51
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Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-based NMR. Proc Natl Acad Sci U S A 2015; 112:8817-23. [PMID: 26124125 DOI: 10.1073/pnas.1510083112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The prototypical chaperonin GroEL assists protein folding through an ATP-dependent encapsulation mechanism. The details of how GroEL folds proteins remain elusive, particularly because encapsulation is not an absolute requirement for successful re/folding. Here we make use of a metastable model protein substrate, comprising a triple mutant of Fyn SH3, to directly demonstrate, by simultaneous analysis of three complementary NMR-based relaxation experiments (lifetime line broadening, dark state exchange saturation transfer, and Carr-Purcell-Meinboom-Gill relaxation dispersion), that apo GroEL accelerates the overall interconversion rate between the native state and a well-defined folding intermediate by about 20-fold, under conditions where the "invisible" GroEL-bound states have occupancies below 1%. This is largely achieved through a 500-fold acceleration in the folded-to-intermediate transition of the protein substrate. Catalysis is modulated by a kinetic deuterium isotope effect that reduces the overall interconversion rate between the GroEL-bound species by about 3-fold, indicative of a significant hydrophobic contribution. The location of the GroEL binding site on the folding intermediate, mapped from (15)N, (1)HN, and (13)Cmethyl relaxation dispersion experiments, is composed of a prominent, surface-exposed hydrophobic patch.
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52
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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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53
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Zhou Y, Yang D. 13Cα CEST experiment on uniformly 13C-labeled proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 61:89-94. [PMID: 25465387 DOI: 10.1007/s10858-014-9888-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 11/26/2014] [Indexed: 06/04/2023]
Abstract
A new HSQC-based (13)Cα CEST pulse scheme is proposed, which is suitable for uniformly (13)C- or (13)C, (15)N-labeled samples in either water or heavy water. Except for Thr and Ser residues, the sensitivity of this scheme for uniformly labeled samples is similar to that of the previous scheme for selectively (13)Cα-labeled samples with 100% isotope enrichment. The experiment is demonstrated on an acyl carrier protein domain. Our (13)Cα CEST data reveal that the minor state of the acyl carrier protein has high helical propensity. The new scheme will facilitate structural characterization of invisible minor states.
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Affiliation(s)
- Yang Zhou
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
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54
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Fawzi NL, Libich DS, Ying J, Tugarinov V, Clore GM. Characterizing methyl-bearing side chain contacts and dynamics mediating amyloid β protofibril interactions using ¹³C(methyl)-DEST and lifetime line broadening. Angew Chem Int Ed Engl 2014; 53:10345-9. [PMID: 25130489 DOI: 10.1002/anie.201405180] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/08/2014] [Indexed: 11/08/2022]
Abstract
Many details pertaining to the formation and interactions of protein aggregates associated with neurodegenerative diseases are invisible to conventional biophysical techniques. We recently introduced (15)N dark-state exchange saturation transfer (DEST) and (15)N lifetime line-broadening to study solution backbone dynamics and position-specific binding probabilities for amyloid β (Aβ) monomers in exchange with large (2-80 MDa) protofibrillar Aβ aggregates. Here we use (13)C(methyl)DEST and lifetime line-broadening to probe the interactions and dynamics of methyl-bearing side chains in the Aβ-protofibril-bound state. We show that all methyl groups of Aβ40 populate direct-contact bound states with a very fast effective transverse relaxation rate, indicative of side-chain-mediated direct binding to the protofibril surface. The data are consistent with position-specific enhancements of (13)C(methyl)-R₂(tethered) values in tethered states, providing further insights into the structural ensemble of the protofibril-bound state.
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Affiliation(s)
- Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912 (USA).
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55
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Fawzi NL, Libich DS, Ying J, Tugarinov V, Clore GM. Characterizing Methyl-Bearing Side Chain Contacts and Dynamics Mediating Amyloid β Protofibril Interactions Using13Cmethyl-DEST and Lifetime Line Broadening. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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56
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Zhao B, Hansen AL, Zhang Q. Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1ρ) NMR spectroscopy. J Am Chem Soc 2013; 136:20-3. [PMID: 24299272 DOI: 10.1021/ja409835y] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R(1ρ) relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R(1ρ) RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR "invisible" state. The utility of CEST and low spin-lock field R(1ρ) RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s(-1).
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Affiliation(s)
- Bo Zhao
- Department of Biochemistry and Biophysics and ‡Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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57
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Bouvignies G, Vallurupalli P, Kay LE. Visualizing side chains of invisible protein conformers by solution NMR. J Mol Biol 2013; 426:763-74. [PMID: 24211467 DOI: 10.1016/j.jmb.2013.10.041] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 10/31/2013] [Accepted: 10/31/2013] [Indexed: 11/18/2022]
Abstract
Sparsely populated and transiently formed protein conformers can play key roles in many biochemical processes. Understanding the structure function paradigm requires, therefore, an atomic-resolution description of these rare states. However, they are difficult to study because they cannot be observed using standard biophysical techniques. In the past decade, NMR methods have been developed for structural studies of these elusive conformers, focusing primarily on backbone (1)H, (15)N and (13)C nuclei. Here we extend the methodology to include side chains by developing a (13)C-based chemical exchange saturation transfer experiment for the assignment of side-chain aliphatic (13)C chemical shifts in uniformly (13)C labeled proteins. A pair of applications is provided, involving the folding of β-sheet Fyn SH3 and α-helical FF domains. Over 96% and 89% of the side-chain (13)C chemical shifts for excited states corresponding to the unfolded conformation of the Fyn SH3 domain and a folding intermediate of the FF domain, respectively, have been obtained, providing insight into side-chain packing and dynamics.
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Affiliation(s)
- Guillaume Bouvignies
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Pramodh Vallurupalli
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lewis E Kay
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada; Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5S 1A8, Canada.
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58
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Vallurupalli P, Bouvignies G, Kay LE. A computational study of the effects of (13) C-(13) C scalar couplings on (13) C CEST NMR spectra: towards studies on a uniformly (13) C-labeled protein. Chembiochem 2013; 14:1709-13. [PMID: 23784752 DOI: 10.1002/cbic.201300230] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Indexed: 11/10/2022]
Abstract
Read the label: The NMR CEST experiment can be used to reconstruct spectra of sparsely populated, transiently formed protein conformers so long as they exchange with a highly populated ground state with rates of 20-300 s(-1) . Here we establish that accurate (13) C chemical shifts of side-chain carbon nuclei can be obtained from uniformly (13) C-labeled samples, without interference from the coupled (13) C spin network.
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Affiliation(s)
- Pramodh Vallurupalli
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, 1, King's College Circle, Toronto, Ontario, M5S 1A8 (Canada)
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59
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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.
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Affiliation(s)
- Alexandar L Hansen
- Department of Molecular Genetics, The University of Toronto, Toronto, ON, M5S 1A8, Canada
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60
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Vallurupalli P, Kay LE. Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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61
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Vallurupalli P, Kay LE. Probing slow chemical exchange at carbonyl sites in proteins by chemical exchange saturation transfer NMR spectroscopy. Angew Chem Int Ed Engl 2013; 52:4156-9. [PMID: 23450751 DOI: 10.1002/anie.201209118] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Pramodh Vallurupalli
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario, M5S1A8, Canada.
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62
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Bouvignies G, Kay LE. Measurement of proton chemical shifts in invisible states of slowly exchanging protein systems by chemical exchange saturation transfer. J Phys Chem B 2012. [PMID: 23194058 DOI: 10.1021/jp311109u] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chemical exchange saturation transfer (CEST) NMR spectroscopy has emerged as a powerful technique for studies of transiently formed, sparsely populated (excited) conformational states of protein molecules in slow exchange with a dominant structure. The most popular form of the experiment, and the version originally developed, uses a weak (1)H radio frequency field to perturb longitudinal magnetization of one state with the effect transferred to magnetization in the second conformation via chemical exchange. A significant limitation of the method for protein applications emerges from (1)H magnetization transfer via dipolar relaxation (NOE effect) that can severely complicate analysis of the resulting CEST profile. This is particularly an issue since the (1)H chemical shifts of the excited state, critical for structural studies of these elusive conformers, become difficult to extract. Here we present a method for measurement of these shifts via CEST experiments in which the NOE effect is not an issue. The methodology is illustrated through applications to a pair of exchanging systems where the results are cross-validated.
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Affiliation(s)
- Guillaume Bouvignies
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario, Canada, M5S 1A8.
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63
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Osawa M, Takeuchi K, Ueda T, Nishida N, Shimada I. Functional dynamics of proteins revealed by solution NMR. Curr Opin Struct Biol 2012; 22:660-9. [PMID: 23000032 DOI: 10.1016/j.sbi.2012.08.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 08/28/2012] [Accepted: 08/31/2012] [Indexed: 12/22/2022]
Abstract
Solution NMR spectroscopy can analyze the dynamics of proteins on a wide range of timescales, from picoseconds to even days, in a site-specific manner, and thus its results are complementary to the detailed but largely static structural information obtained by X-ray crystallography. We review recent progresses in a variety of NMR techniques, including relaxation dispersion and paramagnetic relaxation enhancement (PRE), that permit the observation of the low-populated states, which had been 'invisible' with other techniques. In addition, we review how NMR spectroscopy can be used to elucidate functionally relevant protein dynamics.
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Affiliation(s)
- Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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