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Shcherbakov AA, Medeiros-Silva J, Tran N, Gelenter MD, Hong M. From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR. Chem Rev 2021; 122:9848-9879. [PMID: 34694769 DOI: 10.1021/acs.chemrev.1c00662] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional 13C and 15N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance 19F and 1H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on 19F- and 1H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.
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Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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2
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Tognetti J, Trent Franks W, Gallo A, Lewandowski JR. Accelerating 15N and 13C R 1 and R 1ρ relaxation measurements by multiple pathway solid-state NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 331:107049. [PMID: 34508920 DOI: 10.1016/j.jmr.2021.107049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Magic angle spinning (MAS) Solid-state NMR is a powerful technique to probe dynamics of biological systems at atomic resolution. R1 and R1ρ relaxation measurements can provide detailed insight on amplitudes and time scales of motions, especially when information from several different site-specific types of probes is combined. However, such experiments are time-consuming to perform. Shortening the time necessary to record relaxation data for different nuclei will greatly enhance practicality of such approaches. Here, we present staggered acquisition experiments to acquire multiple relaxation experiments from a single excitation to reduce the overall experimental time. Our strategy enables one to collect 15N and 13C relaxation data in a single experiment in a fraction of the time necessary for two separate experiments, with the same signal to noise ratio.
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Affiliation(s)
- Jacqueline Tognetti
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom; Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom; Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom.
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3
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Kupče Ē, Mote KR, Webb A, Madhu PK, Claridge TDW. Multiplexing experiments in NMR and multi-nuclear MRI. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 124-125:1-56. [PMID: 34479710 DOI: 10.1016/j.pnmrs.2021.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 05/22/2023]
Abstract
Multiplexing NMR experiments by direct detection of multiple free induction decays (FIDs) in a single experiment offers a dramatic increase in the spectral information content and often yields significant improvement in sensitivity per unit time. Experiments with multi-FID detection have been designed with both homonuclear and multinuclear acquisition, and the advent of multiple receivers on commercial spectrometers opens up new possibilities for recording spectra from different nuclear species in parallel. Here we provide an extensive overview of such techniques, designed for applications in liquid- and solid-state NMR as well as in hyperpolarized samples. A brief overview of multinuclear MRI is also provided, to stimulate cross fertilization of ideas between the two areas of research (NMR and MRI). It is shown how such techniques enable the design of experiments that allow structure elucidation of small molecules from a single measurement. Likewise, in biomolecular NMR experiments multi-FID detection allows complete resonance assignment in proteins. Probes with multiple RF microcoils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems, effectively reducing the cost of NMR analysis and increasing the information content at the same time. Solid-state NMR experiments have also benefited immensely from both parallel and sequential multi-FID detection in a variety of multi-dimensional pulse schemes. We are confident that multi-FID detection will become an essential component of future NMR methodologies, effectively increasing the sensitivity and information content of NMR measurements.
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Affiliation(s)
- Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research-Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Andrew Webb
- Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Perunthiruthy K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research-Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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Gallo A, Franks WT, Lewandowski JR. A suite of solid-state NMR experiments to utilize orphaned magnetization for assignment of proteins using parallel high and low gamma detection. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 305:219-231. [PMID: 31319283 DOI: 10.1016/j.jmr.2019.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 05/18/2023]
Abstract
We present a suite of two-receiver solid-state NMR experiments for backbone and side chain resonance assignment. The experiments rely on either dipolar coupling or scalar coupling for polarization transfer and are devised to acquire a 1H-detected 3D experiment AND a nested 13C-detected 2D from a shared excitation pulse. In order to compensate for the lower sensitivity of detection on 13C nucleus, 2D rows are signal averaged during 3D planes. The 3D dual receiver experiments do not suffer from any appreciable signal loss compared to their single receiver versions and require no extra optimization. The resulting data is higher in information content with no additional experiment time. The approach is expected to become widespread as multiple receivers become standard for new NMR spectrometers.
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Affiliation(s)
- A Gallo
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - W T Franks
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK; Department of Physics, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - J R Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK.
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Kupče Ē, Mote KR, Madhu PK. Experiments with direct detection of multiple FIDs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 304:16-34. [PMID: 31077929 DOI: 10.1016/j.jmr.2019.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/26/2019] [Accepted: 04/29/2019] [Indexed: 05/04/2023]
Abstract
Pulse schemes with direct observation of multiple free induction decays (FIDs) offer a dramatic increase in the spectral information content of NMR experiments and often yield substantial improvement in measurement sensitivity per unit time. Availability of multiple receivers on the state-of-the-art commercial spectrometers allows spectra from different nuclear species to be recorded in parallel routinely. Experiments with multi-FID detection have been designed with both, homonuclear and multinuclear acquisition. We provide a brief overview of such techniques designed for applications in liquid- and solid- state NMR as well as in hyperpolarized samples. Here we show how these techniques have led to design of experiments that allow structure elucidation of small molecules and resonance assignment in proteins from a single measurement. Probes with multiple RF micro-coils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems. Solid-state NMR experiments have also benefited immensely from both parallel and simultaneous FID acquisition in a variety of multi-dimensional pulse schemes. We believe that multi-FID detection will become an essential component of the future NMR methodologies effectively increasing the information content of NMR experiments and reducing the cost of NMR analysis.
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Affiliation(s)
- Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500107, India
| | - Perunthiruthy K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500107, India
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Demers JP, Vijayan V, Lange A. Recovery of Bulk Proton Magnetization and Sensitivity Enhancement in Ultrafast Magic-Angle Spinning Solid-State NMR. J Phys Chem B 2015; 119:2908-20. [DOI: 10.1021/jp511987y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jean-Philippe Demers
- Department of NMR-Based Structural
Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Vinesh Vijayan
- Department of NMR-Based Structural
Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Adam Lange
- Department of NMR-Based Structural
Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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Das BB, Opella SJ. Multiple acquisition/multiple observation separated local field/chemical shift correlation solid-state magic angle spinning NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 245:98-104. [PMID: 25023566 PMCID: PMC4128693 DOI: 10.1016/j.jmr.2014.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/06/2014] [Accepted: 06/08/2014] [Indexed: 05/12/2023]
Abstract
Multiple acquisition spectroscopy (MACSY) experiments that enable multiple free induction decays to be recorded during individual experiments are demonstrated. In particular, the experiments incorporate separated local field spectroscopy into homonuclear and heteronuclear correlation spectroscopy. The measured heteronuclear dipolar couplings are valuable in structure determination as well as in enhancing resolution by providing an additional frequency axis. In one example four different three-dimensional spectra are obtained in a single experiment, demonstrating that substantial potential saving in experimental time is available when multiple multi-dimensional spectra are required as part of solid-state NMR studies.
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Affiliation(s)
- Bibhuti B Das
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Abstract
In the stationary, aligned samples used in oriented sample (OS) solid-state NMR, (1)H-(1)H homonuclear dipolar couplings are not attenuated as they are in magic angle spinning solid-state NMR; consequently, they are available for participation in dipolar coupling-based spin-exchange processes. Here we describe analytically the pathways of (15)N-(15)N spin-exchange mediated by (1)H-(1)H homonuclear dipolar couplings. The mixed-order proton-relay mechanism can be differentiated from the third spin assisted recoupling mechanism by setting the (1)H to an off-resonance frequency so that it is at the "magic angle" during the spin-exchange interval in the experiment, since the "magic angle" irradiation nearly quenches the former but only slightly attenuates the latter. Experimental spectra from a single crystal of N-acetyl leucine confirm that this proton-relay mechanism plays the dominant role in (15)N-(15)N dilute-spin-exchange in OS solid-state NMR in crystalline samples. Remarkably, the "forbidden" spin-exchange condition under "magic angle" irradiation results in (15)N-(15)N cross-peaks intensities that are comparable to those observed with on-resonance irradiation in applications to proteins. The mechanism of the proton relay in dilute-spin-exchange is crucial for the design of polarization transfer experiments.
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Affiliation(s)
- George J Lu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0307, USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0307, USA
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Ferella L, Luchinat C, Ravera E, Rosato A. SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR. JOURNAL OF BIOMOLECULAR NMR 2013; 57:319-26. [PMID: 24243317 DOI: 10.1007/s10858-013-9795-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 11/11/2013] [Indexed: 05/09/2023]
Abstract
We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity--obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device--into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment.
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Affiliation(s)
- Lucio Ferella
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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Agarwal V, Sardo M, Scholz I, Böckmann A, Ernst M, Meier BH. PAIN with and without PAR: variants for third-spin assisted heteronuclear polarization transfer. JOURNAL OF BIOMOLECULAR NMR 2013; 56:365-377. [PMID: 23807391 DOI: 10.1007/s10858-013-9756-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/17/2013] [Indexed: 06/02/2023]
Abstract
In this article, we describe third-spin assisted heteronuclear recoupling experiments, which play an increasingly important role in measuring long-range heteronuclear couplings, in particular (15)N-(13)C, in proteins. In the proton-assisted insensitive nuclei cross polarization (PAIN-CP) experiment (de Paëpe et al. in J Chem Phys 134:095101, 2011), heteronuclear polarization transfer is always accompanied by homonuclear transfer of the proton-assisted recoupling (PAR) type. We present a phase-alternating experiment that promotes heteronuclear (e.g. (15)N → (13)C) polarization transfer while simultaneously minimizing homonuclear (e.g.(13)C → (13)C) transfer (PAIN without PAR). This minimization of homonuclear polarization transfer is based on the principle of the resonant second-order transfer (RESORT) recoupling scheme where the passive proton spins are irradiated by a phase-alternating sequence and the modulation frequency is matched to an integer multiple of the spinning frequency. The similarities and differences between the PAIN-CP and this het-RESORT experiment are discussed here.
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Affiliation(s)
- Vipin Agarwal
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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Goldbourt A. Biomolecular magic-angle spinning solid-state NMR: recent methods and applications. Curr Opin Biotechnol 2013; 24:705-15. [DOI: 10.1016/j.copbio.2013.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 12/28/2022]
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Bhaumik A, Luchinat C, Parigi G, Ravera E, Rinaldelli M. NMR crystallography on paramagnetic systems: solved and open issues. CrystEngComm 2013. [DOI: 10.1039/c3ce41485j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ren J, Eckert H. Eine homonukleare Rotationsecho-Doppelresonanzmethode zur Messung aufgelöster Abstandsverteilungen inI=1/2-Spinpaaren, -Spinclustern und -Vielspinsystemen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ren J, Eckert H. A Homonuclear Rotational Echo Double-Resonance Method for Measuring Site-Resolved Distance Distributions in I=1/2 Spin Pairs, Clusters, and Multispin Systems. Angew Chem Int Ed Engl 2012; 51:12888-91. [DOI: 10.1002/anie.201207094] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Indexed: 11/05/2022]
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