translational or concerted motion, and only recently have significant advances been made to make it possible to acquire a more holistic representation of the dynamics and structural landscapes of proteins. Here, we briefly revisit our most recent progress in the theory and use of exact nuclear Overhauser enhancements (eNOEs) for the calculation of structural ensembles that describe their conformational space. New developments are primarily targeted at increasing the number and improving the quality of extracted eNOE distance restraints, such that the multi-state structure calculation can be applied to proteins of higher molecular weights. We then review the implications of the exact NOE to the protein dynamics and function of cyclophilin A and the WW domain of Pin1, and finally discuss our current research and future directions.
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Vögeli B, Olsson S, Güntert P, Riek R. The Exact NOE as an Alternative in Ensemble Structure Determination. Biophys J 2016; 110:113-26. [PMID: 26745415 DOI: 10.1016/j.bpj.2015.11.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 10/22/2022] Open
Abstract
The structure-function paradigm is increasingly replaced by the structure-dynamics-function paradigm. All protein activity is steered by the interplay between enthalpy and entropy. Conformational dynamics serves as a proxy of conformational entropy. Therefore, it is essential to study not only the average conformation but also the spatial sampling of a protein on all timescales. To this purpose, we have established a protocol for determining multiple-state ensembles of proteins based on exact nuclear Overhauser effects (eNOEs). We have recently extended our previously reported eNOE data set for the protein GB3 by a very large set of backbone and side-chain residual dipolar couplings and three-bond J couplings. Here, we demonstrate that at least four structural states are required to represent the complete data set by dissecting the contributions to the CYANA target function, which quantifies restraint violations in structure calculation. We present a four-state ensemble of GB3, which largely preserves the characteristics obtained from eNOEs only. Due to the abundance of the input data, the ensemble and χ(1) angles in particular are well suited for cross-validation of the input data and comparison to x-ray structures. Principal component analysis is used to automatically identify and validate relevant states of the ensembles. Overall, our findings suggest that eNOEs are a valuable alternative to traditional NMR probes in spatial elucidation of proteins.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland.
| | - Simon Olsson
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland; Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Frankfurt am Main, Germany; Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
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8
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The Dynamic Basis for Signal Propagation in Human Pin1-WW. Structure 2016; 24:1464-75. [PMID: 27499442 DOI: 10.1016/j.str.2016.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/11/2016] [Accepted: 06/14/2016] [Indexed: 12/23/2022]
Abstract
Allostery is the structural manifestation of information transduction in biomolecules. Its hallmark is conformational change induced by perturbations at a distal site. An increasing body of evidence demonstrates the presence of allostery in very flexible and even disordered proteins, encouraging a thermodynamic description of this phenomenon. Still, resolving such processes at atomic resolution is difficult. Here we establish a protocol to determine atomistic thermodynamic models of such systems using high-resolution solution state nuclear magnetic resonance data and extensive molecular simulations. Using this methodology, we study information transduction in the WW domain of a key cell-cycle regulator Pin1. Pin1 binds promiscuously to phospho-Ser/Thr-Pro motifs, however, disparate structural and dynamic responses have been reported upon binding different ligands. Our model consists of two topologically distinct states whose relative population may be specifically skewed by an incoming ligand. This model provides a canonical basis for the understanding of multi-functionality in Pin1.
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Augustyniak R, Stanek J, Colaux H, Bodenhausen G, Koźmiński W, Herrmann T, Ferrage F. Nuclear overhauser spectroscopy of chiral CHD methylene groups. JOURNAL OF BIOMOLECULAR NMR 2016; 64:27-37. [PMID: 26614488 DOI: 10.1007/s10858-015-0002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure.
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Affiliation(s)
- Rafal Augustyniak
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Henri Colaux
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
| | - Geoffrey Bodenhausen
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
- Ecole Polytechnique Fédérale de Lausanne, Institut des Sciences et Ingénierie Chimiques, BCH, 1015, Lausanne, Switzerland
| | - Wiktor Koźmiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, Université de Lyon/UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Fabien Ferrage
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France.
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France.
- UMR 7203 LBM, CNRS, 75005, Paris, France.
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Strotz D, Orts J, Minges M, Vögeli B. The experimental accuracy of the uni-directional exact NOE. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 259:32-46. [PMID: 26291287 DOI: 10.1016/j.jmr.2015.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/20/2015] [Accepted: 07/25/2015] [Indexed: 06/04/2023]
Abstract
We have established protocols to calculate exact NOEs (eNOE) from NOE data. eNOEs lend unprecedented precision to the calculation of distance restraints used for structure calculation. Moreover, as eNOEs are averaged quantities over all conformations of a molecule, they may contain accessible information of the sampled conformational space. In practice, a prerequisite for an exact interpretation is the evaluation of both NOESY cross-peak buildups. For large molecular sizes, the fraction of NOEs which can only be obtained from one cross peak typically increases. Distance restraints derived from such NOEs must be used with a tolerance for errors associated with the broken symmetry of the individual magnetization transfer pathways. The correct choice of upper and lower limits is particularly important for multiple-state ensemble calculation, where too narrow tolerances may lead to incorrect spatial sampling. In order to dissect these pathways in heavy-atom resolved 3D NOESY experiments, we analyze 2D [(1)H, (1)H]-NOESY experiments, which are the fundamental building blocks of the former. In combination with an analysis of excitation and inversion profiles of pulses on heavy atoms and relaxation effects during HXQC elements, we derive a rule for the correct choice of upper and lower distance limits derived from such uni-directional NOEs. We show that normalization of the cross- to the diagonal-peak intensities of the spins of magnetization destination rather than origin leads to similar errors of the distance restraints. This opens up the prospect of extended collection of unidirectional eNOEs.
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Affiliation(s)
- Dean Strotz
- Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Julien Orts
- Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Martina Minges
- Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Beat Vögeli
- Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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11
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Compiled data set of exact NOE distance limits, residual dipolar couplings and scalar couplings for the protein GB3. Data Brief 2015; 5:99-106. [PMID: 26504890 PMCID: PMC4576366 DOI: 10.1016/j.dib.2015.08.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 01/26/2023] Open
Abstract
We compiled an NMR data set consisting of exact nuclear Overhauser enhancement (eNOE) distance limits, residual dipolar couplings (RDCs) and scalar (J) couplings for GB3, which forms one of the largest and most diverse data set for structural characterization of a protein to date. All data have small experimental errors, which are carefully estimated. We use the data in the research article Vogeli et al., 2015, Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics, J. Struct. Biol., 191, 3, 306–317, doi:10.1016/j.jsb.2015.07.008 [1] for cross-validation in multiple-state structural ensemble calculation. We advocate this set to be an ideal test case for molecular dynamics simulations and structure calculations.
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12
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Vögeli B, Olsson S, Riek R, Güntert P. Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics. J Struct Biol 2015. [DOI: 10.1016/j.jsb.2015.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Güntert P, Buchner L. Combined automated NOE assignment and structure calculation with CYANA. JOURNAL OF BIOMOLECULAR NMR 2015; 62:453-71. [PMID: 25801209 DOI: 10.1007/s10858-015-9924-9] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/17/2015] [Indexed: 05/12/2023]
Abstract
The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR.
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Affiliation(s)
- Peter Güntert
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, Switzerland.
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
| | - Lena Buchner
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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14
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Vögeli B, Orts J, Strotz D, Chi C, Minges M, Wälti MA, Güntert P, Riek R. Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:53-59. [PMID: 24656080 DOI: 10.1016/j.jmr.2013.11.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
| | - Julien Orts
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Celestine Chi
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Martina Minges
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Graduate School of Science, Tokyo Metropolitan University, Hachioji, 192-0397 Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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