1
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Dreydoppel M, Lichtenecker RJ, Akke M, Weininger U. 1H R 1ρ relaxation dispersion experiments in aromatic side chains. JOURNAL OF BIOMOLECULAR NMR 2021; 75:383-392. [PMID: 34510298 PMCID: PMC8642340 DOI: 10.1007/s10858-021-00382-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamic, since they are often key residues in enzyme active sites and protein binding sites. Dynamic processes on microsecond to millisecond timescales can be studied by relaxation dispersion experiments that attenuate conformational exchange contributions to the transverse relaxation rate by varying the refocusing frequency of applied radio-frequency fields implemented as either CPMG pulse trains or continuous spin-lock periods. Here we present an aromatic 1H R1ρ relaxation dispersion experiment enabling studies of two to three times faster exchange processes than achievable by existing experiments for aromatic side chains. We show that site-specific isotope labeling schemes generating isolated 1H-13C spin pairs with vicinal 2H-12C moieties are necessary to avoid anomalous relaxation dispersion profiles caused by Hartmann-Hahn matching due to the 3JHH couplings and limited chemical shift differences among 1H spins in phenylalanine, tyrosine and the six-ring moiety of tryptophan. This labeling pattern is sufficient in that remote protons do not cause additional complications. We validated the approach by measuring ring-flip kinetics in the small protein GB1. The determined rate constants, kflip, agree well with previous results from 13C R1ρ relaxation dispersion experiments, and yield 1H chemical shift differences between the two sides of the ring in good agreement with values measured under slow-exchange conditions. The aromatic1H R1ρ relaxation dispersion experiment in combination with the site-selective 1H-13C/2H-12C labeling scheme enable measurement of exchange rates up to kex = 2kflip = 80,000 s-1, and serve as a useful complement to previously developed 13C-based methods.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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2
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Liu B, Rangadurai A, Shi H, Al-Hashimi H. Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1H CEST. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:715-731. [PMID: 37905209 PMCID: PMC10539785 DOI: 10.5194/mr-2-715-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/05/2021] [Indexed: 11/01/2023]
Abstract
In duplex DNA, Watson-Crick A-T and G-C base pairs (bp's) exist in dynamic equilibrium with an alternative Hoogsteen conformation, which is low in abundance and short-lived. Measuring how the Hoogsteen dynamics varies across different DNA sequences, structural contexts and physiological conditions is key for identifying potential Hoogsteen hot spots and for understanding the potential roles of Hoogsteen base pairs in DNA recognition and repair. However, such studies are hampered by the need to prepare 13 C or 15 N isotopically enriched DNA samples for NMR relaxation dispersion (RD) experiments. Here, using SELective Optimized Proton Experiments (SELOPE) 1 H CEST experiments employing high-power radiofrequency fields (B 1 > 250 Hz) targeting imino protons, we demonstrate accurate and robust characterization of Watson-Crick to Hoogsteen exchange, without the need for isotopic enrichment of the DNA. For 13 residues in three DNA duplexes under different temperature and pH conditions, the exchange parameters deduced from high-power imino 1 H CEST were in very good agreement with counterparts measured using off-resonance 13 C / 15 N spin relaxation in the rotating frame (R 1 ρ ). It is shown that 1 H-1 H NOE effects which typically introduce artifacts in 1 H-based measurements of chemical exchange can be effectively suppressed by selective excitation, provided that the relaxation delay is short (≤ 100 ms). The 1 H CEST experiment can be performed with ∼ 10× higher throughput and ∼ 100× lower cost relative to 13 C / 15 N R 1 ρ and enabled Hoogsteen chemical exchange measurements undetectable by R 1 ρ . The results reveal an increased propensity to form Hoogsteen bp's near terminal ends and a diminished propensity within A-tract motifs. The 1 H CEST experiment provides a basis for rapidly screening Hoogsteen breathing in duplex DNA, enabling identification of unusual motifs for more in-depth characterization.
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Affiliation(s)
- Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Department of Chemistry, Duke University, Durham, NC, USA
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3
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Xiang X, Hansen AL, Yu L, Jameson G, Bruschweiler-Li L, Yuan C, Brüschweiler R. Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation. J Am Chem Soc 2021; 143:13593-13604. [PMID: 34428032 DOI: 10.1021/jacs.1c04687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amino-acid side-chain properties in proteins are key determinants of protein function. NMR spin relaxation of side chains is an important source of information about local protein dynamics and flexibility. However, traditional solution NMR relaxation methods are most sensitive to sub-nanosecond dynamics lacking information on slower ns-μs time-scale motions. Nanoparticle-assisted NMR spin relaxation (NASR) of methyl-side chains is introduced here as a window into these ns-μs dynamics. NASR utilizes the transient and nonspecific interactions between folded proteins and slowly tumbling spherical nanoparticles (NPs), whereby the increase of the relaxation rates reflects motions on time scales from ps all the way to the overall tumbling correlation time of the NPs ranging from hundreds of ns to μs. The observed motional amplitude of each methyl group can then be expressed by a model-free NASR S2 order parameter. The method is demonstrated for 2H-relaxation of CH2D methyl moieties and cross-correlated relaxation of CH3 groups for proteins Im7 and ubiquitin in the presence of anionic silica-nanoparticles. Both types of relaxation experiments, dominated by either quadrupolar or dipolar interactions, yield highly consistent results. Im7 shows additional dynamics on the intermediate time scales taking place in a functionally important loop, whereas ubiquitin visits the majority of its conformational substates on the sub-ns time scale. These experimental observations are in good agreement with 4-10 μs all-atom molecular dynamics trajectories. NASR probes side-chain dynamics on a much wider range of motional time scales than previously possible, thereby providing new insights into the interplay between protein structure, dynamics, and molecular interactions that govern protein function.
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Affiliation(s)
- Xinyao Xiang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lei Yu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gregory Jameson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
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4
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Pritišanac I, Alderson TR, Güntert P. Automated assignment of methyl NMR spectra from large proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:54-73. [PMID: 32883449 DOI: 10.1016/j.pnmrs.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
Abstract
As structural biology trends towards larger and more complex biomolecular targets, a detailed understanding of their interactions and underlying structures and dynamics is required. The development of methyl-TROSY has enabled NMR spectroscopy to provide atomic-resolution insight into the mechanisms of large molecular assemblies in solution. However, the applicability of methyl-TROSY has been hindered by the laborious and time-consuming resonance assignment process, typically performed with domain fragmentation, site-directed mutagenesis, and analysis of NOE data in the context of a crystal structure. In response, several structure-based automatic methyl assignment strategies have been developed over the past decade. Here, we present a comprehensive analysis of all available methods and compare their input data requirements, algorithmic strategies, and reported performance. In general, the methods fall into two categories: those that primarily rely on inter-methyl NOEs, and those that utilize methyl PRE- and PCS-based restraints. We discuss their advantages and limitations, and highlight the potential benefits from standardizing and combining different methods.
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Affiliation(s)
- Iva Pritišanac
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany; Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland; Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
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5
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Shamshir A, Sparrman T, Westlund PO. Analysis of the behaviour of confined molecules using 2H T1 nuclear magnetic relaxation dispersion. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1645367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Adel Shamshir
- Department of Chemistry, Umeå University, Umeå, Sweden
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6
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Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
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Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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7
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Chao FA, Li Y, Zhang Y, Byrd RA. Probing the Broad Time Scale and Heterogeneous Conformational Dynamics in the Catalytic Core of the Arf-GAP ASAP1 via Methyl Adiabatic Relaxation Dispersion. J Am Chem Soc 2019; 141:11881-11891. [PMID: 31293161 PMCID: PMC7505415 DOI: 10.1021/jacs.9b02602] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Methyl-TROSY is one of the most powerful NMR spectroscopic tools for studying structures and conformational dynamics of large protein complexes in solution. In studying conformational dynamics, side chains usually display heterogeneous dynamics, including collective and local motions, that can be difficult to detect and analyze by conventional relaxation dispersion (RD) approaches. The combination of NH-based heteronuclear adiabatic relaxation dispersion (HARD) experiments and a geometric approximation (geoHARD) has been shown to have several advantages over conventional RD in revealing conformational dynamics over a broad time scale. Here, we demonstrate a new technique that has been developed to detect both heterogeneous and wide time scale conformational dynamics in the hydrophobic interior of large macromolecules utilizing methyl-geoHARD. It is shown that methyl-geoHARD will be feasible at ultrahigh magnetic fields (>1 GHz), when this technology becomes available. For the ZA domain of Arf-GAP ASAP1, with a global correlational time of 24 ns at 15 °C, a wide range of conformational dynamics (exhibiting chemical exchange rates (kex) between 102 and 105 s-1) are observed in the methyl groups of isoleucine, leucine, and valine. The dynamics include collective and independent local motions. Furthermore, portions of the collective motions have been confirmed by single-quantum Carr-Purcell-Meiboom-Gill (SQ-CPMG) RD experiments; however, motions outside of the detectable CPMG window (400-8000 s-1) cannot be accurately determined by SQ-CPMG experiments. The methyl-geoHARD experiment allows the dissection of heterogeneous conformational dynamics and pinpoints important motions that, potentially, can be correlated with important biological functions and recognition.
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Affiliation(s)
- Fa-An Chao
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - Yifei Li
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - Yue Zhang
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - R Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
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8
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Abstract
The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
| | - Hans Koss
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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9
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Boswell ZK, Latham MP. Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes. Biochemistry 2018; 58:144-155. [PMID: 30336000 DOI: 10.1021/acs.biochem.8b00953] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
NMR spectroscopy is particularly adept at site-specifically monitoring dynamic processes in proteins, such as protein folding, domain movements, ligand binding, and side-chain rotations. By coupling the favorable spectroscopic properties of highly dynamic side-chain methyl groups with transverse-relaxation-optimized spectroscopy (TROSY), it is now possible to routinely study such dynamic processes in high-molecular-weight proteins and complexes approaching 1 MDa. In this Perspective, we describe many elegant methyl-based NMR experiments that probe slow (second) to fast (picosecond) dynamics in large systems. To demonstrate the power of these methods, we also provide interesting examples of studies that utilized each methyl-based NMR technique to uncover functionally important dynamics. In many cases, the NMR experiments are paired with site-directed mutagenesis and/or other biochemical assays to put the dynamics and function into context. Our vision of the future of structural biology involves pairing methyl-based NMR spectroscopy with biochemical studies to advance our knowledge of the motions large proteins and macromolecular complexes use to choreograph complex functions. Such studies will be essential in elucidating the critical structural dynamics that underlie function and characterizing alterations in these processes that can lead to human disease.
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Affiliation(s)
- Zachary K Boswell
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79423 , United States
| | - Michael P Latham
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79423 , United States
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10
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Resolving biomolecular motion and interactions by R2 and R1ρ relaxation dispersion NMR. Methods 2018; 148:28-38. [DOI: 10.1016/j.ymeth.2018.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
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11
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Schlagnitweit J, Steiner E, Karlsson H, Petzold K. Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach. Chemistry 2018; 24:6067-6070. [PMID: 29504639 PMCID: PMC5947647 DOI: 10.1002/chem.201800992] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 01/10/2023]
Abstract
The knowledge of structure and dynamics is crucial to explain the function of RNAs. While nuclear magnetic resonance (NMR) is well suited to probe these for complex biomolecules, it requires expensive, isotopically labeled samples, and long measurement times. Here we present SELOPE, a new robust, proton-only NMR method that allows us to obtain site-specific overview of structure and dynamics in an entire RNA molecule using an unlabeled sample. SELOPE simplifies assignment and allows for cost-effective screening of the response of nucleic acids to physiological changes (e.g. ion concentration) or screening of drugs in a high throughput fashion. This single technique allows us to probe an unprecedented range of exchange time scales (the whole μs to ms motion range) with increased sensitivity, surpassing all current experiments to detect chemical exchange. For the first time we could describe an RNA excited state using an unlabeled RNA.
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Affiliation(s)
- Judith Schlagnitweit
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Emilie Steiner
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Hampus Karlsson
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Katja Petzold
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
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12
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Abstract
The measurement of R1ρ , the longitudinal relaxation rate constant in the rotating frame, is one of the few available methods to characterize the μs-ms functional dynamics of biomolecules. Here, we focus on 15N R1ρ experiments for protein NH groups. We present protocols for both on- and off-resonance 15N R1ρ measurements needed for relaxation dispersion studies, and describe the data analysis for extracting kinetic and thermodynamic parameters characterizing the motional processes.
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Affiliation(s)
- Francesca Massi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Jeffrey W Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
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13
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Steiner E, Schlagnitweit J, Lundström P, Petzold K. Capturing Excited States in the Fast-Intermediate Exchange Limit in Biological Systems Using 1H NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Emilie Steiner
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; 10435 Stockholm Sweden
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; 10435 Stockholm Sweden
| | - Patrik Lundström
- Department of Physics, Chemistry and Biology; Linköping University; 58183 Linköping Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; 10435 Stockholm Sweden
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14
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Steiner E, Schlagnitweit J, Lundström P, Petzold K. Capturing Excited States in the Fast-Intermediate Exchange Limit in Biological Systems Using 1 H NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:15869-15872. [PMID: 27860024 DOI: 10.1002/anie.201609102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Changes in molecular structure are essential for the function of biomolecules. Characterization of these structural fluctuations can illuminate alternative states and help in correlating structure to function. NMR relaxation dispersion (RD) is currently the only method for detecting these alternative, high-energy states. In this study, we present a versatile 1 H R1ρ RD experiment that not only extends the exchange timescales at least three times beyond the rate limits of 13 C/15 N R1ρ and ten times for CPMG experiments, but also makes use of easily accessible probes, thus allowing a general description of biologically important excited states. This technique can be used to extract chemical shifts for the structural characterization of excited states and to elucidate complex excited states.
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Affiliation(s)
- Emilie Steiner
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 10435, Stockholm, Sweden
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 10435, Stockholm, Sweden
| | - Patrik Lundström
- Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 10435, Stockholm, Sweden
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15
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Shukla D, Peck A, Pande VS. Conformational heterogeneity of the calmodulin binding interface. Nat Commun 2016; 7:10910. [PMID: 27040077 PMCID: PMC4822001 DOI: 10.1038/ncomms10910] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 01/28/2016] [Indexed: 01/13/2023] Open
Abstract
Calmodulin (CaM) is a ubiquitous Ca(2+) sensor and a crucial signalling hub in many pathways aberrantly activated in disease. However, the mechanistic basis of its ability to bind diverse signalling molecules including G-protein-coupled receptors, ion channels and kinases remains poorly understood. Here we harness the high resolution of molecular dynamics simulations and the analytical power of Markov state models to dissect the molecular underpinnings of CaM binding diversity. Our computational model indicates that in the absence of Ca(2+), sub-states in the folded ensemble of CaM's C-terminal domain present chemically and sterically distinct topologies that may facilitate conformational selection. Furthermore, we find that local unfolding is off-pathway for the exchange process relevant for peptide binding, in contrast to prior hypotheses that unfolding might account for binding diversity. Finally, our model predicts a novel binding interface that is well-populated in the Ca(2+)-bound regime and, thus, a candidate for pharmacological intervention.
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Affiliation(s)
- Diwakar Shukla
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- SIMBIOS NIH Center for Biomedical Computation, Stanford University, Stanford, California 94305, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ariana Peck
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- SIMBIOS NIH Center for Biomedical Computation, Stanford University, Stanford, California 94305, USA
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16
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Ward ME, Ritz E, Ahmed MAM, Bamm VV, Harauz G, Brown LS, Ladizhansky V. Proton detection for signal enhancement in solid-state NMR experiments on mobile species in membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 63:375-388. [PMID: 26494649 DOI: 10.1007/s10858-015-9997-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/15/2015] [Indexed: 05/09/2023]
Abstract
Direct proton detection is becoming an increasingly popular method for enhancing sensitivity in solid-state nuclear magnetic resonance spectroscopy. Generally, these experiments require extensive deuteration of the protein, fast magic angle spinning (MAS), or a combination of both. Here, we implement direct proton detection to selectively observe the mobile entities in fully-protonated membrane proteins at moderate MAS frequencies. We demonstrate this method on two proteins that exhibit different motional regimes. Myelin basic protein is an intrinsically-disordered, peripherally membrane-associated protein that is highly flexible, whereas Anabaena sensory rhodopsin is composed of seven rigid transmembrane α-helices connected by mobile loop regions. In both cases, we observe narrow proton linewidths and, on average, a 10× increase in sensitivity in 2D insensitive nuclear enhancement of polarization transfer-based HSQC experiments when proton detection is compared to carbon detection. We further show that our proton-detected experiments can be easily extended to three dimensions and used to build complete amino acid systems, including sidechain protons, and obtain inter-residue correlations. Additionally, we detect signals which do not correspond to amino acids, but rather to lipids and/or carbohydrates which interact strongly with membrane proteins.
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Affiliation(s)
- Meaghan E Ward
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Emily Ritz
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Mumdooh A M Ahmed
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
- The Department of Physics, Faculty of Science, Suez University, Suez, 43533, Egypt
| | - Vladimir V Bamm
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - George Harauz
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, ON, Canada.
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada.
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17
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Abstract
Myriad biological processes proceed through states that defy characterization by conventional atomic-resolution structural biological methods. The invisibility of these 'dark' states can arise from their transient nature, low equilibrium population, large molecular weight, and/or heterogeneity. Although they are invisible, these dark states underlie a range of processes, acting as encounter complexes between proteins and as intermediates in protein folding and aggregation. New methods have made these states accessible to high-resolution analysis by nuclear magnetic resonance (NMR) spectroscopy, as long as the dark state is in dynamic equilibrium with an NMR-visible species. These methods - paramagnetic NMR, relaxation dispersion, saturation transfer, lifetime line broadening, and hydrogen exchange - allow the exploration of otherwise invisible states in exchange with a visible species over a range of timescales, each taking advantage of some unique property of the dark state to amplify its effect on a particular NMR observable. In this review, we introduce these methods and explore two specific techniques - paramagnetic relaxation enhancement and dark state exchange saturation transfer - in greater detail.
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Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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18
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Hoang J, Prosser RS. Conformational Selection and Functional Dynamics of Calmodulin: A 19F Nuclear Magnetic Resonance Study. Biochemistry 2014; 53:5727-36. [DOI: 10.1021/bi500679c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joshua Hoang
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - R. Scott Prosser
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
- Department
of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S
1A8, Canada
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19
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Weininger U, Brath U, Modig K, Teilum K, Akke M. Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection. JOURNAL OF BIOMOLECULAR NMR 2014; 59:23-9. [PMID: 24706175 PMCID: PMC4003406 DOI: 10.1007/s10858-014-9826-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/25/2014] [Indexed: 05/04/2023]
Abstract
Protein dynamics on the microsecond-millisecond time scales often play a critical role in biological function. NMR relaxation dispersion experiments are powerful approaches for investigating biologically relevant dynamics with site-specific resolution, as shown by a growing number of publications on enzyme catalysis, protein folding, ligand binding, and allostery. To date, the majority of studies has probed the backbone amides or side-chain methyl groups, while experiments targeting other sites have been used more sparingly. Aromatic side chains are useful probes of protein dynamics, because they are over-represented in protein binding interfaces, have important catalytic roles in enzymes, and form a sizable part of the protein interior. Here we present an off-resonance R 1ρ experiment for measuring microsecond to millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimization. Using selective excitation and inversion of the narrow component of the (13)C doublet, the experiment achieves significant sensitivity enhancement in terms of both signal intensity and the fractional contribution from exchange to transverse relaxation; additional signal enhancement is achieved by optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-selected R 1ρ experiment by measuring exchange parameters for Y23 in bovine pancreatic trypsin inhibitor at a temperature of 328 K, where the ring flip is in the fast exchange regime with a mean waiting time between flips of 320 μs. The determined chemical shift difference matches perfectly with that measured from the NMR spectrum at lower temperatures, where separate peaks are observed for the two sites. We further show that potentially complicating effects of strong scalar coupling between protons (Weininger et al. in J Phys Chem B 117: 9241-9247, 2013b) can be accounted for using a simple expression, and provide recommendations for data acquisition when the studied system exhibits this behavior. The present method extends the repertoire of relaxation methods tailored for aromatic side chains by enabling studies of faster processes and improved control over artifacts due to strong coupling.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Ulrika Brath
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
- Present Address: Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Göteborg, Sweden
| | - Kristofer Modig
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Kaare Teilum
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
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