1
|
Zuiderweg ERP. Validating the 15N- 1H HSQC-ROESY experiment for detecting 1HN exchange broadening in proteated proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 363:107676. [PMID: 38815459 DOI: 10.1016/j.jmr.2024.107676] [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: 12/01/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 06/01/2024]
Abstract
It is advantageous to investigate milli-to-micro-second conformational exchange data contained in the solution NMR protein relaxation data other than 15N nuclei. Not only does one search under another lamp post, one also looks at dynamics at other time scales. The HSQC-ROESY 1HN relaxation dispersion experiment for amide protons as introduced by Ishima, et al (1998). J. Am. Soc. 120, 10534-10542, is such an experiment, but has by the authors been advised to only be used for perdeuterated proteins to avoid complication with the 1H-1H multiple-spin effects. This is regretful, since not all proteins can be perdeuterated. Here we analyze in detail the 1HN relaxation terms for this experiment for a fully proteated protein. Indeed, the 1HN relaxation theory is in this case complex and includes dipolar-dipolar relaxation interference and TOCSY transfers. With simulate both of these effects and show that the interference can be exploited for detecting exchange broadening. The TOCSY effect is shown to minor, and when it is not, a solution is provided. We apply the HSQC-ROESY experiment, with a small modification to suppress ROESY crosspeaks, to a 7 kDa GB1 protein that is just 15N and 13C labeled. At 10 °C we cannot detect any conformational exchange broadening: the 1HN R2 relaxation rates with 1.357 kHz spinlock field not larger than those recorded with a 12.136 kHz spinlock field. This means that there is no exchange broadening that can be differentially suppressed with the applied fields. Either there is no broadening, or the broadening is effectively suppressed by all fields, or the broadening cannot be suppressed by either of the fields. While initially this seems to be a disappointing result, we feel that this work establishes that the HSQC-ROESY experiment is very robust. It can indeed be utilized for proteated proteins upto about 30 kDa. This could be opening the study the milli-microsecond conformational dynamics as reported by 1HN exchange broadening for many more proteins.
Collapse
Affiliation(s)
- Erik R P Zuiderweg
- Radboud University, Institute for Molecules and Materials, Nijmegen, XZ 6525, The Netherlands; University of Michigan Medical School, Department of Biological Chemistry, Ann Arbor, MI 41109, USA.
| |
Collapse
|
2
|
Tugarinov V, Okuno Y, Torricella F, Karamanos TK, Clore GM. A "Steady-State" Relaxation Dispersion Nuclear Magnetic Resonance Experiment for Studies of Chemical Exchange in Degenerate 1H Transitions of Methyl Groups. J Phys Chem Lett 2022; 13:11271-11279. [PMID: 36449372 DOI: 10.1021/acs.jpclett.2c02937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Degenerate spin-systems consisting of magnetically equivalent nuclear spins, such as a 1H3 spin-system in selectively 13CH3-labeled proteins, present considerable challenges for the design of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments to characterize chemical exchange on the micro-to-millisecond time-scale. Several approaches have been previously proposed for the elimination of deleterious artifacts observed in methyl 1H CPMG relaxation dispersion profiles obtained for (13C)1H3 groups. We describe an alternative, experimentally simple solution and design a "steady-state" methyl 1H CPMG scheme, where 90° or acute-angle (<90°) 1H radiofrequency pulses are applied after each CPMG echo in-phase with methyl 1H magnetization, resulting in the establishment of a "steady-state" for effective rates of magnetization decay. A simple computational procedure for quantitative analysis of the "steady-state" CPMG relaxation dispersion profiles is developed. The "steady-state" CPMG methodology is applied to two protein systems where exchange between major and minor species occurs in different regimes on the chemical shift time-scale.
Collapse
Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Yusuke Okuno
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Francesco Torricella
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Theodoros K Karamanos
- The Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| |
Collapse
|
3
|
Dayie TK, Olenginski LT, Taiwo KM. Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs. Chem Rev 2022; 122:9357-9394. [PMID: 35442658 PMCID: PMC9136934 DOI: 10.1021/acs.chemrev.1c00845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 02/07/2023]
Abstract
RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.
Collapse
Affiliation(s)
- Theodore K. Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kehinde M. Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
4
|
Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M. Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Pravin Kumar Ankush Jagtap
- Lehrstuhl für Biomolekulare NMR-SpektroskopieTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Sam Asami
- Lehrstuhl für Biomolekulare NMR-SpektroskopieTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Claudia Sippel
- Max Planck Institute of Psychiatry Kraepelinstr. 2–10 80804 Munich Germany
| | - Ville R. I. Kaila
- Department ChemieTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Felix Hausch
- Max Planck Institute of Psychiatry Kraepelinstr. 2–10 80804 Munich Germany
- Present address: Structure-Based Drug ResearchTechnische Universität Darmstadt Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Michael Sattler
- Lehrstuhl für Biomolekulare NMR-SpektroskopieTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| |
Collapse
|
5
|
Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M. Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States. Angew Chem Int Ed Engl 2019; 58:9429-9433. [PMID: 31100184 DOI: 10.1002/anie.201902994] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/24/2019] [Indexed: 12/26/2022]
Abstract
The recently discovered SAFit class of inhibitors against the Hsp90 co-chaperone FKBP51 show greater than 10 000-fold selectivity over its closely related paralogue FKBP52. However, the mechanism underlying this selectivity remained unknown. By combining NMR spectroscopy, biophysical and computational methods with mutational analysis, we show that the SAFit molecules bind to a transient pocket in FKBP51. This represents a weakly populated conformation resembling the inhibitor-bound state of FKBP51, suggesting conformational selection rather than induced fit as the major binding mechanism. The inhibitor-bound conformation of FKBP51 is stabilized by an allosteric network of residues located away from the inhibitor-binding site. These residues stabilize the Phe67 side chain in a dynamic outward conformation and are distinct in FKBP52, thus rationalizing the basis for the selectivity of SAFit inhibitors. Our results represent a paradigm for the selective inhibition of transient binding pockets.
Collapse
Affiliation(s)
- Pravin Kumar Ankush Jagtap
- Lehrstuhl für Biomolekulare NMR-Spektroskopie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Sam Asami
- Lehrstuhl für Biomolekulare NMR-Spektroskopie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Claudia Sippel
- Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Ville R I Kaila
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Felix Hausch
- Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany.,Present address: Structure-Based Drug Research, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Michael Sattler
- Lehrstuhl für Biomolekulare NMR-Spektroskopie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| |
Collapse
|
6
|
Casiraghi M, Point E, Pozza A, Moncoq K, Banères JL, Catoire LJ. NMR analysis of GPCR conformational landscapes and dynamics. Mol Cell Endocrinol 2019; 484:69-77. [PMID: 30690069 DOI: 10.1016/j.mce.2018.12.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/13/2018] [Accepted: 12/24/2018] [Indexed: 12/22/2022]
Abstract
Understanding the signal transduction mechanism mediated by the G Protein-Coupled Receptors (GPCRs) in eukaryote cells represents one of the main issues in modern biology. At the molecular level, various biophysical approaches have provided important insights on the functional plasticity of these complex allosteric machines. In this context, X-ray crystal structures published during the last decade represent a major breakthrough in GPCR structural biology, delivering important information on the activation process of these receptors through the description of the three-dimensional organization of their active and inactive states. In complement to crystals and cryo-electronic microscopy structures, information on the probability of existence of different GPCR conformations and the dynamic barriers separating those structural sub-states is required to better understand GPCR function. Among the panel of techniques available, nuclear magnetic resonance (NMR) spectroscopy represents a powerful tool to characterize both conformational landscapes and dynamics. Here, we will outline the potential of NMR to address such biological questions, and we will illustrate the functional insights that NMR has brought in the field of GPCRs in the recent years.
Collapse
Affiliation(s)
- Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Elodie Point
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Alexandre Pozza
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Jean-Louis Banères
- Institut des Biomoléćules Max Mousseron (IBMM), UMR 5247 CNRS, Université; Montpellier, ENSCM, 15 av. Charles Flahault, 34093, Montpellier, France
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France.
| |
Collapse
|
7
|
Gavrilov Y, Dagan S, Reich Z, Scherf T, Levy Y. An NMR Confirmation for Increased Folded State Entropy Following Loop Truncation. J Phys Chem B 2018; 122:10855-10860. [PMID: 30411894 DOI: 10.1021/acs.jpcb.8b09658] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Previous studies conducted on flexible loop regions in proteins revealed that the energetic consequences of changing loop length predominantly arise from the entropic cost of ordering a loop during folding. However, in an earlier study of human acylphosphatase (hmAcP) using experimental and computational approaches, we showed that thermodynamic stabilization upon loop truncation can be attributed mainly to the increased entropy of the folded state. Here, using 15N NMR spectroscopy, we studied the effect of loop truncation on hmAcP backbone dynamics on the picosecond-nanosecond timescale with the aim of confirming the effect of folded state entropy on protein stability. NMR-relaxation-derived N-H squared generalized order parameters reveal that loop truncation results in a significant increase in protein conformational flexibility. Comparison of these results with previously acquired all-atom molecular dynamics simulation, analyzed here in terms of squared generalized NMR order parameters, demonstrates general agreement between the two methods. The NMR study not only provides direct evidence for the enhanced conformational entropy of the folded state of hmAcP upon loop truncation but also gives a quantitative measure of the observed effects.
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Gopalan AB, Hansen DF, Vallurupalli P. CPMG Experiments for Protein Minor Conformer Structure Determination. Methods Mol Biol 2018; 1688:223-242. [PMID: 29151212 DOI: 10.1007/978-1-4939-7386-6_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
CPMG relaxation dispersion NMR experiments have emerged as a powerful method to characterize protein minor states that are in exchange with a visible dominant conformation, and have lifetimes between ~0.5 and 5 milliseconds (ms) and populations greater than 0.5%. The structure of the minor state can, in favorable cases, be determined from the parameters provided by the CPMG relaxation dispersion experiments. Here, we go through the intricacies of setting up these powerful CPMG experiments.
Collapse
Affiliation(s)
- Anusha B Gopalan
- TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad, 500075, India.
| | - D Flemming Hansen
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Pramodh Vallurupalli
- TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad, 500075, India.
| |
Collapse
|
10
|
Modulation of Hoogsteen dynamics on DNA recognition. Nat Commun 2018; 9:1473. [PMID: 29662229 PMCID: PMC5902632 DOI: 10.1038/s41467-018-03516-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/20/2018] [Indexed: 11/18/2022] Open
Abstract
In naked duplex DNA, G–C and A–T Watson-Crick base pairs exist in dynamic equilibrium with their Hoogsteen counterparts. Here, we used nuclear magnetic resonance (NMR) relaxation dispersion and molecular dynamics (MD) simulations to examine how Watson-Crick/Hoogsteen dynamics are modulated upon recognition of duplex DNA by the bisintercalator echinomycin and monointercalator actinomycin D. In both cases, DNA recognition results in the quenching of Hoogsteen dynamics at base pairs involved in intermolecular base-specific hydrogen bonds. In the case of echinomycin, the Hoogsteen population increased 10-fold for base pairs flanking the chromophore most likely due to intermolecular stacking interactions, whereas actinomycin D minimally affected Hoogsteen dynamics at other sites. Modulation of Hoogsteen dynamics at binding interfaces may be a general phenomenon with important implications for DNA–ligand and DNA–protein recognition. DNA is found in a dynamic equilibrium between standard Watson-Crick (WC) base pairs and non-standard Hoogsteen (HG) base pairs. Here the authors describe the influence of echinomycin and actinomycin D ligands binding on the HG-WC base pair dynamics in DNA.
Collapse
|
11
|
Kitevski-LeBlanc JL, Yuwen T, Dyer PN, Rudolph J, Luger K, Kay LE. Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR. J Am Chem Soc 2018; 140:4774-4777. [DOI: 10.1021/jacs.8b00931] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Julianne L. Kitevski-LeBlanc
- Departments of Chemistry, Molecular Genetics, and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tairan Yuwen
- Departments of Chemistry, Molecular Genetics, and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Pamela N. Dyer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Johannes Rudolph
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Karolin Luger
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Lewis E. Kay
- Departments of Chemistry, Molecular Genetics, and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
12
|
Correy GJ, Carr PD, Meirelles T, Mabbitt PD, Fraser NJ, Weik M, Jackson CJ. Mapping the Accessible Conformational Landscape of an Insect Carboxylesterase Using Conformational Ensemble Analysis and Kinetic Crystallography. Structure 2016; 24:977-87. [PMID: 27210287 DOI: 10.1016/j.str.2016.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 11/26/2022]
Abstract
The proper function of enzymes often depends upon their efficient interconversion between particular conformational sub-states on a free-energy landscape. Experimentally characterizing these sub-states is challenging, which has limited our understanding of the role of protein dynamics in many enzymes. Here, we have used a combination of kinetic crystallography and detailed analysis of crystallographic protein ensembles to map the accessible conformational landscape of an insect carboxylesterase (LcαE7) as it traverses all steps in its catalytic cycle. LcαE7 is of special interest because of its evolving role in organophosphate insecticide resistance. Our results reveal that a dynamically coupled network of residues extends from the substrate-binding site to a surface loop. Interestingly, the coupling of this network that is apparent in the apoenzyme appears to be reduced in the phosphorylated enzyme intermediate. Altogether, the results of this work highlight the importance of protein dynamics to enzyme function and the evolution of new activity.
Collapse
Affiliation(s)
- Galen J Correy
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Paul D Carr
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Tamara Meirelles
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Peter D Mabbitt
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nicholas J Fraser
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Martin Weik
- Institut de Biologie Structurale Jean Pierre Ebel, Commisariat a l'Energie Atomique, Centre de National de la Recherche Scientifique, University Josef Fourier, 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
| |
Collapse
|
13
|
Wang H, Hosoda K, Ishii T, Arai R, Kohno T, Terawaki SI, Wakamatsu K. Protein stabilizer, NDSB-195, enhances the dynamics of the β4 -α2 loop of ubiquitin. J Pept Sci 2016; 22:174-80. [PMID: 26856691 DOI: 10.1002/psc.2855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 12/21/2022]
Abstract
Non-detergent sulfobetaines (NDSBs) are a new group of small, synthetic protein stabilizers, which have advantages over classical compatible osmolytes, such as polyol, amines, and amino acids: they do not increase solution viscosity, unlike polyols, and they are zwitterionic at all pH ranges, unlike amines and amino acids. NDSBs also facilitate the crystallization and refolding of proteins. The mechanism whereby NDSBs exhibit such activities, however, remains elusive. To gain insight into this mechanism, we studied, using nuclear magnetic resonance (NMR), the effects of dimethylethylammonium propane sulfonate (NDSB-195) on the dynamics of ubiquitin, on which a wealth of information has been accumulated. By analyzing the line width of amide proton resonances and the transverse relaxation rates of nitrogen atoms, we found that NDSB-195 enhances the microsecond-millisecond dynamics of a β4 -α2 loop of ubiquitin. Although those compounds that enhance protein dynamics are generally considered to destabilize protein molecules, NDSB-195 enhanced the stability of ubiquitin against guanidium chloride denaturation. Thus, the simultaneous enhancement of stability and flexibility by a single compound can be attained.
Collapse
Affiliation(s)
- Haimei Wang
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Kazuo Hosoda
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Takeshi Ishii
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Ryo Arai
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Toshiyuki Kohno
- Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Shin-Ichi Terawaki
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Kaori Wakamatsu
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| |
Collapse
|
14
|
Toyama Y, Osawa M, Yokogawa M, Shimada I. NMR Method for Characterizing Microsecond-to-Millisecond Chemical Exchanges Utilizing Differential Multiple-Quantum Relaxation in High Molecular Weight Proteins. J Am Chem Soc 2016; 138:2302-11. [PMID: 26855064 DOI: 10.1021/jacs.5b12954] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical exchange processes of proteins on the order of microseconds (μs) to milliseconds (ms) play critical roles in biological functions. Developments in methyl-transverse relaxation optimized spectroscopy (methyl-TROSY), which observes the slowly relaxing multiple quantum (MQ) coherences, have enabled the studies of biologically important large proteins. However, the analyses of μs to ms chemical exchange processes based on the methyl-TROSY principle are still challenging, because the interpretation of the chemical exchange contributions to the MQ relaxation profiles is complicated, as significant chemical shift differences occur in both (1)H and (13)C nuclei. Here, we report a new methyl-based NMR method for characterizing chemical exchanges, utilizing differential MQ relaxation rates and a heteronuclear double resonance pulse technique. The method enables quantitative evaluations of the chemical exchange processes, in which significant chemical shift differences exist in both the (1)H and (13)C nuclei. The versatility of the method is demonstrated with the application to KirBac1.1, with an apparent molecular mass of 200 kDa.
Collapse
Affiliation(s)
- Yuki Toyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Japan Biological Informatics Consortium (JBIC) , Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
15
|
Salvi N. Theoretical tools for the design of NMR relaxation dispersion pulse sequences. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:105-115. [PMID: 26282198 DOI: 10.1016/j.pnmrs.2015.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
Recent decades have witnessed tremendous progress in the development of new experimental methods for studying biomolecules, particularly in the field of NMR relaxation dispersion. Here we review the theoretical frameworks that provided the insights necessary for such progress. The effect of radio-frequency manipulations on spin systems is discussed using Average Hamiltonian Theory (AHT), Average Liouvillian Theory (ALT), and Bloch-Wangsness-Redfield (BWR) relaxation theory. We illustrate these concepts using the case of Heteronuclear Double Resonance (HDR) methods.
Collapse
Affiliation(s)
- Nicola Salvi
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| |
Collapse
|
16
|
Jiang B, Yu B, Zhang X, Liu M, Yang D. A (15)N CPMG relaxation dispersion experiment more resistant to resonance offset and pulse imperfection. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 257:1-7. [PMID: 26037134 DOI: 10.1016/j.jmr.2015.05.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 06/04/2023]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is a powerful NMR method to study protein dynamics on the microsecond-millisecond time scale. J-coupling, resonance offset, radio frequency field inhomogeneity, and pulse imperfection often introduce systematic errors into the measured transverse relaxation rates. Here we proposed a modified continuous wave decoupling CPMG experiment, which is more unaffected by resonance offset and pulse imperfection. We found that it is unnecessary to match the decoupling field strength with the delay between CPMG refocusing pulses, provided that decoupling field is strong enough. The performance of the scheme proposed here was shown by simulations and further demonstrated experimentally on a fatty acid binding protein.
Collapse
Affiliation(s)
- Bin Jiang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, 430071 Wuhan, China.
| | - Binhan Yu
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, 430071 Wuhan, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, 430071 Wuhan, China.
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
| |
Collapse
|
17
|
Wallerstein J, Weininger U, Khan MAI, Linse S, Akke M. Site-specific protonation kinetics of acidic side chains in proteins determined by pH-dependent carboxyl (13)C NMR relaxation. J Am Chem Soc 2015; 137:3093-101. [PMID: 25665463 DOI: 10.1021/ja513205s] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-transfer dynamics plays a critical role in many biochemical processes, such as proton pumping across membranes and enzyme catalysis. The large majority of enzymes utilize acid-base catalysis and proton-transfer mechanisms, where the rates of proton transfer can be rate limiting for the overall reaction. However, measurement of proton-exchange kinetics for individual side-chain carboxyl groups in proteins has been achieved in only a handful of cases, which typically have involved comparative analysis of mutant proteins in the context of reaction network modeling. Here we describe an approach to determine site-specific protonation and deprotonation rate constants (kon and koff, respectively) of carboxyl side chains, based on (13)C NMR relaxation measurements as a function of pH. We validated the method using an extensively studied model system, the B1 domain of protein G, for which we measured rate constants koff in the range (0.1-3) × 10(6) s(-1) and kon in the range (0.6-300) × 10(9) M(-1) s(-1), which correspond to acid-base equilibrium dissociation constants (Ka) in excellent agreement with previous results determined by chemical shift titrations. Our results further reveal a linear free-energy relationship between log kon and pKa, which provides information on the free-energy landscape of the protonation reaction, showing that the variability among residues in these parameters arises primarily from the extent of charge stabilization of the deprotonated state by the protein environment. We find that side-chain carboxyls with extreme values of koff or kon are involved in hydrogen bonding, thus providing a mechanistic explanation for the observed stabilization of the protonated or deprotonated state.
Collapse
Affiliation(s)
- Johan Wallerstein
- Department of Biophysical Chemistry and ‡Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University , P.O. Box 124, SE-221 00 Lund, Sweden
| | | | | | | | | |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Palmer AG. Chemical exchange in biomacromolecules: past, present, and future. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:3-17. [PMID: 24656076 PMCID: PMC4049312 DOI: 10.1016/j.jmr.2014.01.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 05/08/2023]
Abstract
The perspective reviews quantitative investigations of chemical exchange phenomena in proteins and other biological macromolecules using NMR spectroscopy, particularly relaxation dispersion methods. The emphasis is on techniques and applications that quantify the populations, interconversion kinetics, and structural features of sparsely populated conformational states in equilibrium with a highly populated ground state. Applications to folding, molecular recognition, catalysis, and allostery by proteins and nucleic acids are highlighted.
Collapse
Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States.
| |
Collapse
|
20
|
Lukman S, Verma CS, Fuentes G. Exploiting Protein Intrinsic Flexibility in Drug Design. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:245-69. [DOI: 10.1007/978-3-319-02970-2_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
21
|
Lichtenecker RJ. Synthesis of aromatic 13C/2H-α-ketoacid precursors to be used in selective phenylalanine and tyrosine protein labelling. Org Biomol Chem 2014; 12:7551-60. [DOI: 10.1039/c4ob01129e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A synthetic concept to access various 13C/2H patterns of phenylalanine and tyrosine precursors for cell-based protein overexpression systems is presented. The target compounds feature isolated 13C–1H spin systems to be used in NMR probing of protein structure and dynamics.
Collapse
Affiliation(s)
- R. J. Lichtenecker
- Institute of Organic Chemistry
- University of Vienna
- A-1090 Vienna, Austria
| |
Collapse
|
22
|
Micura R, Kreutz C, Breuker K. A personal perspective on chemistry-driven RNA research. Biopolymers 2013; 99:1114-23. [PMID: 23754524 PMCID: PMC4477180 DOI: 10.1002/bip.22299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 05/27/2013] [Indexed: 12/14/2022]
Abstract
In this mini review, we discuss how our understanding of ribonucleic acid (RNA) properties becomes significantly deepened when a broad range of modern chemical and biophysical methods is applied. We span our perspective from RNA solid-phase synthesis and site-specific labeling to single-molecule fluorescence-resonance-energy-transfer imaging and NMR spectroscopy approaches to explore the dynamics of RNA over a broad timescale. We then move on to Fourier-transform-ion-cyclotron-resonance mass spectrometry (FT-ICR-MS) as a powerful technique for RNA sequencing and modification analysis. The novel methodological developments are discussed for selected biological systems that include the thiamine-pyrophosphate riboswitch, HIV and ribosomal A-site RNA, and transfer RNA.
Collapse
Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Center for Chemistry and Biomedicine (CCB), University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | | | | |
Collapse
|
23
|
Hansen AL, Bouvignies G, Kay LE. Probing slowly exchanging protein systems via ¹³Cα-CEST: monitoring folding of the Im7 protein. JOURNAL OF BIOMOLECULAR NMR 2013; 55:279-289. [PMID: 23386228 DOI: 10.1007/s10858-013-9711-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/20/2013] [Indexed: 06/01/2023]
Abstract
A¹³C(α) chemical exchange saturation transfer based experiment is presented for the study of protein systems undergoing slow interconversion between an 'observable' ground state and one or more 'invisible' excited states. Here a labeling strategy whereby [2-(13)C]-glucose is the sole carbon source is exploited, producing proteins with ¹³C at the C(α) position, while the majority of residues remain unlabeled at CO or C(β). The new experiment is demonstrated with an application to the folding reaction of the Im7 protein that involves an on-pathway excited state. The obtained excited state (13)C(α) chemical shifts are cross validated by comparison to values extracted from analysis of CPMG relaxation dispersion profiles, establishing the utility of the methodology.
Collapse
Affiliation(s)
- Alexandar L Hansen
- Department of Molecular Genetics, The University of Toronto, Toronto, ON, M5S 1A8, Canada
| | | | | |
Collapse
|
24
|
Baldwin AJ, Kay LE. An R(1ρ) expression for a spin in chemical exchange between two sites with unequal transverse relaxation rates. JOURNAL OF BIOMOLECULAR NMR 2013; 55:211-8. [PMID: 23340732 DOI: 10.1007/s10858-012-9694-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 12/06/2012] [Indexed: 05/22/2023]
Abstract
An analytical expression is derived for the rotating frame relaxation rate, R(1ρ), of a spin exchanging between two sites with different transverse relaxation times. A number of limiting cases are examined, with the equation reducing to formulae derived previously under the assumption of equivalent relaxation rates at each site. The measurement of a pair off-resonance R(1ρ) values, with the carrier displaced equally on either side of the observed correlation, forms the basis of one of the approaches for obtaining signs of chemical shift differences, Δω, of exchanging nuclei. The results presented here establish that this method is relatively insensitive to differential transverse relaxation rates between the exchaning states, greatly simplifying the calculation of optimal parameters in R(1ρ) based experiments that are used for measurement of signs of Δω.
Collapse
Affiliation(s)
- Andrew J Baldwin
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | | |
Collapse
|
25
|
Protein activity regulation by conformational entropy. Nature 2012; 488:236-40. [PMID: 22801505 DOI: 10.1038/nature11271] [Citation(s) in RCA: 392] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 05/31/2012] [Indexed: 12/11/2022]
Abstract
How the interplay between protein structure and internal dynamics regulates protein function is poorly understood. Often, ligand binding, post-translational modifications and mutations modify protein activity in a manner that is not possible to rationalize solely on the basis of structural data. It is likely that changes in the internal motions of proteins have a major role in regulating protein activity, but the nature of their contributions remains elusive, especially in quantitative terms. Here we show that changes in conformational entropy can determine whether protein-ligand interactions will occur, even among protein complexes with identical binding interfaces. We have used NMR spectroscopy to determine the changes in structure and internal dynamics that are elicited by the binding of DNA to several variants of the catabolite activator protein (CAP) that differentially populate the inactive and active DNA-binding domain states. We found that the CAP variants have markedly different affinities for DNA, despite the CAP−DNA-binding interfaces being essentially identical in the various complexes. Combined with thermodynamic data, the results show that conformational entropy changes can inhibit the binding of CAP variants that are structurally poised for optimal DNA binding or can stimulate the binding activity of CAP variants that only transiently populate the DNA-binding-domain active state. Collectively, the data show how changes in fast internal dynamics (conformational entropy) and slow internal dynamics (energetically excited conformational states) can regulate binding activity in a way that cannot be predicted on the basis of the protein's ground-state structure.
Collapse
|
26
|
In silico-screening approaches for lead generation: identification of novel allosteric modulators of human-erythrocyte pyruvate kinase. Methods Mol Biol 2012; 796:351-67. [PMID: 22052500 DOI: 10.1007/978-1-61779-334-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Identification of allosteric binding site modulators have gained increased attention lately for their potential to be developed as selective agents with a novel chemotype and targeting perhaps a new and unique binding site with probable fewer side effects. Erythrocyte pyruvate kinase (R-PK) is an important glycolytic enzyme that can be pharmacologically modulated through its allosteric effectors for the treatment of hemolytic anemia, sickle-cell anemia, hypoxia-related diseases, and other disorders arising from erythrocyte PK malfunction. An in-silico screening approach was applied to identify novel allosteric modulators of pyruvate kinase. A small-molecules database of the National Cancer Institute (NCI), was virtually screened based on structure/ligand-based pharmacophore. The virtual screening campaign led to the identification of several compounds with similar pharmacophoric features as fructose-1,6-bisphosphate (FBP), the natural allosteric activator of the kinase. The compounds were subsequently docked into the FBP-binding site using the programs FlexX and GOLD, and their interactions with the protein were analyzed with the energy-scoring function of HINT. Seven promising candidates were obtained from the NCI and subjected to kinetics analysis, which revealed both activators and inhibitors of the R-isozyme of PK (R-PK).
Collapse
|
27
|
Vallurupalli P, Bouvignies G, Kay LE. Studying “Invisible” Excited Protein States in Slow Exchange with a Major State Conformation. J Am Chem Soc 2012; 134:8148-61. [DOI: 10.1021/ja3001419] [Citation(s) in RCA: 353] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pramodh Vallurupalli
- Departments of Molecular
Genetics,
Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Guillaume Bouvignies
- Departments of Molecular
Genetics,
Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Lewis E. Kay
- Departments of Molecular
Genetics,
Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario, Canada M5S 1A8
- Program in Molecular Structure
and Function, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| |
Collapse
|
28
|
Interdomain dynamics and coactivation of the mRNA decapping enzyme Dcp2 are mediated by a gatekeeper tryptophan. Proc Natl Acad Sci U S A 2012; 109:2872-7. [PMID: 22323607 DOI: 10.1073/pnas.1113620109] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Conformational dynamics in bilobed enzymes can be used to regulate their activity. One such enzyme, the eukaryotic decapping enzyme Dcp2, controls the half-life of mRNA by cleaving the 5' cap structure, which exposes a monophosphate that is efficiently degraded by exonucleases. Decapping by Dcp2 is thought to be controlled by an open-to-closed transition involving formation of a composite active site with two domains sandwiching substrate, but many details of this process are not understood. Here, using NMR spectroscopy and enzyme kinetics, we show that Trp43 of Schizosaccharomyces pombe Dcp2 is a conserved gatekeeper of this open-to-closed transition. We find that Dcp2 samples multiple conformations in solution on the millisecond-microsecond timescale. Mutation of the gatekeeper tryptophan abolishes the dynamic behavior of Dcp2 and attenuates coactivation by a yeast enhancer of decapping (Edc1). Our results determine the dynamics of the open-to-closed transition in Dcp2, suggest a structural pathway for coactivation, predict that Dcp1 directly contacts the catalytic domain of Dcp2, and show that coactivation of decapping by Dcp2 is linked to formation of the composite active site.
Collapse
|
29
|
Kleckner IR, Foster MP. GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data. JOURNAL OF BIOMOLECULAR NMR 2012; 52:11-22. [PMID: 22160811 PMCID: PMC3593345 DOI: 10.1007/s10858-011-9589-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/25/2011] [Indexed: 05/20/2023]
Abstract
Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15 years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial μs-ms time window. However, analysis of RD data is challenging because datasets are often large and require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation. Hence, we present the open-source software package GUARDD (Graphical User-friendly Analysis of Relaxation Dispersion Data), which is designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD data ( http://code.google.com/p/guardd/). This MATLAB-based program includes a graphical user interface, permits global fitting to multi-field, multi-temperature, multi-coherence data, and implements χ (2)-mapping procedures, via grid-search and Monte Carlo methods, to enhance and assess fitting accuracy. The presentation features allow users to seamlessly traverse the large amount of results, and the RD Simulator feature can help design future experiments as well as serve as a teaching tool for those unfamiliar with RD phenomena. Based on these innovative features, we expect that GUARDD will fill a well-defined gap in service of the RD NMR community.
Collapse
Affiliation(s)
- Ian R. Kleckner
- Biophysics Program, The Ohio State University, 484 West 12th Ave Room 776, Columbus, OH 43210, USA,
| | - Mark P. Foster
- Biochemistry Department, The Ohio State University, 484 West 12th Ave Room 776, Columbus, OH 43210, USA,
| |
Collapse
|
30
|
Abstract
Motions are essential for protein function, and knowledge of protein dynamics is a key to our understanding the mechanisms underlying protein folding and stability, ligand recognition, allostery, and catalysis. In the last two decades, NMR relaxation measurements have become a powerful tool for characterizing backbone and side chain dynamics in complex biological macromolecules such as proteins and nucleic acids. Accurate analysis of the experimental data in terms of motional parameters is an essential prerequisite for developing physical models of motions to paint an adequate picture of protein dynamics. Here, I describe in detail how to use the software package DYNAMICS that was developed for accurate characterization of the overall tumbling and local dynamics in a protein from nuclear spin-relaxation rates measured by NMR. Step-by-step instructions are provided and illustrated through an analysis of (15)N relaxation data for protein G.
Collapse
Affiliation(s)
- David Fushman
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, USA.
| |
Collapse
|
31
|
Baldwin AJ, Hilton GR, Lioe H, Bagnéris C, Benesch JL, Kay LE. Quaternary Dynamics of αB-Crystallin as a Direct Consequence of Localised Tertiary Fluctuations in the C-Terminus. J Mol Biol 2011; 413:310-20. [DOI: 10.1016/j.jmb.2011.07.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 07/08/2011] [Accepted: 07/11/2011] [Indexed: 11/16/2022]
|
32
|
Torchia DA. Dynamics of biomolecules from picoseconds to seconds at atomic resolution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 212:1-10. [PMID: 21840740 DOI: 10.1016/j.jmr.2011.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/14/2011] [Indexed: 05/31/2023]
Abstract
Although biomolecular dynamics has been investigated using NMR for at least 40 years, only in the past 20 years have internal motions been characterized at atomic resolution throughout proteins and nucleic acids. This development was made possible by multidimensional heteronuclear NMR approaches that provide near complete sequential signal assignments of uniformly labeled biomolecules. Recent methodological advances have enabled characterization of internal dynamics on timescales ranging from picoseconds to seconds, both in solution and in the solid state. The size, complexity and functional significance of biomolecules investigated by NMR continue to grow, as do the insights that have been obtained about function. In this article I review a number of recent advances that have made such studies possible, and provide a few examples of where NMR either by itself or in combination with other approaches has paved the way to a better understanding of the complex relationship between dynamics and biomolecular function. Finally, I discuss prospects for further advances in this field.
Collapse
|
33
|
Clore GM. Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation. Protein Sci 2011; 20:229-46. [PMID: 21280116 DOI: 10.1002/pro.576] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sparsely populated states of macromolecules, characterized by short lifetimes and high free-energies relative to the predominant ground state, often play a key role in many biological, chemical, and biophysical processes. In this review, we briefly summarize various new developments in NMR spectroscopy that permit these heretofore invisible, sparsely populated states to be detected, characterized, and in some instances visualized. Relaxation dispersion spectroscopy yields detailed kinetic information on processes involving species characterized by distinct chemical shifts with lifetimes in the ∼50 μs-10 ms range and populations as low as 0.5%. In the fast exchange regime (time scale less than ∼250-500 μs), the footprint of sparsely populated states can be observed on paramagnetic relaxation enhancement profiles measured on the resonances of the major species, thereby yielding structural information that is directly related to paramagnetic center-nuclei distances from which it is possible, under suitable circumstances, to compute a structure or ensemble of structures for the minor species. Finally, differential transverse relaxation measurements can be used to detect lifetime broadening effects that directly reflect the unidirectional rates for the conversion of NMR-visible into high-molecular weight NMR-invisible species. Examples of these various approaches are presented.
Collapse
Affiliation(s)
- 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.
| |
Collapse
|
34
|
Hansen DF, Kay LE. Determining Valine Side-Chain Rotamer Conformations in Proteins from Methyl 13C Chemical Shifts: Application to the 360 kDa Half-Proteasome. J Am Chem Soc 2011; 133:8272-81. [DOI: 10.1021/ja2014532] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
35
|
Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
| | | | | | | | | |
Collapse
|
36
|
Bouvignies G, Hansen DF, Vallurupalli P, Kay LE. Divided-Evolution-Based Pulse Scheme for Quantifying Exchange Processes in Proteins: Powerful Complement to Relaxation Dispersion Experiments. J Am Chem Soc 2011; 133:1935-45. [DOI: 10.1021/ja109589y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guillaume Bouvignies
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - D. Flemming Hansen
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Pramodh Vallurupalli
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario, Canada M5S 1A8
| |
Collapse
|
37
|
Ulzega S, Salvi N, Segawa TF, Ferrage F, Bodenhausen G. Control of Cross Relaxation of Multiple-Quantum Coherences Induced by Fast Chemical Exchange under Heteronuclear Double-Resonance Irradiation. Chemphyschem 2010; 12:333-41. [DOI: 10.1002/cphc.201000699] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Indexed: 11/09/2022]
|
38
|
Otten R, Villali J, Kern D, Mulder FAA. Probing microsecond time scale dynamics in proteins by methyl (1)H Carr-Purcell-Meiboom-Gill relaxation dispersion NMR measurements. Application to activation of the signaling protein NtrC(r). J Am Chem Soc 2010; 132:17004-14. [PMID: 21058670 PMCID: PMC2991065 DOI: 10.1021/ja107410x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Indexed: 11/29/2022]
Abstract
To study microsecond processes by relaxation dispersion NMR spectroscopy, low power deposition and short pulses are crucial and encourage the development of experiments that employ (1)H Carr-Purcell-Meiboom-Gill (CPMG) pulse trains. Herein, a method is described for the comprehensive study of microsecond to millisecond time scale dynamics of methyl groups in proteins, exploiting their high abundance and favorable relaxation properties. In our approach, protein samples are produced using [(1)H, (13)C]-d-glucose in ∼100% D(2)O, which yields CHD(2) methyl groups for alanine, valine, threonine, isoleucine, leucine, and methionine residues with high abundance, in an otherwise largely deuterated background. Methyl groups in such samples can be sequence-specifically assigned to near completion, using (13)C TOCSY NMR spectroscopy, as was recently demonstrated (Otten, R.; et al. J. Am. Chem. Soc. 2010, 132, 2952-2960). In this Article, NMR pulse schemes are presented to measure (1)H CPMG relaxation dispersion profiles for CHD(2) methyl groups, in a vein similar to that of backbone relaxation experiments. Because of the high deuteration level of methyl-bearing side chains, artifacts arising from proton scalar coupling during the CPMG pulse train are negligible, with the exception of Ile-δ1 and Thr-γ2 methyl groups, and a pulse scheme is described to remove the artifacts for those residues. Strong (13)C scalar coupling effects, observed for several leucine residues, are removed by alternative biochemical and NMR approaches. The methodology is applied to the transcriptional activator NtrC(r), for which an inactive/active state transition was previously measured and the motions in the microsecond time range were estimated through a combination of backbone (15)N CPMG dispersion NMR spectroscopy and a collection of experiments to determine the exchange-free component to the transverse relaxation rate. Exchange contributions to the (1)H line width were detected for 21 methyl groups, and these probes were found to collectively report on a local structural rearrangement around the phosphorylation site, with a rate constant of (15.5 ± 0.5) × 10(3) per second (i.e., τ(ex) = 64.7 ± 1.9 μs). The affected methyl groups indicate that, already before phosphorylation, a substantial, transient rearrangement takes place between helices 3 and 4 and strands 4 and 5. This conformational equilibrium allows the protein to gain access to the active, signaling state in the absence of covalent modification through a shift in a pre-existing dynamic equilibrium. Moreover, the conformational switching maps exactly to the regions that differ between the solution NMR structures of the fully inactive and active states. These results demonstrate that a cost-effective and quantitative study of protein methyl group dynamics by (1)H CPMG relaxation dispersion NMR spectroscopy is possible and can be applied to study functional motions on the microsecond time scale that cannot be accessed by backbone (15)N relaxation dispersion NMR. The use of methyl groups as dynamics probes extends such applications also to larger proteins.
Collapse
|
39
|
Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:942-68. [PMID: 21059410 DOI: 10.1016/j.bbapap.2010.10.012] [Citation(s) in RCA: 339] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 01/15/2023]
Abstract
Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Collapse
Affiliation(s)
- Ian R Kleckner
- The Ohio State University Biophysics Program, 484 West 12th Ave Room 776, Columbus, OH 43210, USA
| | | |
Collapse
|
40
|
Ho MR, Lou YC, Wei SY, Luo SC, Lin WC, Lyu PC, Chen C. Human RegIV protein adopts a typical C-type lectin fold but binds mannan with two calcium-independent sites. J Mol Biol 2010; 402:682-95. [PMID: 20692269 DOI: 10.1016/j.jmb.2010.07.061] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 07/30/2010] [Accepted: 07/31/2010] [Indexed: 10/19/2022]
Abstract
Human RegIV protein, which contains a sequence motif homologous to calcium-dependent (C-type) lectin-like domain, is highly expressed in mucosa cells of the gastrointestinal tract during pathogen infection and carcinogenesis and may be applied in both diagnosis and treatment of gastric and colon cancers. Here, we provide evidence that, unlike other C-type lectins, human RegIV binds to polysaccharides, mannan, and heparin in the absence of calcium. To elucidate the structural basis for carbohydrate recognition by NMR, we generated the mutant with Pro91 replaced by Ser (hRegIV-P91S) and showed that the structural property and carbohydrate binding ability of hRegIV-P91S are almost identical with those of wild-type protein. The solution structure of hRegIV-P91S was determined, showing that it adopts a typical fold of C-type lectin. Based on the chemical shift perturbations of amide resonances, two calcium-independent mannan-binding sites were proposed. One site is similar to the calcium-independent sugar-binding site on human RegIII and Langerin. Interestingly, the other site is adjacent to the conserved calcium-dependent site at position Ca-2 of typical C-type lectins. Moreover, model-free analysis of (15)N relaxation parameters and simplified Carr-Purcell-Meiboom-Gill relaxation dispersion experiments showed that a slow microsecond-to-millisecond time-scale backbone motion is involved in mannan binding by this site, suggesting a potential role for specific carbohydrate recognition. Our findings shed light on the sugar-binding mode of Reg family proteins, and we postulate that Reg family proteins evolved to bind sugar without calcium to keep the carbohydrate recognition activity under low-pH environments in the gastrointestinal tract.
Collapse
Affiliation(s)
- Meng-Ru Ho
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | | | | | | | | | | | | |
Collapse
|
41
|
Auer R, Hansen DF, Neudecker P, Korzhnev DM, Muhandiram DR, Konrat R, Kay LE. Measurement of signs of chemical shift differences between ground and excited protein states: a comparison between H(S/M)QC and R1rho methods. JOURNAL OF BIOMOLECULAR NMR 2010; 46:205-216. [PMID: 20033258 DOI: 10.1007/s10858-009-9394-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 12/01/2009] [Indexed: 05/28/2023]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond exchange processes between a major, populated ground state and one or more minor, low populated and often invisible 'excited' conformers. Analysis of CPMG data-sets also provides the magnitudes of the chemical shift difference(s) between exchanging states (|Deltavarpi|), that inform on the structural properties of the excited state(s). The sign of Deltavarpi is, however, not available from CPMG data. Here we present one-dimensional NMR experiments for measuring the signs of (1)H(N) and (13)C(alpha) Deltavarpi values using weak off-resonance R (1rho ) relaxation measurements, extending the spin-lock approach beyond previous applications focusing on the signs of (15)N and (1)H(alpha) shift differences. The accuracy of the method is established by using an exchanging system where the invisible, excited state can be converted to the visible, ground state by altering conditions so that the signs of Deltavarpi values obtained from the spin-lock approach can be validated with those measured directly. Further, the spin-lock experiments are compared with the established H(S/M)QC approach for measuring the signs of chemical shift differences. For the Abp1p and Fyn SH3 domains considered here it is found that while H(S/M)QC measurements provide signs for more residues than the spin-lock data, the two different methodologies are complementary, so that combining both approaches frequently produces signs for more residues than when the H(S/M)QC method is used alone.
Collapse
Affiliation(s)
- Renate Auer
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, 1030, Vienna, Austria
| | | | | | | | | | | | | |
Collapse
|
42
|
Abstract
Molecular dynamics are essential for protein function. In some cases these dynamics involve the interconversion between ground state, highly populated conformers and less populated higher energy structures ('excited states') that play critical roles in biochemical processes. Here we describe recent advances in NMR spectroscopy methods that enable studies of these otherwise invisible excited states at an atomic level and that help elucidate their important relation to function. We discuss a range of examples from molecular recognition, ligand binding, enzyme catalysis and protein folding that illustrate the role that motion plays in 'funneling' conformers along preferred pathways that facilitate their biological function.
Collapse
Affiliation(s)
- Andrew J Baldwin
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario, Canada
| | | |
Collapse
|
43
|
Sheppard D, Sprangers R, Tugarinov V. Experimental approaches for NMR studies of side-chain dynamics in high-molecular-weight proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:1-45. [PMID: 20633347 DOI: 10.1016/j.pnmrs.2009.07.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 07/29/2009] [Indexed: 05/29/2023]
Affiliation(s)
- Devon Sheppard
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | | | | |
Collapse
|
44
|
Baldwin AJ, Hansen DF, Vallurupalli P, Kay LE. Measurement of methyl axis orientations in invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. J Am Chem Soc 2009; 131:11939-48. [PMID: 19627152 DOI: 10.1021/ja903896p] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Few detailed studies of transiently populated conformations of biological molecules have emerged despite the fact that such states are often important to processes such as protein folding, enzyme catalysis, molecular recognition and binding. A major limitation has been the lack of experimental tools to study these often invisible, short-lived conformers. Recent advances in relaxation dispersion NMR spectroscopy are changing this paradigm with the potential to generate high resolution structural information which is necessary for a rigorous characterization of these states. In this study, we present an experimental method for establishing the relative orientations of methyl groups in invisible, excited states of proteins by measuring methyl (1)H-(13)C residual dipolar couplings (RDCs). In our approach, four two-dimensional spectra are acquired at a pair of static magnetic fields. Each spectrum contains one of the four isolated multiplet components of a coupled methyl carbon, whose signal intensities, modulated by the pulsing frequency of a Carr-Purcell-Meiboom-Gill (CPMG) element, are sensitive to both chemical shift and RDC differences between exchanging states. In addition, data sets from a CPMG experiment which monitors the decay of in-phase methyl (13)C magnetization are recorded, that are sensitive only to the differences in chemical shifts between the states. Using our methodology, RDC values obtained from an invisible state in an exchanging system are shown to be in good agreement with the corresponding values measured under conditions where the invisible state is stabilized to become the highly populated ground state. The approach allows the measurement of anisotropic restraints at methyl positions in excited states and complements previously developed experiments focusing on the protein backbone.
Collapse
Affiliation(s)
- Andrew J Baldwin
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | | | | | | |
Collapse
|
45
|
Ulzega S, Verde M, Ferrage F, Bodenhausen G. Heteronuclear double resonance in nuclear magnetic resonance spectroscopy: Relaxation of multiple-quantum coherences. J Chem Phys 2009; 131:224503. [DOI: 10.1063/1.3269044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
46
|
Hansen DF, Feng H, Zhou Z, Bai Y, Kay LE. Selective characterization of microsecond motions in proteins by NMR relaxation. J Am Chem Soc 2009; 131:16257-65. [PMID: 19842628 PMCID: PMC7386800 DOI: 10.1021/ja906842s] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The three-dimensional structures of macromolecules fluctuate over a wide range of time-scales. Separating the individual dynamic processes according to frequency is of importance in relating protein motions to biological function and stability. We present here a general NMR method for the specific characterization of microsecond motions at backbone positions in proteins even in the presence of other dynamics such as large-amplitude nanosecond motions and millisecond chemical exchange processes. The method is based on measurement of relaxation rates of four bilinear coherences and relies on the ability of strong continuous radio frequency fields to quench millisecond chemical exchange. The utility of the methodology is demonstrated and validated through two specific examples focusing on the thermo-stable proteins, ubiquitin and protein L, where it is found that small-amplitude microsecond dynamics are more pervasive than previously thought. Specifically, these motions are localized to alpha helices, loop regions, and regions along the rim of beta sheets in both of the proteins examined. A third example focuses on a 28 kDa ternary complex of the chaperone Chz1 and the histones H2A.Z/H2B, where it is established that pervasive microsecond motions are localized to a region of the chaperone that is important for stabilizing the complex. It is further shown that these motions can be well separated from extensive millisecond dynamics that are also present and that derive from exchange of Chz1 between bound and free states. The methodology is straightforward to implement, and data recorded at only a single static magnetic field are required.
Collapse
Affiliation(s)
- D Flemming Hansen
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | | | | | | | | |
Collapse
|
47
|
Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
| |
Collapse
|
48
|
Lundström P, Lin H, Kay LE. Measuring 13Cbeta chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2009; 44:139-155. [PMID: 19448976 DOI: 10.1007/s10858-009-9321-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 04/20/2009] [Indexed: 05/26/2023]
Abstract
A labeling scheme is introduced that facilitates the measurement of accurate (13)C(beta) chemical shifts of invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. The approach makes use of protein over-expression in a strain of E. coli in which the TCA cycle enzyme succinate dehydrogenase is knocked out, leading to the production of samples with high levels of (13)C enrichment (30-40%) at C(beta) side-chain carbon positions for 15 of the amino acids with little (13)C label at positions one bond removed (approximately 5%). A pair of samples are produced using [1-(13)C]-glucose/NaH(12)CO(3) or [2-(13)C]-glucose as carbon sources with isolated and enriched (>30%) (13)C(beta) positions for 11 and 4 residues, respectively. The efficacy of the labeling procedure is established by NMR spectroscopy. The utility of such samples for measurement of (13)C(beta) chemical shifts of invisible, excited states in exchange with visible, ground conformations is confirmed by relaxation dispersion studies of a protein-ligand binding exchange reaction in which the extracted chemical shift differences from dispersion profiles compare favorably with those obtained directly from measurements on ligand free and fully bound protein samples.
Collapse
Affiliation(s)
- Patrik Lundström
- Molecular Biotechnology/IFM, Linköping University, 581 83, Linköping, Sweden
| | | | | |
Collapse
|
49
|
Lundström P, Hansen DF, Vallurupalli P, Kay LE. Accurate measurement of alpha proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy. J Am Chem Soc 2009; 131:1915-26. [PMID: 19152327 DOI: 10.1021/ja807796a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carr-Purcell-Meiboom-Gill relaxation dispersion NMR spectroscopy can provide detailed information about low populated, invisible states of protein molecules, including backbone chemical shifts of the invisible conformer and bond vector orientations that can be used as structural constraints. Notably, the measurement of 1Halpha chemical shifts in excited protein states has not been possible to date because, in the absence of suitable labeling, the homonuclear proton scalar coupling network in side chains of proteins leads to a significant degradation in the performance of proton-based relaxation dispersion experiments. Here we have overcome this problem through a labeling scheme in which proteins are prepared with U-2H glucose and 50% D2O/50% H2O that results in deuteration levels of between 50-88% at the Cbeta carbon. Effects from residual 1Halpha-1Hbeta scalar couplings can be suppressed through a new NMR experiment that is presented here. The utility of the methodology is demonstrated on a ligand binding exchanging system and it is shown that 1Halpha chemical shifts extracted from dispersion profiles are, on average, accurate to 0.03 ppm, an order of magnitude better than they can be predicted from structure using a database approach. The ability to measure 1Halpha chemical shifts of invisible conformers is particularly important because such shifts are sensitive to both secondary and tertiary structure. Thus, the methodology presented is a valuable addition to a growing list of experiments for characterizing excited protein states that are difficult to study using the traditional techniques of structural biology.
Collapse
Affiliation(s)
- Patrik Lundström
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | | | | | | |
Collapse
|
50
|
Neudecker P, Lundström P, Kay LE. Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding. Biophys J 2009; 96:2045-54. [PMID: 19289032 PMCID: PMC2717354 DOI: 10.1016/j.bpj.2008.12.3907] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Revised: 12/11/2008] [Accepted: 12/12/2008] [Indexed: 11/16/2022] Open
Abstract
Characterization of the mechanisms by which proteins fold into their native conformations is important not only for protein structure prediction and design but also because protein misfolding intermediates may play critical roles in fibril formation that are commonplace in neurodegenerative disorders. In practice, the study of folding pathways is complicated by the fact that for the most part intermediates are low-populated and short-lived so that biophysical studies are difficult. Due to recent methodological advances, relaxation dispersion NMR spectroscopy has emerged as a particularly powerful tool to obtain high-resolution structural information about protein folding events on the millisecond timescale. Applications of the methodology to study the folding of SH3 domains have shown that folding proceeds via previously undetected on-pathway intermediates, sometimes stabilized by nonnative long-range interactions. The relaxation dispersion approach provides a detailed kinetic and thermodynamic description of the folding process as well as the promise of obtaining an atomic level structural description of intermediate states. We review the concerted application of a variety of recently developed NMR relaxation dispersion experiments to obtain a "high-resolution" picture of the folding pathway of the A39V/N53P/V55L Fyn SH3 domain.
Collapse
Affiliation(s)
| | | | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|