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Roth FA, Schmidts V, Rettig J, Thiele CM. Model free analysis of experimental residual dipolar couplings in small organic compounds. Phys Chem Chem Phys 2021; 24:281-286. [PMID: 34881759 DOI: 10.1039/d1cp02324a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Residual dipolar couplings (RDCs) contain information on the relative arrangement and dynamics of internuclear spin vectors in chemical compounds. Classically, RDC data is analyzed by fitting to structure models, while model-free approaches (MFA) directly relate RDCs to the corresponding internuclear vectors. The recently introduced software TITANIA implements the MFA and extracts structure and dynamics parameters directly from RDCs to facilitate de novo structure refinement for small organic compounds. Encouraged by our previous results on simulated data, we herein focus on the prerequisites and challenges faced when using purely experimental data for this approach. These concern mainly the fact that not all couplings are accessible in all media, leading to voids in the RDC matrix and the concomitant effects on the structure refinement. It is shown that RDC data sets obtained experimentally from currently available alignment media and measurement methods are of sufficient quality to allow relative configuration determination even when the relative configuration of the analyte is completely unknown.
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Affiliation(s)
- Felix A Roth
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
| | - Jan Rettig
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
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2
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Roth FA, Schmidts V, Thiele CM. TITANIA: Model-Free Interpretation of Residual Dipolar Couplings in the Context of Organic Compounds. J Org Chem 2021; 86:15387-15402. [PMID: 34677977 DOI: 10.1021/acs.joc.1c01926] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) become increasingly important as additional NMR parameters in the structure elucidation of organic compounds but are usually used in fitting procedures to discriminate between (computed) structures that are in accordance with RDCs and others that can be ruled out. Thus, the determination of configurations requires prior structural information. The direct use of RDCs as restraints to construct structures based on RDCs has only recently begun also in organic compounds. No protocol has been published though that uses the vector and dynamics information available in multialignment data sets directly for the joint determination of conformation and configuration of organic compounds. This is proposed in the current study. We show that by employing these data, even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. The requirements in terms of the number of RDCs and alignment media necessary are discussed in detail.
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Affiliation(s)
- Felix A Roth
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
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3
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Vögeli B, Vugmeyster L. Distance-independent Cross-correlated Relaxation and Isotropic Chemical Shift Modulation in Protein Dynamics Studies. Chemphyschem 2018; 20:178-196. [PMID: 30110510 DOI: 10.1002/cphc.201800602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 01/09/2023]
Abstract
Cross-correlated relaxation (CCR) in multiple-quantum coherences differs from other relaxation phenomena in its theoretical ability to be mediated across an infinite distance. The two interfering relaxation mechanisms may be dipolar interactions, chemical shift anisotropies, chemical shift modulations or quadrupolar interactions. These properties make multiple-quantum CCR an attractive probe for structure and dynamics of biomacromolecules not accessible from other measurements. Here, we review the use of multiple-quantum CCR measurements in dynamics studies of proteins. We compile a list of all experiments proposed for CCR rate measurements, provide an overview of the theory with a focus on protein dynamics, and present applications to various protein systems.
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Affiliation(s)
- Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, 12801 East 17th Avenue, Aurora, CO, 80045, United States
| | - Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, 1201 Laurimer Street Denver, CO, 80204, United States
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4
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Sabo TM, Gapsys V, Walter KFA, Fenwick RB, Becker S, Salvatella X, de Groot BL, Lee D, Griesinger C. Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 2018; 138-139:85-92. [PMID: 29656081 DOI: 10.1016/j.ymeth.2018.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/02/2018] [Accepted: 04/10/2018] [Indexed: 11/30/2022] Open
Abstract
Dipole-dipole cross-correlated relaxation (CCR) between two spin pairs is rich with macromolecular structural and dynamic information on inter-nuclear bond vectors. Measurement of short range dipolar CCR rates has been demonstrated for a variety of inter-nuclear vector spin pairs in proteins and nucleic acids, where the multiple quantum coherence necessary for observing the CCR rate is created by through-bond scalar coupling. In principle, CCR rates can be measured for any pair of inter-nuclear vectors where coherence can be generated between one spin of each spin pair, regardless of both the distance between the two spin pairs and the distance of the two spins forming the multiple quantum coherence. In practice, however, long range CCR (lrCCR) rates are challenging to measure due to difficulties in linking spatially distant spin pairs. By utilizing through-space relaxation allowed coherence transfer (RACT), we have developed a new method for the measurement of lrCCR rates involving CαHα bonds on opposing anti-parallel β-strands. The resulting lrCCR rates are straightforward to interpret since only the angle between the two vectors modulates the strength of the interference effect. We applied our lrCCR measurement to the third immunoglobulin-binding domain of the streptococcal protein G (GB3) and utilize published NMR ensembles and static NMR/X-ray structures to highlight the relationship between the lrCCR rates and the CαHα-CαHα inter-bond angle and bond mobility. Furthermore, we employ the lrCCR rates to guide the selection of sub-ensembles from the published NMR ensembles for enhancing the structural and dynamic interpretation of the data. We foresee this methodology for measuring lrCCR rates as improving the generation of structural ensembles by providing highly accurate details concerning the orientation of CαHα bonds on opposing anti-parallel β-strands.
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Affiliation(s)
- T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
| | - Vytautas Gapsys
- Department for Computational Biomolecular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Korvin F A Walter
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - R Bryn Fenwick
- Department of Integrative Structural and Computational Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Stefan Becker
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis AvanÅats (ICREA), Barcelona, Spain
| | - Bert L de Groot
- Department for Computational Biomolecular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
| | - Christian Griesinger
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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6
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Schmidts V. Perspectives in the application of residual dipolar couplings in the structure elucidation of weakly aligned small molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:54-60. [PMID: 27743456 DOI: 10.1002/mrc.4543] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 05/28/2023]
Abstract
This perspective article aims to review the general methodology in the application of residual dipolar couplings (RDCs) in the structure elucidation of small molecules and give the author's view on challenges for future applications. Recent improvements in the availability of alignment media, new pulse sequences for the measurement of couplings and improvements in the analysis software have garnered widespread interest in the technique. However, further generalization is needed in order to make RDC analysis into a truly "routine" method. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
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7
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Chakrabarti KS, Ban D, Pratihar S, Reddy JG, Becker S, Griesinger C, Lee D. High-power (1)H composite pulse decoupling provides artifact free exchange-mediated saturation transfer (EST) experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 269:65-69. [PMID: 27240144 DOI: 10.1016/j.jmr.2016.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/16/2016] [Accepted: 05/20/2016] [Indexed: 05/25/2023]
Abstract
Exchange-mediated saturation transfer (EST) provides critical information regarding dynamics of molecules. In typical applications EST is studied by either scanning a wide range of (15)N chemical shift offsets where the applied (15)N irradiation field strength is on the order of hundreds of Hertz or, scanning a narrow range of (15)N chemical shift offsets where the applied (15)N irradiation field-strength is on the order of tens of Hertz during the EST period. The (1)H decoupling during the EST delay is critical as incomplete decoupling causes broadening of the EST profile, which could possibly result in inaccuracies of the extracted kinetic parameters and transverse relaxation rates. Currently two different (1)H decoupling schemes have been employed, intermittently applied 180° pulses and composite-pulse-decoupling (CPD), for situations where a wide range, or narrow range of (15)N chemical shift offsets are scanned, respectively. We show that high-power CPD provides artifact free EST experiments, which can be universally implemented regardless of the offset range or irradiation field-strengths.
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Affiliation(s)
- Kalyan S Chakrabarti
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - David Ban
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Supriya Pratihar
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jithender G Reddy
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Donghan Lee
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
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8
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Fenwick RB, Schwieters CD, Vögeli B. Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions. J Am Chem Soc 2016; 138:8412-21. [PMID: 27331619 PMCID: PMC5055379 DOI: 10.1021/jacs.6b01447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synchronization of native state motions as they transition between microstates influences catalysis kinetics, mediates allosteric interactions, and reduces the conformational entropy of proteins. However, it has proven difficult to describe native microstates because they are usually minimally frustrated and may interconvert on the micro- to millisecond time scale. Direct observation of concerted equilibrium fluctuations would therefore be an important tool for describing protein native states. Here we propose a strategy that relates NMR cross-correlated relaxation (CCR) rates between dipolar interactions to residual dipolar couplings (RDCs) of individual consecutive H(N)-N and H(α)-C(α) bonds, which act as a proxy for the peptide planes and the side chains, respectively. Using Xplor-NIH ensemble structure calculations restrained with the RDC and CCR data, we observe collective motions on time scales slower than nanoseconds in the backbone for GB3. To directly access the correlations from CCR, we develop a structure-free data analysis. The resulting dynamic correlation map is consistent with the ensemble-restrained simulations and reveals a complex network. In general, we find that the bond motions are on average slightly correlated and that the local environment dominates many observations. Despite this, some patterns are typical over entire secondary structure elements. In the β-sheet, nearly all bonds are weakly correlated, and there is an approximately binary alternation in correlation intensity corresponding to the solvent exposure/shielding alternation of the side chains. For α-helices, there is also a weak correlation in the H(N)-N bonds. The degree of correlation involving H(α)-C(α) bonds is directly affected by side-chain fluctuations, whereas loops show complex and nonuniform behavior.
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Affiliation(s)
- R. Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Spain
- The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Building 12A Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - Beat Vögeli
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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9
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Pratihar S, Sabo TM, Ban D, Fenwick RB, Becker S, Salvatella X, Griesinger C, Lee D. Kinetics of the Antibody Recognition Site in the Third IgG-Binding Domain of Protein G. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Supriya Pratihar
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - T. Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
| | - R. Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Department of Integrative Structural and Computational Biology; Skaggs Institute for Chemical Biology, The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
| | - Stefan Becker
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Barcelona Spain
| | - Christian Griesinger
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - Donghan Lee
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
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10
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Pratihar S, Sabo TM, Ban D, Fenwick RB, Becker S, Salvatella X, Griesinger C, Lee D. Kinetics of the Antibody Recognition Site in the Third IgG-Binding Domain of Protein G. Angew Chem Int Ed Engl 2016; 55:9567-70. [PMID: 27345359 DOI: 10.1002/anie.201603501] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 05/20/2016] [Indexed: 12/31/2022]
Abstract
Protein dynamics occurring on a wide range of timescales play a crucial role in governing protein function. Particularly, motions between the globular rotational correlation time (τc ) and 40 μs (supra-τc window), strongly influence molecular recognition. This supra-τc window was previously hidden, owing to a lack of experimental methods. Recently, we have developed a high-power relaxation dispersion (RD) experiment for measuring kinetics as fast as 4 μs. For the first time, this method, performed under super-cooled conditions, enabled us to detect a global motion in the first β-turn of the third IgG-binding domain of protein G (GB3), which was extrapolated to 371±115 ns at 310 K. Furthermore, the same residues show the plasticity in the model-free residual dipolar coupling (RDC) order parameters and in an ensemble encoding the supra-τc dynamics. This β-turn is involved in antibody binding, exhibiting the potential link of the observed supra-τc motion with molecular recognition.
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Affiliation(s)
- Supriya Pratihar
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
| | - R Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.,Department of Integrative Structural and Computational Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Donghan Lee
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany. .,Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA.
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11
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Allosteric switch regulates protein-protein binding through collective motion. Proc Natl Acad Sci U S A 2016; 113:3269-74. [PMID: 26961002 DOI: 10.1073/pnas.1519609113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Many biological processes depend on allosteric communication between different parts of a protein, but the role of internal protein motion in propagating signals through the structure remains largely unknown. Through an experimental and computational analysis of the ground state dynamics in ubiquitin, we identify a collective global motion that is specifically linked to a conformational switch distant from the binding interface. This allosteric coupling is also present in crystal structures and is found to facilitate multispecificity, particularly binding to the ubiquitin-specific protease (USP) family of deubiquitinases. The collective motion that enables this allosteric communication does not affect binding through localized changes but, instead, depends on expansion and contraction of the entire protein domain. The characterization of these collective motions represents a promising avenue for finding and manipulating allosteric networks.
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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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Olsson S, Vögeli BR, Cavalli A, Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K, Hamelryck T. Probabilistic Determination of Native State Ensembles of Proteins. J Chem Theory Comput 2014; 10:3484-91. [DOI: 10.1021/ct5001236] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Olsson
- Bioinformatics
Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Beat Rolf Vögeli
- Laboratory
of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Wouter Boomsma
- Structural
Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Ferkinghoff-Borg
- Cellular
Signal Integration Group, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Hamelryck
- Bioinformatics
Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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14
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Bibow S, Carneiro MG, Sabo TM, Schwiegk C, Becker S, Riek R, Lee D. Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings. Protein Sci 2014; 23:851-6. [PMID: 24752984 DOI: 10.1002/pro.2482] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 11/11/2022]
Abstract
Membrane proteins are involved in numerous vital biological processes. To understand membrane protein functionality, accurate structural information is required. Usually, structure determination and dynamics of membrane proteins are studied in micelles using either solution state NMR or X-ray crystallography. Even though invaluable information has been obtained by this approach, micelles are known to be far from ideal mimics of biological membranes often causing the loss or decrease of membrane protein activity. Recently, nanodiscs, which are composed of a lipid bilayer surrounded by apolipoproteins, have been introduced as a more physiological alternative than micelles for NMR investigations on membrane proteins. Here, we show that membrane protein bond orientations in nanodiscs can be obtained by measuring residual dipolar couplings (RDCs) with the outer membrane protein OmpX embedded in nanodiscs using Pf1 phage as an alignment medium. The presented collection of membrane protein RDCs in nanodiscs represents an important step toward more comprehensive structural and dynamical NMR-based investigations of membrane proteins in a natural bilayer environment.
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Affiliation(s)
- Stefan Bibow
- Laboratory for Physical Chemistry, ETH Zürich, CH-8093, Zürich, Switzerland
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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: 31] [Impact Index Per Article: 2.8] [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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