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Schönzart J, Han R, Gennett T, Rienstra CM, Stringer JA. Magnetic Susceptibility Modeling of Magic-Angle Spinning Modules for Part Per Billion Scale Field Homogeneity. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 364:107704. [PMID: 38879926 DOI: 10.1016/j.jmr.2024.107704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/18/2024]
Abstract
Magic-angle spinning (MAS) solid-state NMR methods are crucial in many areas of biology and materials science. Conventional probe designs have often been specified with 0.1 part per million (ppm) or 100 part per billion (ppb) magnetic field resolution, which is a limitation for many modern scientific applications. Here we describe a novel 5-mm MAS module design that significantly improves the linewidth and line shape for solid samples by an improved understanding of the magnetic susceptibility of probe materials and geometrical symmetry considerations, optimized to minimize the overall perturbation to the applied magnetic field (B0). The improved spinning module requires only first and second order shimming adjustments to achieve a sub-Hz resolution of 13C resonances of adamantane at 150 MHz Larmor frequency (14.1Tesla magnetic field). Minimal use of third and higher order shims improves experimental reproducibility upon sample changes and the exact placement within the magnet. Furthermore, the shimming procedure is faster, and the required gradients smaller, thus minimizing thermal drift of the room temperature (RT) shims. We demonstrate these results with direct polarization (Bloch decay) and cross polarization experiments on adamantane over a range of sample geometries and with multiple superconducting magnet systems. For a direct polarization experiment utilizing the entire active sample volume of a 5-mm rotor (90 µl), we achieved full width at half maximum (FWHM) of 0.76 Hz (5 ppb) and baseline resolved the 13C satellite peaks for adamantane as a consequent of the 7.31 Hz (59 ppb) width at 2% intensity. We expect these approaches to be increasingly pivotal for high-resolution solid-state NMR spectroscopy at and above 1 GHz 1H frequencies.
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Affiliation(s)
- Jasmin Schönzart
- Department of Chemistry, Colorado School of Mines, Golden, CO 80501, USA; PhoenixNMR, LLC, Loveland, CO 80503, USA.
| | - Ruixian Han
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI 53706, USA
| | - Thomas Gennett
- Department of Chemistry, Colorado School of Mines, Golden, CO 80501, USA
| | - Chad M Rienstra
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin -Madison, Madison, WI 53706, USA; National Magnetic Resonance Facility at Madison, University of Wisconsin - Madison Madison, WI 53706, USA
| | - John A Stringer
- Department of Chemistry, Colorado School of Mines, Golden, CO 80501, USA; PhoenixNMR, LLC, Loveland, CO 80503, USA.
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2
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Harding BD, Barclay AM, Piehl DW, Hiett A, Warmuth OA, Han R, Henzler-Wildman K, Rienstra CM. Cross polarization stability in multidimensional NMR spectroscopy of biological solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107724. [PMID: 38991266 DOI: 10.1016/j.jmr.2024.107724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 06/03/2024] [Accepted: 06/16/2024] [Indexed: 07/13/2024]
Abstract
Magic-angle spinning (MAS) solid-state nuclear magnetic resonance (SSNMR) spectroscopy is a powerful and versatile technique for probing structure and dynamics in large, insoluble biological systems at atomic resolution. With many recent advances in instrumentation and polarization methods, technology development in SSNMR remains an active area of research and presents opportunities to further improve data collection, processing, and analysis of samples with low sensitivity and complex tertiary and quaternary structures. SSNMR spectra are often collected as multidimensional data, requiring stable experimental conditions to minimize signal fluctuations (t1 noise). In this work, we examine the factors adversely affecting signal stability as well as strategies used to mitigate them, considering laboratory environmental requirements, configuration of amplifiers, and pulse sequence parameter selection. We show that Thermopad® temperature variable attenuators (TVAs) can partially compensate for the changes in amplifier output power as a function of temperature and thereby ameliorate one significant source of instability for some spectrometers and pulse sequences. We also consider the selection of tangent ramped cross polarization (CP) waveform shapes, to balance the requirements of sensitivity and instrumental stability. These findings collectively enable improved stability and overall performance for CP-based multidimensional spectra of microcrystalline, membrane, and fibrous proteins performed at multiple magnetic field strengths.
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Affiliation(s)
- Benjamin D Harding
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Alexander M Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dennis W Piehl
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ashley Hiett
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Owen A Warmuth
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ruixian Han
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Chad M Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706 USA; Morgridge Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706 USA.
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3
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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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4
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Ganesan A, Leisen J, Thyagarajan R, Sholl DS, Nair S. Hierarchical ZIF-8 Materials via Acid Gas-Induced Defect Sites: Synthesis, Characterization, and Functional Properties. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40623-40632. [PMID: 37595023 PMCID: PMC10472435 DOI: 10.1021/acsami.3c08344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023]
Abstract
Microporous metal-organic frameworks (MOFs) have been widely studied for molecular separation and catalysis. The uniform micropores of MOFs (<2 nm) can introduce diffusion limitations and render the interiors of the crystal inaccessible to target molecules. The introduction of hierarchical porosity (interconnected micro and mesopores) can enhance intra-crystalline diffusion while maintaining the separation/catalytic selectivity. Conventional hierarchical MOF synthesis involves complex strategies such as elongated linkers, soft templating, and sacrificial templates. Here, we demonstrate a more general approach using our controlled acid gas-enabled degradation and reconstruction (Solvent-Assisted Crystal Redemption) strategy. Selective linker labilization of ZIF-8 is shown to generate a hierarchical pore structure with mesoporous cages (∼50 nm) while maintaining microporosity. Detailed structural and spectroscopic characterization of the controlled degradation, linker insertion, and subsequent linker thermolysis is presented to show the clustering of acid gas-induced defects and the generation of mesopores. These findings indicate the generality of controlled degradation and reconstruction as a means for linker insertion in a wider variety of MOFs and creating hierarchical porosity. Enhanced molecular diffusion and catalytic activity in the hierarchical ZIF-8 are demonstrated by the adsorption kinetics of 1-butanol and a Knoevenagel condensation reaction.
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Affiliation(s)
- Arvind Ganesan
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Johannes Leisen
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Raghuram Thyagarajan
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David S. Sholl
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Oak
Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Sankar Nair
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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5
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Akbey Ü. Site-specific protein backbone deuterium 2H α quadrupolar patterns by proton-detected quadruple-resonance 3D 2H αc αNH MAS NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 125:101861. [PMID: 36989552 DOI: 10.1016/j.ssnmr.2023.101861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/23/2023] [Accepted: 03/06/2023] [Indexed: 06/11/2023]
Abstract
A novel deuterium-excited and proton-detected quadruple-resonance three-dimensional (3D) 2HαcαNH MAS nuclear magnetic resonance (NMR) method is presented to obtain site-specific 2Hα deuterium quadrupolar couplings from protein backbone, as an extension to the 2D version of the experiment reported earlier. Proton-detection results in high sensitivity compared to the heteronuclei detection methods. Utilizing four independent radiofrequency (RF) channels (quadruple-resonance), we managed to excite the 2Hα, then transfer deuterium polarization to its attached Cα, followed by polarization transfers to the neighboring backbone nitrogen and then to the amide proton for detection. This experiment results in an easy to interpret HSQC-like 2D 1H-15N fingerprint NMR spectrum, which contains site-specific deuterium quadrupolar patterns in the indirect third dimension. Provided that four-channel NMR probe technology is available, the setup of the 2HαcαNH experiment is relatively straightforward, by using low power deuterium excitation and polarization transfer schemes we have been developing. To our knowledge, this is the first demonstration of a quadruple-resonance MAS NMR experiment to link 2Hα quadrupolar couplings to proton-detection, extending our previous triple-resonance demonstrations. Distortion-free excitation and polarization transfer of ∼160-170 kHz 2Hα quadrupolar coupling were presented by using a deuterium RF strength of ∼20 kHz. From these 2Hα patterns, an average backbone order parameter of S = 0.92 was determined on a deuterated SH3 sample, with an average η = 0.22. These indicate that SH3 backbone represents sizable dynamics in the microsecond timescale where the 2Hα lineshape is sensitive. Moreover, site-specific 2Hα T1 relaxation times were obtained for a proof of concept. This 3D 2HαcαNH NMR experiment has the potential to determine structure and dynamics of perdeuterated proteins by utilizing deuterium as a novel reporter.
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Affiliation(s)
- Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, 15261, United States.
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6
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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: 22] [Impact Index Per Article: 22.0] [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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7
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Cerofolini L, Parigi G, Ravera E, Fragai M, Luchinat C. Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101828. [PMID: 36240720 DOI: 10.1016/j.ssnmr.2022.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.
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Affiliation(s)
- Linda Cerofolini
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy; Florence Data Science, Università degli Studi di Firenze, Italy.
| | - Marco Fragai
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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Cell-free synthesis of amyloid fibrils with infectious properties and amenable to sub-milligram magic-angle spinning NMR analysis. Commun Biol 2022; 5:1202. [DOI: 10.1038/s42003-022-04175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractStructural investigations of amyloid fibrils often rely on heterologous bacterial overexpression of the protein of interest. Due to their inherent hydrophobicity and tendency to aggregate as inclusion bodies, many amyloid proteins are challenging to express in bacterial systems. Cell-free protein expression is a promising alternative to classical bacterial expression to produce hydrophobic proteins and introduce NMR-active isotopes that can improve and speed up the NMR analysis. Here we implement the cell-free synthesis of the functional amyloid prion HET-s(218-289). We present an interesting case where HET-s(218-289) directly assembles into infectious fibril in the cell-free expression mixture without the requirement of denaturation procedures and purification. By introducing tailored 13C and 15N isotopes or CF3 and 13CH2F labels at strategic amino-acid positions, we demonstrate that cell-free synthesized amyloid fibrils are readily amenable to high-resolution magic-angle spinning NMR at sub-milligram quantity.
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9
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Blahut J, Brandl MJ, Pradhan T, Reif B, Tošner Z. Sensitivity-Enhanced Multidimensional Solid-State NMR Spectroscopy by Optimal-Control-Based Transverse Mixing Sequences. J Am Chem Soc 2022; 144:17336-17340. [PMID: 36074981 DOI: 10.1021/jacs.2c06568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, proton-detected magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy has become an attractive tool to study the structure and dynamics of insoluble proteins at atomic resolution. The sensitivity of the employed multidimensional experiments can be systematically improved when both transversal components of the magnetization are transferred simultaneously after an evolution period. The method of preservation of equivalent pathways has been explored in solution-state NMR; however, it does not find widespread application due to relaxation issues connected with increased molecular size. We present here for the first time heteronuclear transverse mixing sequences for correlation experiments at moderate and fast MAS frequencies. Optimal control allows to boost the signal-to-noise ratio (SNR) beyond the expected factor of 2 for each indirect dimension. In addition to the carbon-detected sensitivity-enhanced 2D NCA experiment, we present a novel proton-detected, doubly sensitivity-enhanced 3D hCANH pulse sequence for which we observe a 3-fold improvement in SNR compared to the conventional experimental implementation. The sensitivity gain turned out to be essential to unambiguously characterize a minor fibril polymorph of a human lambda-III immunoglobulin light chain protein that escaped detection so far.
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Affiliation(s)
- Jan Blahut
- Department of Chemistry, Faculty of Science, Charles University, Albertov 6, 12842 Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16610, Prague, Czech Republic
| | - Matthias J Brandl
- Bayerisches NMR Zentrum (BNMRZ) at Department Chemie, Technische Universität München (TUM), 85747 Garching, Germany
| | - Tejaswini Pradhan
- Bayerisches NMR Zentrum (BNMRZ) at Department Chemie, Technische Universität München (TUM), 85747 Garching, Germany
| | - Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at Department Chemie, Technische Universität München (TUM), 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, 85764 Neuherberg, Germany
| | - Zdeněk Tošner
- Department of Chemistry, Faculty of Science, Charles University, Albertov 6, 12842 Prague, Czech Republic
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Zhang Z, Su Y, Xiao H, Yang J. Selective Nuclear Magnetic Resonance Method for Enhancing Long-Range Heteronuclear Correlations in Solids. J Phys Chem Lett 2022; 13:6376-6382. [PMID: 35796704 DOI: 10.1021/acs.jpclett.2c01527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The long-range heteronuclear correlation remains a significant challenge in solid-state nuclear magnetic resonance (NMR), which is critical in the structural elucidation of biomolecular, material, and pharmaceutical solids. We propose a selective NMR method, heteronuclear selective phase-optimized recoupling (hetSPR), to selectively enhance long-range correlations of interest by utilizing characteristic chemical shifts. Compared to conventional methods, hetSPR can selectively enhance desired heteronuclear correlations (e.g., 1H-13C and 1H-19F) by factors up to 5 and largely suppress the unwanted ones. The method proves useful by enhancing the long-range correlation from an intermolecular 1H-19F distance of 4.8 Å by a factor of 2.4 in a fluorinated pharmaceutical drug, bicalutamide, under fast magic-angle spinning. It does not use selective pulses and is thus user-friendly even for nonexperts. The new method is expected to boost solid-state NMR to elucidate the structures of various solids.
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Affiliation(s)
- Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yongchao Su
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, the University of Texas at Austin, Austin, Texas 78712, United States
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Hang Xiao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
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11
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Akbey Ü, Andreasen M. Functional amyloids from bacterial biofilms - structural properties and interaction partners. Chem Sci 2022; 13:6457-6477. [PMID: 35756505 PMCID: PMC9172111 DOI: 10.1039/d2sc00645f] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/05/2022] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation and amyloid formation have historically been linked with various diseases such as Alzheimer's and Parkinson's disease, but recently functional amyloids have gained a great deal of interest in not causing a disease and having a distinct function in vivo. Functional bacterial amyloids form the structural scaffold in bacterial biofilms and provide a survival strategy for the bacteria along with antibiotic resistance. The formation of functional amyloids happens extracellularly which differs from most disease related amyloids. Studies of functional amyloids have revealed several distinctions compared to disease related amyloids including primary structures designed to optimize amyloid formation while still retaining a controlled assembly of the individual subunits into classical cross-β-sheet structures, along with a unique cross-α-sheet amyloid fold. Studies have revealed that functional amyloids interact with components found in the extracellular matrix space such as lipids from membranes and polymers from the biofilm. Intriguingly, a level of complexity is added as functional amyloids also interact with several disease related amyloids and a causative link has even been established between functional amyloids and neurodegenerative diseases. It is hence becoming increasingly clear that functional amyloids are not inert protein structures found in bacterial biofilms but interact with many different components including human proteins related to pathology. Gaining a clear understanding of the factors governing the interactions will lead to improved strategies to combat biofilm associated infections and the correlated antibiotic resistance. In the current review we summarize the current state of the art knowledge on this exciting and fast growing research field of biofilm forming bacterial functional amyloids, their structural features and interaction partners.
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Affiliation(s)
- Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh Pittsburgh PA 15261 USA
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University Wilhelm Meyers Allé 3 8000 Aarhus Denmark
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12
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Xue K, Sarkar R, Tošner Z, Reif B. Field and magic angle spinning frequency dependence of proton resonances in rotating solids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:47-61. [PMID: 36113917 DOI: 10.1016/j.pnmrs.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Proton detection in solid state NMR is continuously developing and allows one to gain new insights in structural biology. Overall, this progress is a result of the synergy between hardware development, new NMR methodology and new isotope labeling strategies, to name a few factors. Even though current developments are rapid, it is worthwhile to summarize what can currently be achieved employing proton detection in biological solids. We illustrate this by analysing the signal-to-noise ratio (SNR) for spectra obtained for a microcrystalline α-spectrin SH3 domain protein sample by (i) employing different degrees of chemical dilution to replace protons by incorporating deuterons in different sites, by (ii) variation of the magic angle spinning (MAS) frequencies between 20 and 110 kHz, and by (iii) variation of the static magnetic field B0. The experimental SNR values are validated with numerical simulations employing up to 9 proton spins. Although in reality a protein would contain far more than 9 protons, in a deuterated environment this is a sufficient number to achieve satisfactory simulations consistent with the experimental data. The key results of this analysis are (i) with current hardware, deuteration is still necessary to record spectra of optimum quality; (ii) 13CH3 isotopomers for methyl groups yield the best SNR when MAS frequencies above 100 kHz are available; and (iii) sensitivity increases with a factor beyond B0 3/2 with the static magnetic field due to a transition of proton-proton dipolar interactions from a strong to a weak coupling limit.
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Affiliation(s)
- Kai Xue
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology, Am Fassberg. 11, Goettingen, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
| | - Zdeněk Tošner
- Department of Chemistry, Faculty of Science, Charles University, Hlavova 8, 12842 Praha 2, Czech Republic
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.
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13
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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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14
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Akbey Ü. Site-specific protein methyl deuterium quadrupolar patterns by proton-detected 3D 2H- 13C- 1H MAS NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2022; 76:23-28. [PMID: 34997409 DOI: 10.1007/s10858-021-00388-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Determination of protein structure and dynamics is key to understand the mechanism of protein action. Perdeuterated proteins have been used to obtain high resolution/sensitivty NMR experiments via proton-detection. These methods utilizes 1H, 13C and 15N nuclei for chemical shift dispersion or relaxation probes, despite the existing abundant deuterons. However, a high-sensitivity NMR method to utilize deuterons and e.g. determine site-specific deuterium quadrupolar pattern information has been lacking due to technical difficulties associated with deuterium's large quadrupolar couplings. Here, we present a novel deuterium-excited and proton-detected three-dimensional 2H-13C-1H MAS NMR experiment to utilize deuterons and to obtain site-specific methyl 2H quadrupolar patterns on detuterated proteins for the first time. A high-resolution fingerprint 1H-15N HSQC-spectrum is correlated with the anisotropic deuterium quadrupolar tensor in the third dimension. Results from a model perdeuterated protein has been shown.
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Affiliation(s)
- Ümit Akbey
- Radboud University, Magnetic Resonance Research Center, Institute for Molecules and Materials, Nijmegen, The Netherlands.
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, USA.
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15
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Paluch P, Augustyniak R, Org ML, Vanatalu K, Kaldma A, Samoson A, Stanek J. NMR Assignment of Methyl Groups in Immobilized Proteins Using Multiple-Bond 13C Homonuclear Transfers, Proton Detection, and Very Fast MAS. Front Mol Biosci 2022; 9:828785. [PMID: 35425812 PMCID: PMC9002630 DOI: 10.3389/fmolb.2022.828785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
In nuclear magnetic resonance spectroscopy of proteins, methyl protons play a particular role as extremely sensitive reporters on dynamics, allosteric effects, and protein–protein interactions, accessible even in high-molecular-weight systems approaching 1 MDa. The notorious issue of their chemical shift assignment is addressed here by a joint use of solid-state 1H-detected methods at very fast (nearly 100 kHz) magic-angle spinning, partial deuteration, and high-magnetic fields. The suitability of a series of RF schemes is evaluated for the efficient coherence transfer across entire 13C side chains of methyl-containing residues, which is key for establishing connection between methyl and backbone 1H resonances. The performance of ten methods for recoupling of either isotropic 13C–13C scalar or anisotropic dipolar interactions (five variants of TOBSY, FLOPSY, DIPSI, WALTZ, RFDR, and DREAM) is evaluated experimentally at two state-of-the-art magic-angle spinning (55 and 94.5 kHz) and static magnetic field conditions (18.8 and 23.5 T). Model isotopically labeled compounds (alanine and Met-Leu-Phe tripeptide) and ILV-methyl and amide-selectively protonated, and otherwise deuterated chicken α-spectrin SH3 protein are used as convenient reference systems. Spin dynamics simulations in SIMPSON are performed to determine optimal parameters of these RF schemes, up to recently experimentally attained spinning frequencies (200 kHz) and B0 field strengths (28.2 T). The concept of linearization of 13C side chain by appropriate isotope labeling is revisited and showed to significantly increase sensitivity of methyl-to-backbone correlations. A resolution enhancement provided by 4D spectroscopy with non-uniform (sparse) sampling is demonstrated to remove ambiguities in simultaneous resonance assignment of methyl proton and carbon chemical shifts.
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Affiliation(s)
- Piotr Paluch
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Łódź, Poland
| | | | - Mai-Liis Org
- Tallin University of Technology, Tallinn, Estonia
| | | | - Ats Kaldma
- Tallin University of Technology, Tallinn, Estonia
| | - Ago Samoson
- Tallin University of Technology, Tallinn, Estonia
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- *Correspondence: Jan Stanek,
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16
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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17
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Klein A, Vasa SK, Söldner B, Grohe K, Linser R. Unambiguous Side-Chain Assignments for Solid-State NMR Structure Elucidation of Nondeuterated Proteins via a Combined 5D/4D Side-Chain-to-Backbone Experiment. J Phys Chem Lett 2022; 13:1644-1651. [PMID: 35147439 DOI: 10.1021/acs.jpclett.1c04075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Owing to fast-magic-angle-spinning technology, proton-detected solid-state NMR has been facilitating the analysis of insoluble, crystalline, sedimented, and membrane proteins. However, potential applications have been largely restricted by limited access to side-chain resonances. The recent availability of spinning frequencies exceeding 100 kHz in principle now allows direct probing of all protons without the need for partial deuteration. This potentiates both the number of accessible target proteins and possibilities to exploit side-chain protons as reporters on distances and interactions. Their low dispersion, however, has severely compromised their chemical-shift assignment, which is a prerequisite for their use in downstream applications. Herein, we show that unambiguous correlations are obtained from 5D methodology by which the side-chain resonances are directly connected with the backbone. When further concatenated with simultaneous 4D intra-side-chain correlations, this yields comprehensive assignments in the side chains and hence allows a high density of distance restraints for high-resolution structure calculation from minimal amounts of protein.
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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
| | - Benedikt Söldner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Kristof Grohe
- 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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18
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Najbauer EE, Tekwani Movellan K, Giller K, Benz R, Becker S, Griesinger C, Andreas LB. Structure and Gating Behavior of the Human Integral Membrane Protein VDAC1 in a Lipid Bilayer. J Am Chem Soc 2022; 144:2953-2967. [PMID: 35164499 PMCID: PMC8874904 DOI: 10.1021/jacs.1c09848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The voltage-dependent
anion channel (VDAC), the most abundant protein
in the outer mitochondrial membrane, is responsible for the transport
of all ions and metabolites into and out of mitochondria. Larger than
any of the β-barrel structures determined to date by magic-angle
spinning (MAS) NMR, but smaller than the size limit of cryo-electron
microscopy (cryo-EM), VDAC1’s 31 kDa size has long been a bottleneck
in determining its structure in a near-native lipid bilayer environment.
Using a single two-dimensional (2D) crystalline sample of human VDAC1
in lipids, we applied proton-detected fast magic-angle spinning NMR
spectroscopy to determine the arrangement of β strands. Combining
these data with long-range restraints from a spin-labeled sample,
chemical shift-based secondary structure prediction, and previous
MAS NMR and atomic force microscopy (AFM) data, we determined the
channel’s structure at a 2.2 Å root-mean-square deviation
(RMSD). The structure, a 19-stranded β-barrel, with an N-terminal
α-helix in the pore is in agreement with previous data in detergent,
which was questioned due to the potential for the detergent to perturb
the protein’s functional structure. Using a quintuple mutant
implementing the channel’s closed state, we found that dynamics
are a key element in the protein’s gating behavior, as channel
closure leads to the destabilization of not only the C-terminal barrel
residues but also the α2 helix. We showed that cholesterol,
previously shown to reduce the frequency of channel closure, stabilizes
the barrel relative to the N-terminal helix. Furthermore, we observed
channel closure through steric blockage by a drug shown to selectively
bind to the channel, the Bcl2-antisense oligonucleotide G3139.
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Affiliation(s)
- Eszter E Najbauer
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Roland Benz
- Life Sciences and Chemistry, Jacobs University of Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
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19
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Nimerovsky E, Najbauer EE, Movellan KT, Xue K, Becker S, Andreas LB. Modest Offset Difference Internuclear Selective Transfer via Homonuclear Dipolar Coupling. J Phys Chem Lett 2022; 13:1540-1546. [PMID: 35133845 PMCID: PMC8859849 DOI: 10.1021/acs.jpclett.1c03871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Homonuclear dipolar recoupling is routinely used for magic-angle spinning NMR-based structure determination. In fully protonated samples, only short proton-proton distances are accessible to broadband recoupling approaches because of high proton density. Selective methods allow detection of longer distances by directing polarization to a subset of spins. Here we introduce the selective pulse sequence MODIST, which recouples spins that have a modest chemical shift offset difference, and demonstrate it to selectively record correlations between amide protons. The sequence was selected for good retention of total signal, leading to up to twice the intensity for proton-proton correlations compared with other selective methods. The sequence is effective across a range of spinning conditions and magnetic fields, here tested at 55.555 and 100 kHz magic-angle spinning and at proton Larmor frequencies from 600 to 1200 MHz. For influenza A M2 in lipid bilayers, cross-peaks characteristic of a helical conformation are observed.
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20
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Klein A, Rovó P, Sakhrani VV, Wang Y, Holmes JB, Liu V, Skowronek P, Kukuk L, Vasa SK, Güntert P, Mueller LJ, Linser R. Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR. Proc Natl Acad Sci U S A 2022; 119:e2114690119. [PMID: 35058365 PMCID: PMC8795498 DOI: 10.1073/pnas.2114690119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/13/2021] [Indexed: 02/07/2023] Open
Abstract
NMR chemical shifts provide detailed information on the chemical properties of molecules, thereby complementing structural data from techniques like X-ray crystallography and electron microscopy. Detailed analysis of protein NMR data, however, often hinges on comprehensive, site-specific assignment of backbone resonances, which becomes a bottleneck for molecular weights beyond 40 to 45 kDa. Here, we show that assignments for the (2x)72-kDa protein tryptophan synthase (665 amino acids per asymmetric unit) can be achieved via higher-dimensional, proton-detected, solid-state NMR using a single, 1-mg, uniformly labeled, microcrystalline sample. This framework grants access to atom-specific characterization of chemical properties and relaxation for the backbone and side chains, including those residues important for the catalytic turnover. Combined with first-principles calculations, the chemical shifts in the β-subunit active site suggest a connection between active-site chemistry, the electrostatic environment, and catalytically important dynamics of the portal to the β-subunit from solution.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Petra Rovó
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
| | - Varun V Sakhrani
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Yangyang Wang
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Jacob B Holmes
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Viktoriia Liu
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Patricia Skowronek
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
| | - Laura Kukuk
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Rasmus Linser
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany;
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
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21
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Xue K, Nimerovsky E, Tekwani Movellan KA, Becker S, Andreas LB. Backbone Torsion Angle Determination Using Proton Detected Magic-Angle Spinning Nuclear Magnetic Resonance. J Phys Chem Lett 2022; 13:18-24. [PMID: 34957837 PMCID: PMC8762656 DOI: 10.1021/acs.jpclett.1c03267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Protein torsion angles define the backbone secondary structure of proteins. Magic-angle spinning (MAS) NMR methods using carbon detection have been developed to measure torsion angles by determining the relative orientation between two anisotropic interactions─dipolar coupling or chemical shift anisotropy. Here we report a new proton-detection based method to determine the backbone torsion angle by recoupling NH and CH dipolar couplings within the HCANH pulse sequence, for protonated or partly deuterated samples. We demonstrate the efficiency and precision of the method with microcrystalline chicken α spectrin SH3 protein and the influenza A matrix 2 (M2) membrane protein, using 55 or 90 kHz MAS. For M2, pseudo-4D data detect a turn between transmembrane and amphipathic helices.
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22
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Tognetti J, Franks WT, Lewandowski JR, Brown SP. Optimisation of 1H PMLG homonuclear decoupling at 60 kHz MAS to enable 15N-1H through-bond heteronuclear correlation solid-state NMR spectroscopy. Phys Chem Chem Phys 2022; 24:20258-20273. [PMID: 35975627 PMCID: PMC9429863 DOI: 10.1039/d2cp01041k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Lee–Goldburg condition for homonuclear decoupling in 1H magic-angle spinning (MAS) solid-state NMR sets the angle θ, corresponding to arctan of the ratio of the rf nutation frequency, ν1, to the rf offset, to be the magic angle, θm, equal to tan−1(√2) = 54.7°. At 60 kHz MAS, we report enhanced decoupling compared to MAS alone in a 1H spectrum of 15N-glycine with at θ = 30° for a ν1 of ∼100 kHz at a 1H Larmor frequency, ν0, of 500 MHz and 1 GHz, corresponding to a high chemical shift scaling factor (λCS) of 0.82. At 1 GHz, we also demonstrate enhanced decoupling compared to 60 kHz MAS alone for a lower ν1 of 51 kHz, i.e., a case where the nutation frequency is less than the MAS frequency, with θ = 18°, λCS = 0.92. The ratio of the rotor period to the decoupling cycle time, Ψ = τr/τc, is in the range 0.53 to 0.61. Windowed decoupling using the optimised parameters for a ν1 of ∼100 kHz also gives good performance in a 1H spin-echo experiment, enabling implementation in a 1H-detected 15N–1H cross polarisation (CP)-refocused INEPT heteronuclear correlation NMR experiment. Specifically, initial 15N transverse magnetisation as generated by 1H–15N CP is transferred back to 1H using a refocused INEPT pulse sequence employing windowed 1H decoupling. Such an approach ensures the observation of through-bond N–H connectivities. For 15N-glycine, while the CP-refocused INEPT experiment has a lower sensitivity (∼50%) as compared to a double CP experiment (with a 200 μs 15N to 1H CP contact time), there is selectivity for the directly bonded NH3+ moiety, while intensity is observed for the CH21H resonances in the double CP experiment. Two-dimensional 15N–1H correlation MAS NMR spectra are presented for the dipeptide β-AspAla and the pharmaceutical cimetidine at 60 kHz MAS, both at natural isotopic abundance. For the dipeptide β-AspAla, different build-up dependence on the first spin-echo duration is observed for the NH and NH3+ moieties demonstrating that the experiment could be used to distinguish resonances for different NHx groups. 15N–1H heteronuclear NMR correlation at natural abundance in the solid state via J couplings is enabled by optimisation of phase-modulated Lee–Goldburg (PMLG) 1H homonuclear decoupling during the spin echoes, far from the ideal magic-angle condition.![]()
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Affiliation(s)
- Jacqueline Tognetti
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
| | - W Trent Franks
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
| | | | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
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23
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Baldus M. Biological solid-state NMR: Integrative across different scientific disciplines. J Struct Biol X 2022; 6:100075. [PMID: 36185734 PMCID: PMC9523391 DOI: 10.1016/j.yjsbx.2022.100075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/18/2022] [Accepted: 09/25/2022] [Indexed: 11/29/2022] Open
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24
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Franks WT, Tatman BP, Trenouth J, Lewandowski JR. Dipolar Order Parameters in Large Systems With Fast Spinning. Front Mol Biosci 2021; 8:791026. [PMID: 34957221 PMCID: PMC8699854 DOI: 10.3389/fmolb.2021.791026] [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: 10/07/2021] [Accepted: 11/05/2021] [Indexed: 12/01/2022] Open
Abstract
Order parameters are a useful tool for quantifying amplitudes of molecular motions. Here we measure dipolar order parameters by recoupling heteronuclear dipole-dipole couplings under fast spinning. We apply symmetry based recoupling methods to samples spinning under magic angle at 60 kHz by employing a variable flip angle compound inversion pulse. We validate the methods by measuring site-specific 15N-1H order parameters of a microcrystalline protein over a small temperature range and the same protein in a large, precipitated complex with antibody. The measurements of the order parameters in the complex are consistent with the observed protein undergoing overall motion within the assembly.
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Affiliation(s)
- W Trent Franks
- Department of Physics, University of Warwick, Coventry, United Kingdom.,Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Ben P Tatman
- Department of Physics, University of Warwick, Coventry, United Kingdom.,Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Jonah Trenouth
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
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25
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Cukkemane A, Becker N, Zielinski M, Frieg B, Lakomek NA, Heise H, Schröder GF, Willbold D, Weiergräber OH. Conformational heterogeneity coupled with β-fibril formation of a scaffold protein involved in chronic mental illnesses. Transl Psychiatry 2021; 11:639. [PMID: 34921141 PMCID: PMC8683410 DOI: 10.1038/s41398-021-01765-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/23/2021] [Accepted: 12/07/2021] [Indexed: 12/17/2022] Open
Abstract
Chronic mental illnesses (CMIs) pose a significant challenge to global health due to their complex and poorly understood etiologies and hence, absence of causal therapies. Research of the past two decades has revealed dysfunction of the disrupted in schizophrenia 1 (DISC1) protein as a predisposing factor involved in several psychiatric disorders. DISC1 is a multifaceted protein that serves myriads of functions in mammalian cells, for instance, influencing neuronal development and synapse maintenance. It serves as a scaffold hub forming complexes with a variety (~300) of partners that constitute its interactome. Herein, using combinations of structural and biophysical tools, we demonstrate that the C-region of the DISC1 protein is highly polymorphic, with important consequences for its physiological role. Results from solid-state NMR spectroscopy and electron microscopy indicate that the protein not only forms symmetric oligomers but also gives rise to fibrils closely resembling those found in certain established amyloid proteinopathies. Furthermore, its aggregation as studied by isothermal titration calorimetry (ITC) is an exergonic process, involving a negative enthalpy change that drives the formation of oligomeric (presumably tetrameric) species as well as β-fibrils. We have been able to narrow down the β-core region participating in fibrillization to residues 716-761 of full-length human DISC1. This region is absent in the DISC1Δ22aa splice variant, resulting in reduced association with proteins from the dynein motor complex, viz., NDE-like 1 (NDEL1) and lissencephaly 1 (LIS1), which are crucial during mitosis. By employing surface plasmon resonance, we show that the oligomeric DISC1 C-region has an increased affinity and shows cooperativity in binding to LIS1 and NDEL1, in contrast to the noncooperative binding mode exhibited by the monomeric version. Based on the derived structural models, we propose that the association between the binding partners involves two neighboring subunits of DISC1 C-region oligomers. Altogether, our findings highlight the significance of the DISC1 C-region as a crucial factor governing the balance between its physiological role as a multifunctional scaffold protein and aggregation-related aberrations with potential significance for disease.
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Affiliation(s)
- Abhishek Cukkemane
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Nina Becker
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Mara Zielinski
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Benedikt Frieg
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Nils-Alexander Lakomek
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Henrike Heise
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Gunnar F. Schröder
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany. .,Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.
| | - Oliver H. Weiergräber
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
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26
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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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27
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Liang L, Ji Y, Zhao Z, Quinn CM, Han X, Bao X, Polenova T, Hou G. Accurate heteronuclear distance measurements at all magic-angle spinning frequencies in solid-state NMR spectroscopy. Chem Sci 2021; 12:11554-11564. [PMID: 34567504 PMCID: PMC8409495 DOI: 10.1039/d1sc03194e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 07/20/2021] [Indexed: 11/21/2022] Open
Abstract
Heteronuclear dipolar coupling is indispensable in revealing vital information related to the molecular structure and dynamics, as well as intermolecular interactions in various solid materials. Although numerous approaches have been developed to selectively reintroduce heteronuclear dipolar coupling under MAS, most of them lack universality and can only be applied to limited spin systems. Herein, we introduce a new and robust technique dubbed phase modulated rotary resonance (PMRR) for reintroducing heteronuclear dipolar couplings while suppressing all other interactions under a broad range of MAS conditions. The standard PMRR requires the radiofrequency (RF) field strength of only twice the MAS frequency, can efficiently recouple the dipolar couplings with a large scaling factor of 0.50, and is robust to experimental imperfections. Moreover, the adjustable window modification of PMRR, dubbed wPMRR, can improve its performance remarkably, making it well suited for the accurate determination of dipolar couplings in various spin systems. The robust performance of such pulse sequences has been verified theoretically and experimentally via model compounds, at different MAS frequencies. The application of the PMRR technique was demonstrated on the H-ZSM-5 zeolite, where the interaction between the Brønsted acidic hydroxyl groups of H-ZSM-5 and the absorbed trimethylphosphine oxide (TMPO) were probed, revealing the detailed configuration of super acid sites.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, 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 Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yi Ji
- State Key Laboratory of Catalysis, 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 Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, 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 Dalian 116023 China
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware Newark Delaware 19716 USA
| | - Xiuwen Han
- State Key Laboratory of Catalysis, 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 Dalian 116023 China
| | - Xinhe Bao
- State Key Laboratory of Catalysis, 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 Dalian 116023 China
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware Newark Delaware 19716 USA
| | - Guangjin Hou
- State Key Laboratory of Catalysis, 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 Dalian 116023 China
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28
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Akbey Ü. Dynamics of uniformly labelled solid proteins between 100 and 300 K: A 2D 2H- 13C MAS NMR approach. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106974. [PMID: 33823335 DOI: 10.1016/j.jmr.2021.106974] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
We describe a 2H based MAS nuclear magnetic resonance (NMR) method to obtain site-specific molecular dynamics of biomolecules. The method utilizes the use of deuterium nucleus as a spin label that is proven to be very useful in dynamics studies of solid biological and functional materials. The aim is to understand overall characteristics of protein backbone and side-chain motions for CD3, CD2 and CD groups, in terms of timescale, type and activation energy of the underlying processes. Variable temperature two-dimensional (2D) 2H-13C correlation MAS NMR spectra were recorded for the uniformly 2H,13C,15N labelled Alanine and microcrystalline SH3 at a broad temperature range, from 320 K down to 100 K. First, the deuterium quadrupolar-coupling constant from specific D-C sites is obtained with the 2D experiment by utilizing carbon chemical shifts. Second, the static quadrupolar patterns are obtained at 100 K. Third, variable temperature approach enabled the observation of quadrupolar pattern over different motional regimes; slow, intermediate and fast. And finally, the apparent activation energies for C-D sites are determined and compared, by evaluating the temperature induced signal intensities. This information led to the determination of the dynamic processes for different D-C sites at a broad range of temperature and motional timescales. This is a first representation of 2D 2H-13C MAS NMR approach applied to fully isotope labelled deuterated protein covering 220 K temperature range.
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Affiliation(s)
- Ümit Akbey
- Weizmann Institute of Science, Department of Chemical and Biological Physics, Perlman Chemical Sciences Building, P.O. Box 26, Rehovot 76100, Israel.
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29
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Nimerovsky E, Movellan KT, Zhang XC, Forster MC, Najbauer E, Xue K, Dervişoǧlu R, Giller K, Griesinger C, Becker S, Andreas LB. Proton Detected Solid-State NMR of Membrane Proteins at 28 Tesla (1.2 GHz) and 100 kHz Magic-Angle Spinning. Biomolecules 2021; 11:752. [PMID: 34069858 PMCID: PMC8157399 DOI: 10.3390/biom11050752] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/25/2022] Open
Abstract
The available magnetic field strength for high resolution NMR in persistent superconducting magnets has recently improved from 23.5 to 28 Tesla, increasing the proton resonance frequency from 1 to 1.2 GHz. For magic-angle spinning (MAS) NMR, this is expected to improve resolution, provided the sample preparation results in homogeneous broadening. We compare two-dimensional (2D) proton detected MAS NMR spectra of four membrane proteins at 950 and 1200 MHz. We find a consistent improvement in resolution that scales superlinearly with the increase in magnetic field for three of the four examples. In 3D and 4D spectra, which are now routinely acquired, this improvement indicates the ability to resolve at least 2 and 2.5 times as many signals, respectively.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Loren B. Andreas
- Department for NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany; (E.N.); (K.T.M.); (X.C.Z.); (M.C.F.); (E.N.); (K.X.); (R.D.); (K.G.); (C.G.); (S.B.)
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30
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Narasimhan S, Pinto C, Lucini Paioni A, van der Zwan J, Folkers GE, Baldus M. Characterizing proteins in a native bacterial environment using solid-state NMR spectroscopy. Nat Protoc 2021; 16:893-918. [PMID: 33442051 DOI: 10.1038/s41596-020-00439-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 01/29/2023]
Abstract
For a long time, solid-state nuclear magnetic resonance (ssNMR) has been employed to study complex biomolecular systems at the detailed chemical, structural, or dynamic level. Recent progress in high-resolution and high-sensitivity ssNMR, in combination with innovative sample preparation and labeling schemes, offers novel opportunities to study proteins in their native setting irrespective of the molecular tumbling rate. This protocol describes biochemical preparation schemes to obtain cellular samples of both soluble as well as insoluble or membrane-associated proteins in bacteria. To this end, the protocol is suitable for studying a protein of interest in both whole cells and in cell envelope or isolated membrane preparations. In the first stage of the procedure, an appropriate strain of Escherichia coli (DE3) is transformed with a plasmid of interest harboring the protein of interest under the control of an inducible T7 promoter. Next, the cells are adapted to grow in minimal (M9) medium. Before the growth enters stationary phase, protein expression is induced, and shortly thereafter, the native E. coli RNA polymerase is inhibited using rifampicin for targeted labeling of the protein of interest. The cells are harvested after expression and prepared for ssNMR rotor filling. In addition to conventional 13C/15N-detected ssNMR, we also outline how these preparations can be readily subjected to multidimensional ssNMR experiments using dynamic nuclear polarization (DNP) or proton (1H) detection schemes. We estimate that the entire preparative procedure until NMR experiments can be started takes 3-5 days.
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Cecilia Pinto
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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31
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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: 155] [Impact Index Per Article: 51.7] [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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32
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Solid-state NMR approaches to investigate large enzymes in complex with substrates and inhibitors. Biochem Soc Trans 2020; 49:131-144. [PMID: 33367567 DOI: 10.1042/bst20200099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022]
Abstract
Enzyme catalysis is omnipresent in the cell. The mechanisms by which highly evolved protein folds enable rapid and specific chemical transformation of substrates belong to the marvels of structural biology. Targeting of enzymes with inhibitors has immediate application in drug discovery, from chemotherapeutics over antibiotics to antivirals. NMR spectroscopy combines multiple assets for the investigation of enzyme function. The non-invasive technique can probe enzyme structure and dynamics and map interactions with substrates, cofactors and inhibitors at the atomic level. With experiments performed at close to native conditions, catalytic transformations can be monitored in real time, giving access to kinetic parameters. The power of NMR in the solid state, in contrast with solution, lies in the absence of fundamental size limitations, which is crucial for enzymes that are either membrane-embedded or assemble into large soluble complexes exceeding hundreds of kilodaltons in molecular weight. Here we review recent progress in solid-state NMR methodology, which has taken big leaps in the past years due to steady improvements in hardware design, notably magic angle spinning, and connect it to parallel biochemical advances that enable isotope labelling of increasingly complex enzymes. We first discuss general concepts and requirements of the method and then highlight the state-of-the-art in sample preparation, structure determination, dynamics and interaction studies. We focus on examples where solid-state NMR has been instrumental in elucidating enzyme mechanism, alone or in integrative studies.
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33
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Krushelnitsky A, Saalwächter K. Relaxation-induced dipolar exchange with recoupling (RIDER) distortions in CODEX experiments. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:247-259. [PMID: 37904827 PMCID: PMC10500706 DOI: 10.5194/mr-1-247-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/22/2020] [Indexed: 11/01/2023]
Abstract
Chemical shift anisotropy (CSA) and dipolar CODEX (Cenralband Only Detection of EXchange) experiments enable abundant quantitative information on the reorientation of the CSA and dipolar tensors to be obtained on millisecond-second timescales. At the same time, proper performance of the experiments and data analysis can often be a challenge since CODEX is prone to some interfering effects that may lead to incorrect interpretation of the experimental results. One of the most important such effects is RIDER (relaxation-induced dipolar exchange with recoupling). It appears due to the dipolar interaction of the observed X nuclei with some other nuclei, which causes an apparent decay in the mixing time dependence of the signal intensity reflecting not molecular motion, but spin flips of the adjacent nuclei. This may hamper obtaining correct values of the parameters of molecular mobility. In this contribution we consider in detail the reasons why the RIDER distortions remain even under decoupling conditions and propose measures to eliminate them. That is, we suggest (1) using an additional Z filter between the cross-polarization (CP) section and the CODEX recoupling blocks that suppresses the interfering anti-phase coherence responsible for the X -H RIDER and (2) recording only the cosine component of the CODEX signal since it is less prone to the RIDER distortions in comparison to the sine component. The experiments were conducted on rigid model substances as well as microcrystalline 2 H / 15 N-enriched proteins (GB1 and SH3) with a partial back-exchange of labile protons. Standard CSA and dipolar CODEX experiments reveal a fast-decaying component in the mixing time dependence of 15 N nuclei in proteins, which can be misinterpreted as a slow overall protein rocking motion. However, the RIDER-free experimental setup provides flat mixing time dependences, meaning that the studied proteins do not undergo global motions on the millisecond timescale.
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Affiliation(s)
- Alexey Krushelnitsky
- Institute of Physics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Kay Saalwächter
- Institute of Physics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
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34
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Zhang Z, Oss A, Org ML, Samoson A, Li M, Tan H, Su Y, Yang J. Selectively Enhanced 1H- 1H Correlations in Proton-Detected Solid-State NMR under Ultrafast MAS Conditions. J Phys Chem Lett 2020; 11:8077-8083. [PMID: 32880459 DOI: 10.1021/acs.jpclett.0c02412] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Proton-detected solid-state NMR has emerged as a powerful analytical technique in structural elucidation via 1H-1H correlations, which are mostly established by broadband methods. We propose a new class of frequency-selective homonuclear recoupling methods to selectively enhance 1H-1H correlations of interest under ultrafast magic-angle spinning (MAS). These methods, dubbed as selective phase-optimized recoupling (SPR), can provide a sensitivity enhancement by a factor of ∼3 over the widely used radio-frequency-driven recoupling (RFDR) to observe 1HN-1HN contacts in a protonated tripeptide N-formyl-Met-Leu-Phe (fMLF) under 150 kHz MAS and are successfully utilized to probe a long-range 1H-1H contact in a pharmaceutical molecule, the hydrochloride form of pioglitazone (PIO-HCl). SPR is not only highly efficient in frequency-selective recoupling but also easy to implement, imparting to it great potential to probe 1H-1H contacts for the structural elucidation of organic solids such as proteins and pharmaceuticals under ultrafast MAS conditions.
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Affiliation(s)
- Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Andres Oss
- Tallinn University of Technology, Tallinn 19086, Estonia
| | - Mai-Liis Org
- Tallinn University of Technology, Tallinn 19086, Estonia
| | - Ago Samoson
- Tallinn University of Technology, Tallinn 19086, Estonia
| | - Mingyue Li
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Huan Tan
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
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35
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Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies. Viruses 2020; 12:v12101069. [PMID: 32987909 PMCID: PMC7599928 DOI: 10.3390/v12101069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Structural virology reveals the architecture underlying infection. While notably electron microscopy images have provided an atomic view on viruses which profoundly changed our understanding of these assemblies incapable of independent life, spectroscopic techniques like NMR enter the field with their strengths in detailed conformational analysis and investigation of dynamic behavior. Typically, the large assemblies represented by viral particles fall in the regime of biological high-resolution solid-state NMR, able to follow with high sensitivity the path of the viral proteins through their interactions and maturation steps during the viral life cycle. We here trace the way from first solid-state NMR investigations to the state-of-the-art approaches currently developing, including applications focused on HIV, HBV, HCV and influenza, and an outlook to the possibilities opening in the coming years.
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Gopinath T, Weber DK, Veglia G. Multi-receiver solid-state NMR using polarization optimized experiments (POE) at ultrafast magic angle spinning. JOURNAL OF BIOMOLECULAR NMR 2020; 74:267-285. [PMID: 32333193 PMCID: PMC7236978 DOI: 10.1007/s10858-020-00316-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/11/2020] [Indexed: 05/04/2023]
Abstract
Ultrafast magic angle spinning (MAS) technology and 1H detection have dramatically enhanced the sensitivity of solid-state NMR (ssNMR) spectroscopy of biopolymers. We previously showed that, when combined with polarization optimized experiments (POE), these advancements enable the simultaneous acquisition of multi-dimensional 1H- or 13C-detected experiments using a single receiver. Here, we propose a new sub-class within the POE family, namely HC-DUMAS, HC-MEIOSIS, and HC-MAeSTOSO, that utilize dual receiver technology for the simultaneous detection of 1H and 13C nuclei. We also expand this approach to record 1H-, 13C-, and 15N-detected homonuclear 2D spectra simultaneously using three independent receivers. The combination of POE and multi-receiver technology will further shorten the total experimental time of ssNMR experiments for biological solids.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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Friedrich D, Perodeau J, Nieuwkoop AJ, Oschkinat H. MAS NMR detection of hydrogen bonds for protein secondary structure characterization. JOURNAL OF BIOMOLECULAR NMR 2020; 74:247-256. [PMID: 32185644 PMCID: PMC7211791 DOI: 10.1007/s10858-020-00307-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/09/2020] [Indexed: 05/26/2023]
Abstract
Hydrogen bonds are essential for protein structure and function, making experimental access to long-range interactions between amide protons and heteroatoms invaluable. Here we show that measuring distance restraints involving backbone hydrogen atoms and carbonyl- or α-carbons enables the identification of secondary structure elements based on hydrogen bonds, provides long-range contacts and validates spectral assignments. To this end, we apply specifically tailored, proton-detected 3D (H)NCOH and (H)NCAH experiments under fast magic angle spinning (MAS) conditions to microcrystalline samples of SH3 and GB1. We observe through-space, semi-quantitative correlations between protein backbone carbon atoms and multiple amide protons, enabling us to determine hydrogen bonding patterns and thus to identify β-sheet topologies and α-helices in proteins. Our approach shows the value of fast MAS and suggests new routes in probing both secondary structure and the role of functionally-relevant protons in all targets of solid-state MAS NMR.
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Affiliation(s)
- Daniel Friedrich
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA, 02215, USA
| | - Jacqueline Perodeau
- Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Rd., Piscataway, NJ, 08854, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Rd., Piscataway, NJ, 08854, United States.
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany.
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Kaur H, Grahl A, Hartmann JB, Hiller S. Sample Preparation and Technical Setup for NMR Spectroscopy with Integral Membrane Proteins. Methods Mol Biol 2020; 2127:373-396. [PMID: 32112334 DOI: 10.1007/978-1-0716-0373-4_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
NMR spectroscopy is a method of choice to characterize structure, function, and dynamics of integral membrane proteins at atomic resolution. Here, we describe protocols for sample preparation and characterization by NMR spectroscopy of two integral membrane proteins with different architecture, the α-helical membrane protein MsbA and the β-barrel membrane protein BamA. The protocols describe recombinant expression in E. coli, protein refolding, purification, and reconstitution in suitable membrane mimetics, as well as key setup steps for basic NMR experiments. These include experiments on protein samples in the solid state under magic angle spinning (MAS) conditions and experiments on protein samples in aqueous solution. Since MsbA and BamA are typical examples of their respective architectural classes, the protocols presented here can also serve as a reference for other integral membrane proteins.
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Affiliation(s)
- Hundeep Kaur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
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Burakova E, Vasa SK, Klein A, Linser R. Non-uniform sampling in quantitative assessment of heterogeneous solid-state NMR line shapes. JOURNAL OF BIOMOLECULAR NMR 2020; 74:71-82. [PMID: 31834579 DOI: 10.1007/s10858-019-00291-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Non-uniform sampling has been successfully used for solution and solid-state NMR of homogeneous samples. In the solid state, protein samples are often dominated by inhomogeneous contributions to the homogeneous line widths. In spite of different technical strategies for peak reconstruction by different methods, we validate that NUS can generally be used also for such situations where spectra are made up of complex peak shapes rather than Lorentian lines. Using the RMSD between subsampled and reconstructed data and those spectra obtained with uniform sampling for a sample comprising a wide conformational distribution, we quantitatively evaluate the identity of inhomogeneous peak patterns. The evaluation comprises Iterative Soft Thresholding (hmsIST implementation) as a method explicitly not assuming Lorentian lineshapes, as well as Sparse Multidimensional Iterative Lineshape Enhanced (SMILE) algorithm and Signal Separation Algorithm (SSA) reconstruction, which do work on the basis of Lorentian lineshape models, with different sampling densities. Even though individual peculiarities are apparent, all methods turn out principally viable to reconstruct the heterogeneously broadened peak shapes.
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Affiliation(s)
- Ekaterina Burakova
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
| | - Suresh K Vasa
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
| | - Alexander Klein
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
| | - Rasmus Linser
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany.
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Jekhmane S, Prachar M, Pugliese R, Fontana F, Medeiros‐Silva J, Gelain F, Weingarth M. Design Parameters of Tissue‐Engineering Scaffolds at the Atomic Scale. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shehrazade Jekhmane
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Marek Prachar
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Raffaele Pugliese
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
| | - Federico Fontana
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
- ASST Grande Ospedale Metropolitano NiguardaCenter for Nanomedicine and Tissue Engineering Piazza dell'Ospedale Maggiore 3 20162 Milan Italy
| | - João Medeiros‐Silva
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Fabrizio Gelain
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
- ASST Grande Ospedale Metropolitano NiguardaCenter for Nanomedicine and Tissue Engineering Piazza dell'Ospedale Maggiore 3 20162 Milan Italy
| | - Markus Weingarth
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
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41
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Asami S, Reif B. Accessing Methyl Groups in Proteins via 1H-detected MAS Solid-state NMR Spectroscopy Employing Random Protonation. Sci Rep 2019; 9:15903. [PMID: 31685894 PMCID: PMC6828780 DOI: 10.1038/s41598-019-52383-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/16/2019] [Indexed: 11/09/2022] Open
Abstract
We recently introduced RAP (reduced adjoining protonation) labelling as an easy to implement and cost-effective strategy to yield selectively methyl protonated protein samples. We show here that even though the amount of H2O employed in the bacterial growth medium is rather low, the intensities obtained in MAS solid-state NMR 1H,13C correlation spectra are comparable to spectra obtained for samples in which α-ketoisovalerate was employed as precursor. In addition to correlations for Leu and Val residues, RAP labelled samples yield also resonances for all methyl containing side chains. The labelling scheme has been employed to quantify order parameters, together with the respective asymmetry parameters. We obtain a very good correlation between the order parameters measured using a GlcRAP (glucose carbon source) and a α-ketoisovalerate labelled sample. The labelling scheme holds the potential to be very useful for the collection of long-range distance restraints among side chain atoms. Experiments are demonstrated using RAP and α-ketoisovalerate labelled samples of the α-spectrin SH3 domain, and are applied to fibrils formed from the Alzheimer's disease Aβ1-40 peptide.
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Affiliation(s)
- Sam Asami
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Bernd Reif
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, 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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42
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Xue K, Sarkar R, Tosner Z, Lalli D, Motz C, Koch B, Pintacuda G, Reif B. MAS dependent sensitivity of different isotopomers in selectively methyl protonated protein samples in solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2019; 73:625-631. [PMID: 31515660 DOI: 10.1007/s10858-019-00274-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Sensitivity and resolution together determine the quality of NMR spectra in biological solids. For high-resolution structure determination with solid-state NMR, proton-detection emerged as an attractive strategy in the last few years. Recent progress in probe technology has extended the range of available MAS frequencies up to above 100 kHz, enabling the detection of resolved resonances from sidechain protons, which are important reporters of structure. Here we characterise the interplay between MAS frequency in the newly available range of 70-110 kHz and proton content on the spectral quality obtainable on a 1 GHz spectrometer for methyl resonances. Variable degrees of proton densities are tested on microcrystalline samples of the α-spectrin SH3 domain with selectively protonated methyl isotopomers (CH3, CH2D, CHD2) in a perdeuterated matrix. The experimental results are supported by simulations that allow the prediction of the sensitivity outside this experimental frequency window. Our results facilitate the selection of the appropriate labelling scheme at a given MAS rotation frequency.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Zdenek Tosner
- Department of Chemistry, Faculty of Science, Charles University, Hlavova 8, 12842, Prague 2, Czech Republic
| | - Daniela Lalli
- Centre de Résonance Magnétique Nucléaire a Très hauts Champs (FRE 2034, CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100, Villeurbanne, France
| | - Carina Motz
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Benita Koch
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire a Très hauts Champs (FRE 2034, CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100, Villeurbanne, France
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale Amedeo Avogadro, Viale Teresa Michel, 15121, Alessandria, Italy
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
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43
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Jekhmane S, Prachar M, Pugliese R, Fontana F, Medeiros-Silva J, Gelain F, Weingarth M. Design Parameters of Tissue-Engineering Scaffolds at the Atomic Scale. Angew Chem Int Ed Engl 2019; 58:16943-16951. [PMID: 31573131 PMCID: PMC6899630 DOI: 10.1002/anie.201907880] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/03/2019] [Indexed: 01/08/2023]
Abstract
Stem-cell behavior is regulated by the material properties of the surrounding extracellular matrix, which has important implications for the design of tissue-engineering scaffolds. However, our understanding of the material properties of stem-cell scaffolds is limited to nanoscopic-to-macroscopic length scales. Herein, a solid-state NMR approach is presented that provides atomic-scale information on complex stem-cell substrates at near physiological conditions and at natural isotope abundance. Using self-assembled peptidic scaffolds designed for nervous-tissue regeneration, we show at atomic scale how scaffold-assembly degree, mechanics, and homogeneity correlate with favorable stem cell behavior. Integration of solid-state NMR data with molecular dynamics simulations reveals a highly ordered fibrillar structure as the most favorable stem-cell scaffold. This could improve the design of tissue-engineering scaffolds and other self-assembled biomaterials.
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Affiliation(s)
- Shehrazade Jekhmane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Marek Prachar
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Raffaele Pugliese
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy
| | - Federico Fontana
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy.,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Fabrizio Gelain
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy.,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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Goldbourt A. Structural characterization of bacteriophage viruses by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:192-210. [PMID: 31779880 DOI: 10.1016/j.pnmrs.2019.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/03/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Magic-angle spinning (MAS) solid-state NMR has provided structural insights into various bacteriophage systems including filamentous, spherical, and tailed bacteriophage viruses. A variety of methodologies have been utilized including elementary two and three-dimensional assignment experiments, proton-detection techniques at fast spinning speeds, non-uniform sampling, structure determination protocols, conformational dynamics revealed by recoupling of anisotropic interactions, and enhancement by dynamic nuclear polarization. This review summarizes most of the studies performed during the last decade by MAS techniques and makes comparisons with prior knowledge obtained from static and solution NMR techniques. Chemical shifts for the capsids of the various systems are reported and analyzed, and DNA shifts are reported and discussed in the context of general high molecular-weight DNA molecules. Chemical shift and torsion angle prediction techniques are compared and applied to the various phage systems. The structures of the intact M13 filamentous bacteriophage and that of the Acinetobacter phage AP205 capsid, determined using MAS-based experimental data, are presented. Finally, filamentous phages, which are highly rigid systems, show interesting dynamics at the interface of the capsid and DNA, and their mutual electrostatic interactions are shown to be mediated by highly mobile positively charged residues. Novel results obtained from recoupling the chemical shift anisotropy of a single arginine in IKe phage, which is in contact with its DNA, further demonstrate this point. MAS NMR thus provides many new insights into phage structure, and on the other hand the richness, complexity and variety of bacteriophage systems provide opportunities for new NMR methodologies and technique developments.
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Affiliation(s)
- Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
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Xue K, Mamone S, Koch B, Sarkar R, Reif B. Determination of methyl order parameters using solid state NMR under off magic angle spinning. JOURNAL OF BIOMOLECULAR NMR 2019; 73:471-475. [PMID: 31407204 DOI: 10.1007/s10858-019-00253-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/07/2019] [Indexed: 06/10/2023]
Abstract
Quantification of dipolar couplings in biological solids is important for the understanding of dynamic processes. Under Magic Angle Spinning (MAS), order parameters are normally obtained by recoupling of anisotropic interactions involving the application of radio frequency pulses. We have recently shown that amide backbone order parameters can be estimated accurately in a spin-echo experiment in case the rotor spinning angle is slightly mis-calibrated. In this work, we apply this method to determine methyl order parameters in a deuterated sample of the SH3 domain of chicken α-spectrin in which the methyl containing side chains valine and leucine are selectively protonated.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Benita Koch
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
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46
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Hwang S, Öster C, Chevelkov V, Giller K, Lange S, Becker S, Lange A. Characterization of H/D exchange in type 1 pili by proton-detected solid-state NMR and molecular dynamics simulations. JOURNAL OF BIOMOLECULAR NMR 2019; 73:281-291. [PMID: 31028572 PMCID: PMC6692446 DOI: 10.1007/s10858-019-00247-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Uropathogenic Escherichia coli invades and colonizes hosts by attaching to cells using adhesive pili on the bacterial surface. Although many biophysical techniques have been used to study the structure and mechanical properties of pili, many important details are still unknown. Here we use proton-detected solid-state NMR experiments to investigate solvent accessibility and structural dynamics. Deuterium back-exchange at labile sites of the perdeuterated, fully proton back-exchanged pili was conducted to investigate hydrogen/deuterium (H/D) exchange patterns of backbone amide protons in pre-assembled pili. We found distinct H/D exchange patterns in lateral and axial intermolecular interfaces in pili. Amide protons protected from H/D exchange in pili are mainly located in the core region of the monomeric subunit and in the lateral intermolecular interface, whereas the axial intermolecular interface and the exterior region of pili are highly exposed to H/D exchange. Additionally, we performed molecular dynamics simulations of the type 1 pilus rod and estimated the probability of H/D exchange based on hydrogen bond dynamics. The comparison of the experimental observables and simulation data provides insights into stability and mechanical properties of pili.
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Affiliation(s)
- Songhwan Hwang
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
- Institut für Biologie, Humboldt-Universität Zu Berlin, Berlin, Germany.
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Zhang R, Duong NT, Nishiyama Y. Resolution enhancement and proton proximity probed by 3D TQ/DQ/SQ proton NMR spectroscopy under ultrafast magic-angle-spinning beyond 70 kHz. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 304:78-86. [PMID: 31146121 DOI: 10.1016/j.jmr.2019.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/15/2019] [Accepted: 05/18/2019] [Indexed: 06/09/2023]
Abstract
Proton nuclear magnetic resonance (NMR) in solid state has gained significant attention in recent years due to the remarkable resolution and sensitivity enhancement afforded by ultrafast magic-angle-spinning (MAS). In spite of the substantial suppression of 1H-1H dipolar couplings, the proton spectral resolution is still poor compared to that of 13C or 15N NMR, rendering it challenging for the structural and conformational analysis of complex chemicals or biological solids. Herein, by utilizing the benefits of double-quantum (DQ) and triple-quantum (TQ) coherences, we propose a 3D single-channel pulse sequence that correlates proton triple-quantum/double-quantum/single-quantum (TQ/DQ/SQ) chemical shifts. In addition to the two-spin proximity information, this 3D TQ/DQ/SQ pulse sequence enables more reliable extraction of three-spin proximity information compared to the regular 2D TQ/SQ correlation experiment, which could aid in revealing the proton network in solids. Furthermore, the TQ/DQ slice taken at a specific SQ chemical shift only reveals the local correlations to the corresponding SQ chemical shift, and thus it enables accurate assignments of the proton peaks along the TQ and DQ dimensions and simplifies the interpretation of proton spectra especially for dense proton networks. The high performance of this 3D pulse sequence is well demonstrated on small compounds, L-alanine and a tripeptide, N-formyl-L-methionyl-L-leucyl-L-phenylalanine (MLF). We expect that this new methodology can inspire the development of multidimensional solid-state NMR pulse sequences using the merits of TQ and DQ coherences and enable high-throughput investigations of complex solids using abundant protons.
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Affiliation(s)
- Rongchun Zhang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, PR China.
| | - Nghia Tuan Duong
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Nishiyama
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
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Shcherbakov AA, Mandala VS, Hong M. High-Sensitivity Detection of Nanometer 1H- 19F Distances for Protein Structure Determination by 1H-Detected Fast MAS NMR. J Phys Chem B 2019; 123:4387-4391. [PMID: 31034230 PMCID: PMC7012536 DOI: 10.1021/acs.jpcb.9b03812] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein structure determination by solid-state NMR requires the measurement of many interatomic distances through dipole-dipole couplings. To obtain multiple long-range distance restraints rapidly and with high sensitivity, here we demonstrate a new 1H-detected fast magic-angle-spinning NMR technique that yields many long distances in a two-dimensional (2D)-resolved fashion. The distances are measured up to ∼15 Å, with an accuracy of better than 10%, between 1H and 19F, two nuclear spins that have the highest gyromagnetic ratios. Exogenous fluorines are sparsely introduced into the aromatic residues of the protein, which is perdeuterated and back-exchanged to give amide protons. This 1H-19F distance experiment, termed 2D heteronuclear single-quantum coherence rotational-echo double-resonance (HSQC-REDOR), is demonstrated on the singly fluorinated model protein, GB1. We extracted 33 distances between 5-19F-Trp43 and backbone amide protons, using 2D spectral series that were measured in less than 3 days. Combining these 1H-19F distance restraints with 13C-19F distances and chemical shifts, we calculated a GB1 structure with a backbone root-mean-square deviation of 1.73 Å from the high-resolution structure. This 1H-detected 1H-19F distance technique promises to provide a highly efficient tool for constraining the three-dimensional structures of proteins and protein-ligand complexes, with not only precise and fast measurements but also access to truly long-range distances.
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Affiliation(s)
- Alexander A. Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Venkata Shiva Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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Vasa SK, Singh H, Grohe K, Linser R. Charakterisierung eines großen Enzym‐Wirkstoff‐Komplexes mittels protonendetektierter Festkörper‐NMR ohne Deuterierung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Suresh K. Vasa
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Himanshu Singh
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
- Fakultät für Chemie und Chemische BiologieTechnische Universität Dortmund Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Kristof Grohe
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Rasmus Linser
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
- Fakultät für Chemie und Chemische BiologieTechnische Universität Dortmund Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
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Pell AJ, Pintacuda G, Grey CP. Paramagnetic NMR in solution and the solid state. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 111:1-271. [PMID: 31146806 DOI: 10.1016/j.pnmrs.2018.05.001] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 05/22/2023]
Abstract
The field of paramagnetic NMR has expanded considerably in recent years. This review addresses both the theoretical description of paramagnetic NMR, and the way in which it is currently practised. We provide a review of the theory of the NMR parameters of systems in both solution and the solid state. Here we unify the different languages used by the NMR, EPR, quantum chemistry/DFT, and magnetism communities to provide a comprehensive and coherent theoretical description. We cover the theory of the paramagnetic shift and shift anisotropy in solution both in the traditional formalism in terms of the magnetic susceptibility tensor, and using a more modern formalism employing the relevant EPR parameters, such as are used in first-principles calculations. In addition we examine the theory first in the simple non-relativistic picture, and then in the presence of spin-orbit coupling. These ideas are then extended to a description of the paramagnetic shift in periodic solids, where it is necessary to include the bulk magnetic properties, such as magnetic ordering at low temperatures. The description of the paramagnetic shift is completed by describing the current understanding of such shifts due to lanthanide and actinide ions. We then examine the paramagnetic relaxation enhancement, using a simple model employing a phenomenological picture of the electronic relaxation, and again using a more complex state-of-the-art theory which incorporates electronic relaxation explicitly. An additional important consideration in the solid state is the impact of bulk magnetic susceptibility effects on the form of the spectrum, where we include some ideas from the field of classical electrodynamics. We then continue by describing in detail the solution and solid-state NMR methods that have been deployed in the study of paramagnetic systems in chemistry, biology, and the materials sciences. Finally we describe a number of case studies in paramagnetic NMR that have been specifically chosen to highlight how the theory in part one, and the methods in part two, can be used in practice. The systems chosen include small organometallic complexes in solution, solid battery electrode materials, metalloproteins in both solution and the solid state, systems containing lanthanide ions, and multi-component materials used in pharmaceutical controlled-release formulations that have been doped with paramagnetic species to measure the component domain sizes.
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Affiliation(s)
- Andrew J Pell
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106 91 Stockholm, Sweden.
| | - Guido Pintacuda
- Institut des Sciences Analytiques (CNRS UMR 5280, ENS de Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Clare P Grey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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