1
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Klein A, Vasa SK, Linser R. 5D solid-state NMR spectroscopy for facilitated resonance assignment. JOURNAL OF BIOMOLECULAR NMR 2023; 77:229-245. [PMID: 37943392 PMCID: PMC10687145 DOI: 10.1007/s10858-023-00424-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023]
Abstract
1H-detected solid-state NMR spectroscopy has been becoming increasingly popular for the characterization of protein structure, dynamics, and function. Recently, we showed that higher-dimensionality solid-state NMR spectroscopy can aid resonance assignments in large micro-crystalline protein targets to combat ambiguity (Klein et al., Proc. Natl. Acad. Sci. U.S.A. 2022). However, assignments represent both, a time-limiting factor and one of the major practical disadvantages within solid-state NMR studies compared to other structural-biology techniques from a very general perspective. Here, we show that 5D solid-state NMR spectroscopy is not only justified for high-molecular-weight targets but will also be a realistic and practicable method to streamline resonance assignment in small to medium-sized protein targets, which such methodology might not have been expected to be of advantage for. Using a combination of non-uniform sampling and the signal separating algorithm for spectral reconstruction on a deuterated and proton back-exchanged micro-crystalline protein at fast magic-angle spinning, direct amide-to-amide correlations in five dimensions are obtained with competitive sensitivity compatible with common hardware and measurement time commitments. The self-sufficient backbone walks enable efficient assignment with very high confidence and can be combined with higher-dimensionality sidechain-to-backbone correlations from protonated preparations into minimal sets of experiments to be acquired for simultaneous backbone and sidechain assignment. The strategies present themselves as potent alternatives for efficient assignment compared to the traditional assignment approaches in 3D, avoiding user misassignments derived from ambiguity or loss of overview and facilitating automation. This will ease future access to NMR-based characterization for the typical solid-state NMR targets at fast MAS.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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2
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Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Curr Opin Struct Biol 2023; 82:102660. [PMID: 37536064 DOI: 10.1016/j.sbi.2023.102660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies.
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Affiliation(s)
- Federico Napoli
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria. https://twitter.com/iomichiamofede
| | - Lea Marie Becker
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria. https://twitter.com/bckrlea
| | - Paul Schanda
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria.
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3
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Vugmeyster L, Rodgers A, Ostrovsky D, James McKnight C, Fu R. Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107493. [PMID: 37271094 PMCID: PMC10330767 DOI: 10.1016/j.jmr.2023.107493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
We demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO 80204, USA
| | - C James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, United States
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL 32310, USA
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4
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Tatman BP, Franks WT, Brown SP, Lewandowski JR. Nuclear spin diffusion under fast magic-angle spinning in solid-state NMR. J Chem Phys 2023; 158:2890210. [PMID: 37171196 DOI: 10.1063/5.0142201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Solid-state nuclear spin diffusion is the coherent and reversible process through which spin order is transferred via dipolar couplings. With the recent increases in magic-angle spinning (MAS) frequencies and magnetic fields becoming routinely applied in solid-state nuclear magnetic resonance, understanding how the increased 1H resolution obtained affects spin diffusion is necessary for interpretation of several common experiments. To investigate the coherent contributions to spin diffusion with fast MAS, we have developed a low-order correlation in Liouville space model based on the work of Dumez et al. (J. Chem. Phys. 33, 224501, 2010). Specifically, we introduce a new method for basis set selection, which accounts for the resonance-offset dependence at fast MAS. Furthermore, we consider the necessity of including chemical shift, both isotropic and anisotropic, in the modeling of spin diffusion. Using this model, we explore how different experimental factors change the nature of spin diffusion. Then, we show case studies to exemplify the issues that arise in using spin diffusion techniques at fast spinning. We show that the efficiency of polarization transfer via spin diffusion occurring within a deuterated and 100% back-exchanged protein sample at 60 kHz MAS is almost entirely dependent on resonance offset. We additionally identify temperature-dependent magnetization transfer in beta-aspartyl L-alanine, which could be explained by the influence of an incoherent relaxation-based nuclear Overhauser effect.
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Affiliation(s)
- Ben P Tatman
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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5
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Shcherbakov AA, Brousseau M, Henzler-Wildman KA, Hong M. Microsecond Motion of the Bacterial Transporter EmrE in Lipid Bilayers. J Am Chem Soc 2023; 145:10104-10115. [PMID: 37097985 PMCID: PMC10905379 DOI: 10.1021/jacs.3c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The bacterial transporter EmrE is a homo-dimeric membrane protein that effluxes cationic polyaromatic substrates against the concentration gradient by coupling to proton transport. As the archetype of the small multidrug resistance family of transporters, EmrE structure and dynamics provide atomic insights into the mechanism of transport by this family of proteins. We recently determined high-resolution structures of EmrE in complex with a cationic substrate, tetra(4-fluorophenyl)phosphonium (F4-TPP+), using solid-state NMR spectroscopy and an S64V-EmrE mutant. The substrate-bound protein exhibits distinct structures at acidic and basic pH, reflecting changes upon binding or release of a proton from residue E14, respectively. To obtain insight into the protein dynamics that mediate substrate transport, here we measure 15N rotating-frame spin-lattice relaxation (R1ρ) rates of F4-TPP+-bound S64V-EmrE in lipid bilayers under magic-angle spinning (MAS). Using perdeuterated and back-exchanged protein and 1H-detected 15N spin-lock experiments under 55 kHz MAS, we measured 15N R1ρ rates site-specifically. Many residues show spin-lock field-dependent 15N R1ρ relaxation rates. This relaxation dispersion indicates the presence of backbone motions at a rate of about 6000 s-1 at 280 K for the protein at both acidic and basic pH. This motional rate is 3 orders of magnitude faster than the alternating access rate but is within the range estimated for substrate binding. We propose that these microsecond motions may allow EmrE to sample different conformations to facilitate substrate binding and release from the transport pore.
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Affiliation(s)
- Alexander A. Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Merissa Brousseau
- Department of Biochemistry, University of Wisconsin at Madison, Madison, WI 53706, United States
| | | | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
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6
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Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR. J Am Chem Soc 2023; 145:10700-10711. [PMID: 37140345 DOI: 10.1021/jacs.3c01200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.
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Affiliation(s)
- Laura Troussicot
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
| | - Alicia Vallet
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Department of Life Sciences, Chalmers University of Technology, SE-405 30 Göteborg, Sweden
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Paul Schanda
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
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7
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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
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Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
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8
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Keeler EG, McDermott AE. Rotating Frame Relaxation in Magic Angle Spinning Solid State NMR, a Promising Tool for Characterizing Biopolymer Motion. Chem Rev 2022; 122:14940-14953. [PMID: 36099021 PMCID: PMC10122933 DOI: 10.1021/acs.chemrev.2c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Magic angle spinning NMR rotating frame relaxation measurements provide a unique experimental window into biomolecules dynamics, as is illustrated by numerous recent applications. We discuss experimental strategies for this class of experiments, with a particular focus on systems where motion-driven modulation of the chemical shift interaction is the main mechanism for relaxation. We also explore and describe common strategies for interpreting the data sets to extract motion time scale, activation energy, and angle or order parameters from rotating frame relaxation data. Using model free analysis and numerical simulations, including time domain treatment, we explore conditions under which it is possible to obtain accurate and precise information about the time scales of motions. Overall, with rapid technical advances in solid state NMR, there is a bright future for this class of studies.
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Affiliation(s)
- Eric G Keeler
- New York Structural Biology Center, New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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9
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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10
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Vugmeyster L, Ostrovsky D, Greenwood A, Fu R. Deuteron rotating frame relaxation for the detection of slow motions in rotating solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 337:107171. [PMID: 35219160 PMCID: PMC8994516 DOI: 10.1016/j.jmr.2022.107171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 06/06/2023]
Abstract
We demonstrate experimental and computational approaches for measuring 2H rotating frame NMR relaxation for solid samples under magic angle spinning (MAS) conditions. The relaxation properties of the deuterium spin-1 system are dominated by the reorientation of the anisotropic quadrupolar tensors, with the effective quadrupolar coupling constant around 55 kHz for methyl groups. The technique is demonstrated using the model compound dimethyl-sulfone at MAS rates of 10 and 60 kHz as well as for an amyloid fibril sample comprising an amyloid-β (1-40) protein with a selective methyl group labeled in the disordered domain of the fibrils, at an MAS rate of 8 kHz. For both systems, the motional parameters fall well within the ranges determined by other techniques, thus validating its feasibility. Experimental and computational factors such as i) the probe's radio frequency inhomogeneity profiles, ii) rotary resonances at conditions for which the spin-lock field strength matches the half- or full-integer of the MAS rate, iii) the choice of MAS rates and spin-lock field strengths, and iv) simulations that account for the interconversion of multiple coherences for the spin-1 system under MAS and deviations from the analytical Redfield treatment are thoroughly considered.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO 80204, USA
| | - Alexander Greenwood
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL 32310, USA
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11
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Reif B. Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR. Chem Rev 2021; 122:10019-10035. [PMID: 34870415 DOI: 10.1021/acs.chemrev.1c00681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
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Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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12
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Vugmeyster L, Ostrovsky D, Greenwood A, Fu R. Deuteron Chemical Exchange Saturation Transfer for the Detection of Slow Motions in Rotating Solids. Front Mol Biosci 2021; 8:705572. [PMID: 34386521 PMCID: PMC8353179 DOI: 10.3389/fmolb.2021.705572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/12/2021] [Indexed: 01/10/2023] Open
Abstract
We utilized the 2H Chemical Exchange Saturation Transfer (CEST) technique under magic angle spinning (MAS) conditions to demonstrate the feasibility of the method for studies of slow motions in the solid state. For the quadrupolar anisotropic interaction, the essence of CEST is to scan the saturation pattern over a range of offsets corresponding to the entire spectral region(s) for all conformational states involved, which translates into a range of −60–+ 60 kHz for methyl groups. Rotary resonances occur when the offsets are at half-and full-integer of the MAS rates. The choice of the optimal MAS rate is governed by the condition to reduce the number of rotary resonances in the CEST profile patterns and retain a sufficiently large quadrupolar interaction active under MAS to maintain sensitivity to motions. As examples, we applied this technique to a well-known model compound dimethyl-sulfone (DMS) as well as amyloid-β fibrils selectively deuterated at a single methyl group of A2 belonging to the disordered domain. It is demonstrated that the obtained exchange rate between the two rotameric states of DMS at elevated temperatures fell within known ranges and the fitted model parameters for the fibrils agree well with the previously obtained value using static 2H NMR techniques. Additionally, for the fibrils we have observed characteristic broadening of rotary resonances in the presence of conformational exchange, which provides implications for model selection and refinement. This work sets the stage for future potential extensions of the 2H CEST under MAS technique to multiple-labeled samples in small molecules and proteins.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, United States
| | - Alexander Greenwood
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL, United States
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13
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Busi B, Yarava JR, Bertarello A, Freymond F, Adamski W, Maurin D, Hiller M, Oschkinat H, Blackledge M, Emsley L. Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation. J Phys Chem B 2021; 125:2212-2221. [PMID: 33635078 DOI: 10.1021/acs.jpcb.0c10188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R1) measurements to determine the hierarchical activation energies of motions of four different proteins: two small globular proteins (GB1 and the SH3 domain of α-spectrin), an intrinsically disordered protein (the C-terminus of the nucleoprotein of the Sendai virus, Sendai Ntail), and an outer membrane protein (OmpG). The activation energies map the motions occurring in the side chains, in the backbone, and in the hydration shells of the proteins. We were able to identify similarities and differences in the average motions of the proteins. We find that the NMR relaxation properties of the four proteins do share similar features. The data characterizing average backbone motions are found to be very similar, the same for methyl group rotations, and similar activation energies are measured. The main observed difference occurs for the intrinsically disordered Sendai Ntail, where we observe much lower energy of activation for motions of protons associated with the protein-solvent interface as compared to the others. We also observe variability between the proteins regarding side chain 15N relaxation of lysine residues, with a higher activation energy observed in OmpG. This hints at strong interactions with negatively charged lipids in the bilayer and provides a possible mechanistic clue for the "positive-inside" rule for helical membrane proteins. Overall, these observations refine the understanding of the similarities and differences between hierarchical dynamics in proteins.
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Affiliation(s)
- Baptiste Busi
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Jayasubba Reddy Yarava
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Andrea Bertarello
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - François Freymond
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Wiktor Adamski
- Université Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Damien Maurin
- Université Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Matthias Hiller
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | | | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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14
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Vugmeyster L. Recent developments in deuterium solid-state NMR for the detection of slow motions in proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 111:101710. [PMID: 33450712 PMCID: PMC7903970 DOI: 10.1016/j.ssnmr.2020.101710] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 05/14/2023]
Abstract
Slow timescale dynamics in proteins are essential for a variety of biological functions spanning ligand binding, enzymatic catalysis, protein folding and misfolding regulations, as well as protein-protein and protein-nucleic acid interactions. In this review, we focus on the experimental and theoretical developments of 2H static NMR methods applicable for studies of microsecond to millisecond motional modes in proteins, particularly rotating frame relaxation dispersion (R1ρ), quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation dispersion, and quadrupolar chemical exchange saturation transfer NMR experiments (Q-CEST). With applications chosen from amyloid-β fibrils, we show the complementarity of these approaches for elucidating the complexities of conformational ensembles in disordered domains in the non-crystalline solid state, with the employment of selective deuterium labels. Combined with recent advances in relaxation dispersion backbone measurements for 15N/13C/1H nuclei, these techniques provide powerful tools for studies of biologically relevant timescale dynamics in disordered domains in the solid state.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, 80204, USA.
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15
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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16
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Vallet A, Favier A, Brutscher B, Schanda P. ssNMRlib: a comprehensive library and tool box for acquisition of solid-state nuclear magnetic resonance experiments on Bruker spectrometers. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:331-345. [PMID: 37904819 PMCID: PMC10500710 DOI: 10.5194/mr-1-331-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/16/2020] [Indexed: 11/01/2023]
Abstract
We introduce ssNMRlib, a comprehensive suite of pulse sequences and jython scripts for user-friendly solid-state nuclear magnetic resonance (NMR) data acquisition, parameter optimization and storage on Bruker spectrometers. ssNMRlib allows the straightforward setup of even highly complex multi-dimensional solid-state NMR experiments with a few clicks from an intuitive graphical interface directly from the Bruker Topspin acquisition software. ssNMRlib allows the setup of experiments in a magnetic-field-independent manner and thus facilitates the workflow in a multi-spectrometer setting with a centralized library. Safety checks furthermore assist the user in experiment setup. Currently hosting more than 140 1D to 4D experiments, primarily for biomolecular solid-state NMR, the library can be easily customized and new experiments are readily added as new templates. ssNMRlib is part of the previously introduced NMRlib library, which comprises many solution-NMR pulse sequences and macros.
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Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Adrien Favier
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Bernhard Brutscher
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
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17
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Site-Specific Tryptophan Labels Reveal Local Microsecond-Millisecond Motions of Dihydrofolate Reductase. Molecules 2020; 25:molecules25173819. [PMID: 32842574 PMCID: PMC7503464 DOI: 10.3390/molecules25173819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Many enzymes are known to change conformations during their catalytic cycle, but the role of these protein motions is not well understood. Escherichia coli dihydrofolate reductase (DHFR) is a small, flexible enzyme that is often used as a model system for understanding enzyme dynamics. Recently, native tryptophan fluorescence was used as a probe to study micro- to millisecond dynamics of DHFR. Yet, because DHFR has five native tryptophans, the origin of the observed conformational changes could not be assigned to a specific region within the enzyme. Here, we use DHFR mutants, each with a single tryptophan as a probe for temperature jump fluorescence spectroscopy, to further inform our understanding of DHFR dynamics. The equilibrium tryptophan fluorescence of the mutants shows that each tryptophan is in a different environment and that wild-type DHFR fluorescence is not a simple summation of all the individual tryptophan fluorescence signatures due to tryptophan–tryptophan interactions. Additionally, each mutant exhibits a two-phase relaxation profile corresponding to ligand association/dissociation convolved with associated conformational changes and a slow conformational change that is independent of ligand association and dissociation, similar to the wild-type enzyme. However, the relaxation rate of the slow phase depends on the location of the tryptophan within the enzyme, supporting the conclusion that the individual tryptophan fluorescence dynamics do not originate from a single collective motion, but instead report on local motions throughout the enzyme.
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18
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Rovó P. Recent advances in solid-state relaxation dispersion techniques. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 108:101665. [PMID: 32574905 DOI: 10.1016/j.ssnmr.2020.101665] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
This review describes two rotating-frame (R1ρ) relaxation dispersion methods, namely the Bloch-McConnell Relaxation Dispersion and the Near-rotary Resonance Relaxation Dispersion, which enable the study of microsecond time-scale conformational fluctuations in the solid state using magic-angle-spinning nuclear magnetic resonance spectroscopy. The goal is to provide the reader with key ideas, experimental descriptions, and practical considerations associated with R1ρ measurements that are needed for analyzing relaxation dispersion and quantifying conformational exchange. While the focus is on protein motion, many presented concepts can be equally well adapted to study the microsecond time-scale dynamics of other bio- (e.g. lipids, polysaccharides, nucleic acids), organic (e.g. pharmaceutical compounds), or inorganic molecules (e.g., metal organic frameworks). This article summarizes the essential contributions made by recent theoretical and experimental solid-state NMR studies to our understanding of protein motion. Here we discuss recent advances in fast MAS applications that enable the observation and atomic level characterization of sparsely populated conformational states which are otherwise inaccessible for other experimental methods. Such high-energy states are often associated with protein functions such as molecular recognition, ligand binding, or enzymatic catalysis, as well as with disease-related properties such as misfolding and amyloid formation.
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Affiliation(s)
- Petra Rovó
- Department of Chemistry, Ludwig Maximilian University Munich, Butenandtstr. 5-13, 81377, Munich, Germany; Center for NanoScience (CeNS), Schellingstr. 4, 80799, Munich, Germany.
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19
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Grohe K, Patel S, Hebrank C, Medina S, Klein A, Rovó P, Vasa SK, Singh H, Vögeli B, Schäfer LV, Linser R. Protein Motional Details Revealed by Complementary Structural Biology Techniques. Structure 2020; 28:1024-1034.e3. [PMID: 32579946 DOI: 10.1016/j.str.2020.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 01/16/2023]
Abstract
Proteins depend on defined molecular plasticity for their functionality. How to comprehensively capture dynamics correctly is of ubiquitous biological importance. Approaches commonly used to probe protein dynamics include model-free elucidation of site-specific motion by NMR relaxation, molecular dynamics (MD)-based approaches, and capturing the substates within a dynamic ensemble by recent eNOE-based multiple-structure approaches. Even though MD is sometimes combined with ensemble-averaged NMR restraints, these approaches have largely been developed and used individually. Owing to the different underlying concepts and practical requirements, it has remained unclear how they compare, and how they cross-validate and complement each other. Here, we extract and compare the differential information contents of MD simulations, NMR relaxation measurements, and eNOE-based multi-state structures for the SH3 domain of chicken α-spectrin. The data show that a validated, consistent, and detailed picture is feasible both for timescales and actual conformational states sampled in the dynamic ensemble. This includes the biologically important side-chain plasticity, for which experimentally cross-validated assessment is a significant challenge.
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Affiliation(s)
- Kristof Grohe
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Snehal Patel
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Cornelia Hebrank
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Sara Medina
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Alexander Klein
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Petra Rovó
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Suresh K Vasa
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Himanshu Singh
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Rasmus Linser
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany.
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20
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Hernando M, Orriss G, Perodeau J, Lei S, Ferens FG, Patel TR, Stetefeld J, Nieuwkoop AJ, O'Neil JD. Solution structure and oligomeric state of the E. coliglycerol facilitator. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183191. [PMID: 31953232 DOI: 10.1016/j.bbamem.2020.183191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/05/2019] [Accepted: 01/10/2020] [Indexed: 12/11/2022]
Abstract
Protein dynamics at atomic resolution can provide deep insights into the biological activities of proteins and enzymes but they can also make structure and dynamics studies challenging. Despite their well-known biological and pharmaceutical importance, integral membrane protein structure and dynamics studies lag behind those of water-soluble proteins mainly owing to solubility problems that result upon their removal from the membrane. Escherichia coli glycerol facilitator (GF) is a member of the aquaglyceroporin family that allows for the highly selective passive diffusion of its substrate glycerol across the inner membrane of the bacterium. Previous molecular dynamics simulations and hydrogen-deuterium exchange studies suggested that protein dynamics play an important role in the passage of glycerol through the protein pore. With the aim of studying GF dynamics by solution and solid-state nuclear magnetic resonance (NMR) spectroscopy we optimized the expression of isotope-labelled GF and explored various solubilizing agents including detergents, osmolytes, amphipols, random heteropolymers, lipid nanodiscs, bicelles and other buffer additives to optimize the solubility and polydispersity of the protein. The GF protein is most stable and soluble in lauryl maltose neopentyl glycol (LMNG), where it exists in a tetramer-octamer equilibrium. The solution structures of the GF tetramer and octamer were determined by negative-stain transmission electron microscopy (TEM), size-exclusion chromatography small-angle X-ray scattering (SEC-SAXS) and solid-state magic-angle spinning NMR spectroscopy. Although NMR sample preparation still needs optimization for full structure and dynamics studies, negative stain TEM and SEC-SAXS revealed low-resolution structures of the detergent-solubilized tetramer and octamer particles. The non-native octamer appears to form from the association of the cytoplasmic faces of two tetramers, the interaction apparently mediated by their disordered N- and C-termini. This information may be useful in future studies directed at reducing the heterogeneity and self-association of the protein.
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Affiliation(s)
- Mary Hernando
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - George Orriss
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Jacqueline Perodeau
- Department of Chemistry and Chemical Biology, Rutgers School of Arts and Sciences, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Shixing Lei
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Fraser G Ferens
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Trushar R Patel
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, Lethbridge University, 4401 University Drive, Lethbridge, Alberta T1K 3M4, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers School of Arts and Sciences, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Joe D O'Neil
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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21
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Singh H, Vasa SK, Jangra H, Rovó P, Päslack C, Das CK, Zipse H, Schäfer LV, Linser R. Fast Microsecond Dynamics of the Protein–Water Network in the Active Site of Human Carbonic Anhydrase II Studied by Solid-State NMR Spectroscopy. J Am Chem Soc 2019; 141:19276-19288. [DOI: 10.1021/jacs.9b05311] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Himanshu Singh
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Suresh K. Vasa
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Harish Jangra
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Petra Rovó
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Christopher Päslack
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Hendrik Zipse
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
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22
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Gallo A, Franks WT, Lewandowski JR. A suite of solid-state NMR experiments to utilize orphaned magnetization for assignment of proteins using parallel high and low gamma detection. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 305:219-231. [PMID: 31319283 DOI: 10.1016/j.jmr.2019.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 05/18/2023]
Abstract
We present a suite of two-receiver solid-state NMR experiments for backbone and side chain resonance assignment. The experiments rely on either dipolar coupling or scalar coupling for polarization transfer and are devised to acquire a 1H-detected 3D experiment AND a nested 13C-detected 2D from a shared excitation pulse. In order to compensate for the lower sensitivity of detection on 13C nucleus, 2D rows are signal averaged during 3D planes. The 3D dual receiver experiments do not suffer from any appreciable signal loss compared to their single receiver versions and require no extra optimization. The resulting data is higher in information content with no additional experiment time. The approach is expected to become widespread as multiple receivers become standard for new NMR spectrometers.
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Affiliation(s)
- A Gallo
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - W T Franks
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK; Department of Physics, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - J R Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK.
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23
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Öster C, Kosol S, Lewandowski JR. Quantifying Microsecond Exchange in Large Protein Complexes with Accelerated Relaxation Dispersion Experiments in the Solid State. Sci Rep 2019; 9:11082. [PMID: 31366983 PMCID: PMC6668460 DOI: 10.1038/s41598-019-47507-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/16/2019] [Indexed: 01/20/2023] Open
Abstract
Solid state NMR is a powerful method to obtain information on the structure and dynamics of protein complexes that, due to solubility and size limitations, cannot be achieved by other methods. Here, we present an approach that allows the quantification of microsecond conformational exchange in large protein complexes by using a paramagnetic agent to accelerate 15N R1ρ relaxation dispersion measurements and overcome sensitivity limitations. The method is validated on crystalline GB1 and then applied to a >300 kDa precipitated complex of GB1 with full length human immunoglobulin G (IgG). The addition of a paramagnetic agent increased the signal to noise ratio per time unit by a factor of 5, which allowed full relaxation dispersion curves to be recorded on a sample containing less than 50 μg of labelled material in 5 and 10 days on 850 and 700 MHz spectrometers, respectively. We discover a similar exchange process across the β-sheet in GB1 in crystals and in complex with IgG. However, the slow motion observed for a number of residues in the α-helix of crystalline GB1 is not detected in the complex.
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Affiliation(s)
- Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Simone Kosol
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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24
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Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H- 13C Labeling and Fast Magic-Angle Spinning NMR. J Am Chem Soc 2019; 141:11183-11195. [PMID: 31199882 DOI: 10.1021/jacs.9b04219] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize the dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artifact-free dynamics measurements, and allows probing motions effectively without molecular weight limitations. The application to the TET2 enzyme assembly of ∼0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (picoseconds to milliseconds). We quantitatively probe ring-flip motions and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as the exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS) , INSERM, CNRS, Université de Montpellier , Montpellier , France
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France.,Departamento de Biomedicina , Faculdade de Medicina da Universidade do Porto , Porto , Portugal.,i3S, Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Tsutomu Terauchi
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,SI Innovation Center , Taiyo Nippon Sanso Corp. , 2008-2 Wada , Tama-city , Tokyo 206-0001 , Japan
| | - David Gajan
- Université de Lyon , Centre de RMN à Hauts Champs de Lyon CRMN, FRE 2034, Université de Lyon, CNRS, ENS Lyon, UCB Lyon 1 , 69100 Villeurbanne , France
| | - Yohei Miyanoiri
- Institute of Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Roman Lichtenecker
- Institute of Organic Chemistry , University of Vienna , Währinger Str. 38 , 1090 Vienna , Austria
| | - Masatsune Kainosho
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
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25
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Vugmeyster L, Au DF, Ostrovsky D, Fu R. Deuteron Solid-State NMR Relaxation Measurements Reveal Two Distinct Conformational Exchange Processes in the Disordered N-Terminal Domain of Amyloid-β Fibrils. Chemphyschem 2019; 20:1680-1689. [PMID: 31087613 PMCID: PMC6663588 DOI: 10.1002/cphc.201900363] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/12/2019] [Indexed: 12/26/2022]
Abstract
We employed deuterium solid-state NMR techniques under static conditions to discern the details of the μs-ms timescale motions in the flexible N-terminal subdomain of Aβ1-40 amyloid fibrils, which spans residues 1-16. In particular, we utilized a rotating frame (R1ρ ) and the newly developed time domain quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation measurements at the selectively deuterated side chains of A2, H6, and G9. The two experiments are complementary in terms of probing somewhat different timescales of motions, governed by the tensor parameters and the sampling window of the magnetization decay curves. The results indicated two mobile "free" states of the N-terminal domain undergoing global diffusive motions, with isotropic diffusion coefficients of 0.7-1 ⋅ 108 and 0.3-3 ⋅ 106 ad2 s-1 . The free states are also involved in the conformational exchange with a single bound state, in which the diffusive motions are quenched, likely due to transient interactions with the structured hydrophobic core. The conformational exchange rate constants are 2-3 ⋅ 105 s-1 and 2-3 ⋅ 104 s-1 for the fast and slow diffusion free states, respectively.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO, USA, 80204
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver CO, USA, 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO, USA, 80204
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL, 32310
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26
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Au DF, Ostrovsky D, Fu R, Vugmeyster L. Solid-state NMR reveals a comprehensive view of the dynamics of the flexible, disordered N-terminal domain of amyloid-β fibrils. J Biol Chem 2019; 294:5840-5853. [PMID: 30737281 DOI: 10.1074/jbc.ra118.006559] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/08/2019] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibril deposits observed in Alzheimer's disease comprise amyloid-β (Aβ) protein possessing a structured hydrophobic core and a disordered N-terminal domain (residues 1-16). The internal flexibility of the disordered domain is likely essential for Aβ aggregation. Here, we used 2H static solid-state NMR methods to probe the dynamics of selected side chains of the N-terminal domain of Aβ1-40 fibrils. Line shape and relaxation data suggested a two-state model in which the domain's free state undergoes a diffusive motion that is quenched in the bound state, likely because of transient interactions with the structured C-terminal domain. At 37 °C, we observed freezing of the dynamics progressively along the Aβ sequence, with the fraction of the bound state increasing and the rate of diffusion decreasing. We also found that without solvation, the diffusive motion is quenched. The solvent acted as a plasticizer reminiscent of its role in the onset of global dynamics in globular proteins. As the temperature was lowered, the fraction of the bound state exhibited sigmoidal behavior. The midpoint of the freezing curve coincided with the bulk solvent freezing for the N-terminal residues and increased further along the sequence. Using 2H R 1ρ measurements, we determined the conformational exchange rate constant between the free and bound states under physiological conditions. Zinc-induced aggregation leads to the enhancement of the dynamics, manifested by the faster conformational exchange, faster diffusion, and lower freezing-curve midpoints.
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Affiliation(s)
- Dan Fai Au
- From the Department of Chemistry, University of Colorado, Denver, Colorado 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado, Denver, Colorado 80204
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, Florida 32310
| | - Liliya Vugmeyster
- From the Department of Chemistry, University of Colorado, Denver, Colorado 80204.
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27
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Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R 1p Relaxation-Dispersion MAS NMR. Chemphyschem 2019; 20:276-284. [PMID: 30444575 PMCID: PMC6354937 DOI: 10.1002/cphc.201800935] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/15/2018] [Indexed: 12/14/2022]
Abstract
Studying protein dynamics on microsecond-to-millisecond (μs-ms) time scales can provide important insight into protein function. In magic-angle-spinning (MAS) NMR, μs dynamics can be visualized by R 1 ρ rotating-frame relaxation dispersion experiments in different regimes of radio-frequency field strengths: at low RF field strength, isotropic-chemical-shift fluctuation leads to "Bloch-McConnell-type" relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R 1 ρ rate constants ("Near-Rotary-Resonance Relaxation Dispersion", NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical-shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.
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Affiliation(s)
- Dominique Marion
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
| | - Diego F. Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
| | - Isabel Ayala
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
| | - Karine Giandoreggio-Barranco
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
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28
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Liliya V, Dmitry O. Deuterium Rotating Frame NMR Relaxation Measurements in the Solid State under Static Conditions for Quantification of Dynamics. Chemphyschem 2019; 20:333-342. [PMID: 30079456 PMCID: PMC6499496 DOI: 10.1002/cphc.201800454] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Indexed: 11/07/2022]
Abstract
The feasibility of static deuterium rotating frame NMR relaxation measurements for characterization of slow timescale motions in powder systems is demonstrated. Using a model compound dimethyl sulfone-d6 , we show that these measurements yield conformational exchange rates and activation energy values in accordance with results obtained with other techniques. Furthermore, we demonstrate that the full Liouvillian approach as opposed to the Redfield approximation is necessary to analyze the experimental data.
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Affiliation(s)
- Vugmeyster Liliya
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Ostrovsky Dmitry
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
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29
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Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques. J Am Chem Soc 2019; 141:858-869. [PMID: 30620186 PMCID: PMC6982537 DOI: 10.1021/jacs.8b09258] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch-McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains.
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Affiliation(s)
- Petra Rovó
- Department Chemie und Pharmazie, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Colin A. Smith
- Wesleyan University, Hall-Atwater Laboratories, Middletown, CT 06459, USA
- Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Diego Gauto
- Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Bert L. de Groot
- Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Paul Schanda
- Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Rasmus Linser
- Wesleyan University, Hall-Atwater Laboratories, Middletown, CT 06459, USA
- Physikalische Chemie, Technische Universität Dortmund, 44227 Dortmund, Germany
- , Phone: +49 (0)89 2180-77652. Fax: +49 (0)89 2180-77646
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30
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Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR. Chemphyschem 2018; 20:311-317. [PMID: 30276945 DOI: 10.1002/cphc.201800779] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 11/08/2022]
Abstract
Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15 N rotating frame (R1ρ ) relaxation dispersion solid-state nuclear magnetic resonance spectroscopy over a wide range of spin-lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two-state exchange process with a common exchange rate of 1000 s-1 , corresponding to protein backbone motion on the timescale of 1 ms, and an excited-state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited-state populations (∼5-15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100-300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.
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Affiliation(s)
- Matthew D Shannon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Dwaipayan Mukhopadhyay
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, 44106, United States
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, 44106, United States
| | | | - Paul Schanda
- Institut de Biologie Structurale (IBS), 38027, Grenoble, France
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210, United States
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31
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Vasa SK, Rovó P, Linser R. Protons as Versatile Reporters in Solid-State NMR Spectroscopy. Acc Chem Res 2018; 51:1386-1395. [PMID: 29763290 DOI: 10.1021/acs.accounts.8b00055] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) is a spectroscopic technique that is used for characterization of molecular properties in the solid phase at atomic resolution. In particular, using the approach of magic-angle spinning (MAS), ssNMR has seen widespread applications for topics ranging from material sciences to catalysis, metabolomics, and structural biology, where both isotropic and anisotropic parameters can be exploited for a detailed assessment of molecular properties. High-resolution detection of protons long represented the holy grail of the field. With its high natural abundance and high gyromagnetic ratio, 1H has naturally been the most important nucleus type for the solution counterpart of NMR spectroscopy. In the solid state, similar benefits are obtained over detection of heteronuclei, however, a rocky road led to its success as their high gyromagnetic ratio has also been associated with various detrimental effects. Two exciting approaches have been developed in recent years that enable proton detection: After partial deuteration of the sample to reduce the proton spin density, the exploitation of protons could begin. Also, faster MAS, nowadays using tiny rotors with frequencies up to 130 kHz, has relieved the need for expensive deuteration. Apart from the sheer gain in sensitivity from choosing protons as the detection nucleus, the proton chemical shift and several other useful aspects of protons have revolutionized the field. In this Account, we are describing the fundamentals of proton detection as well as the arising possibilities for characterization of biomolecules as associated with the developments in our own lab. In particular, we focus on facilitated chemical-shift assignment, structure calculation based on protons, and on assessment of dynamics in solid proteins. For example, the proton chemical-shift dimension adds additional information for resonance assignments in the protein backbone and side chains. Chemical shifts and high gyromagnetic ratio of protons enable direct readout of spatial information over large distances. Dynamics in the protein backbone or side chains can be characterized efficiently using protons as reporters. For all of this, the sample amounts necessary for a given signal-to-noise have drastically shrunk, and new methodology enables assessment of molecules with increasing monomer molecular weight and complexity. Taken together, protons are able to overcome previous limitations, by speeding up processes, enhancing accuracies, and increasing the accessible ranges of ssNMR spectroscopy, as we shall discuss in detail in the following. In particular, these methodological developments have been pushing solid-state NMR into a new regime of biological topics as they realistically allow access to complex cellular molecules, elucidating their functions and interactions in a multitude of ways.
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Affiliation(s)
- Suresh K. Vasa
- Department Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany
- Center for Integrated Protein Science, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Petra Rovó
- Department Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany
- Center for Integrated Protein Science, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Rasmus Linser
- Department Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany
- Center for Integrated Protein Science, Ludwig-Maximilians-Universität, 81377 Munich, Germany
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32
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Jaudzems K, Bertarello A, Chaudhari SR, Pica A, Cala-De Paepe D, Barbet-Massin E, Pell AJ, Akopjana I, Kotelovica S, Gajan D, Ouari O, Tars K, Pintacuda G, Lesage A. Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kristaps Jaudzems
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Bertarello
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Sachin R. Chaudhari
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia I-80126 Naples Italy
| | - Diane Cala-De Paepe
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Emeline Barbet-Massin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrew J. Pell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
- Present address: Department of Materials and Environmental Chemistry; Arrhenius Laboratory; Stockholm University; Svante Arrhenius Väg 16 C SE-106 91 Stockholm Sweden
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - David Gajan
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273; 13397 Marseille cedex 20 France
| | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Guido Pintacuda
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Anne Lesage
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
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33
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Jaudzems K, Bertarello A, Chaudhari SR, Pica A, Cala-De Paepe D, Barbet-Massin E, Pell AJ, Akopjana I, Kotelovica S, Gajan D, Ouari O, Tars K, Pintacuda G, Lesage A. Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning. Angew Chem Int Ed Engl 2018; 57:7458-7462. [DOI: 10.1002/anie.201801016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/06/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Kristaps Jaudzems
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Bertarello
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Sachin R. Chaudhari
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia I-80126 Naples Italy
| | - Diane Cala-De Paepe
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Emeline Barbet-Massin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrew J. Pell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
- Present address: Department of Materials and Environmental Chemistry; Arrhenius Laboratory; Stockholm University; Svante Arrhenius Väg 16 C SE-106 91 Stockholm Sweden
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - David Gajan
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273; 13397 Marseille cedex 20 France
| | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Guido Pintacuda
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Anne Lesage
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
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