1
|
Porat-Dahlerbruch G, Polenova T. Simultaneous recoupling of chemical shift tensors of two nuclei by R-symmetry sequences. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 348:107382. [PMID: 36716616 PMCID: PMC10023370 DOI: 10.1016/j.jmr.2023.107382] [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: 12/08/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 05/18/2023]
Abstract
Chemical shift tensors (CSTs) are sensitive probes of structure and dynamics. R-symmetry pulse sequences (RNCSA) can efficiently recouple CSTs of varying magnitudes in magic angle spinning (MAS) NMR experiments, for a broad range of conditions and MAS frequencies. Herein, we introduce dual-channel R-symmetry pulse sequences for simultaneously recording CSTs of two different nuclei in a single experiment (DORNE-CSA). We demonstrate the performance of DORNE-CSA sequences for simultaneous measurement of 13C and 15N CSTs, on a U-13C,15N-labeled microcrystalline l-histidine. We show that the DORNE-CSA method is robust, provides accurate CST parameters, and takes only half of the measurement time compared to a pair of RNCSA experiments otherwise required for recording the CSTs of individual nuclei. DORNE-CSA approach is broadly applicable to a wide range of biological and inorganic systems.
Collapse
Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States.
| |
Collapse
|
2
|
Franks WT, Tognetti J, Lewandowski JR. Slice & Dice: nested spin-lattice relaxation measurements. Phys Chem Chem Phys 2023; 25:6044-6049. [PMID: 36281524 PMCID: PMC9945929 DOI: 10.1039/d2cp03458a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spin-lattice relaxation rate (R1) measurements are commonly used to characterize protein dynamics. However, the time needed to collect the data can be quite long due to long relaxation times of the low-gamma nuclei, especially in the solid state. We present a method to collect backbone heavy atom relaxation data by nesting the collection of datasets in the solid state. This method results in a factor of 2 to 2.5 times faster data acquisition for backbone R1 relaxation data for the 13C and 15N sites of proteins.
Collapse
Affiliation(s)
- W. Trent Franks
- Department of Chemistry, University of WarwickCoventry CV4 7ALUK,Department of Physics, University of WarwickCoventry CV4 7ALUK
| | - Jacqueline Tognetti
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK. .,Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | | |
Collapse
|
3
|
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: 33] [Impact Index Per Article: 33.0] [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.
Collapse
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
| |
Collapse
|
4
|
Gopinath T, Manu VS, Weber DK, Veglia G. PHRONESIS: a one-shot approach for sequential assignment of protein resonances by ultrafast MAS solid-state NMR spectroscopy. Chemphyschem 2022; 23:e202200127. [PMID: 35499980 PMCID: PMC9400877 DOI: 10.1002/cphc.202200127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/25/2022] [Indexed: 11/09/2022]
Abstract
Solid‐state NMR (ssNMR) spectroscopy has emerged as the method of choice to analyze the structural dynamics of fibrillar, membrane‐bound, and crystalline proteins that are recalcitrant to other structural techniques. Recently, 1H detection under fast magic angle spinning and multiple acquisition ssNMR techniques have propelled the structural analysis of complex biomacromolecules. However, data acquisition and resonance‐specific assignments remain a bottleneck for this technique. Here, we present a comprehensive multi‐acquisition experiment (PHRONESIS) that simultaneously generates up to ten 3D 1H‐detected ssNMR spectra. PHRONESIS utilizes broadband transfer and selective pulses to drive multiple independent polarization pathways. High selectivity excitation and de‐excitation of specific resonances were achieved by high‐fidelity selective pulses that were designed using a combination of an evolutionary algorithm and artificial intelligence. We demonstrated the power of this approach with microcrystalline U‐13C,15N GB1 protein, reaching 100 % of the resonance assignments using one data set of ten 3D experiments. The strategy outlined in this work opens up new avenues for implementing novel 1H‐detected multi‐acquisition ssNMR experiments to speed up and expand the application to larger biomolecular systems.
Collapse
Affiliation(s)
- T Gopinath
- University of Minnesota College of Biological Sciences, Biochemistry, Molecular Biology & Biophysics, UNITED STATES
| | - V S Manu
- University of Minnesota College of Biological Sciences, Biochemistry, Molecular Biology & Biophysics, 321 Church St SE, 55455, Minneapolis, UNITED STATES
| | - Daniel K Weber
- University of Minnesota College of Biological Sciences, Biochemistry, Molecular Biology & Biophysics, UNITED STATES
| | - Gianluigi Veglia
- University of Minnesota, Biochemistry, 321 Church Street SE, 55455, Minneapolis, UNITED STATES
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Gopinath T, Weber D, Wang S, Larsen E, Veglia G. Solid-State NMR of Membrane Proteins in Lipid Bilayers: To Spin or Not To Spin? Acc Chem Res 2021; 54:1430-1439. [PMID: 33655754 DOI: 10.1021/acs.accounts.0c00670] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Membrane proteins mediate a plethora of cellular functions and represent important targets for drug development. Unlike soluble proteins, membrane proteins require native-like environments to fold correctly and be active. Therefore, modern structural biology techniques have aimed to determine the structure and dynamics of these membrane proteins at physiological temperature and in liquid crystalline lipid bilayers. With the flourishing of new NMR methodologies and improvements in sample preparations, magic angle spinning (MAS) and oriented sample solid-state NMR (OS-ssNMR) spectroscopy of membrane proteins is experiencing a new renaissance. Born as antagonistic approaches, these techniques nowadays offer complementary information on the structural topology and dynamics of membrane proteins reconstituted in lipid membranes. By spinning biosolid samples at the magic angle (θ = 54.7°), MAS NMR experiments remove the intrinsic anisotropy of the NMR interactions, increasing spectral resolution. Internuclear spin interactions (spin exchange) are reintroduced by RF pulses, providing distances and torsion angles to determine secondary, tertiary, and quaternary structures of membrane proteins. OS-ssNMR, on the other hand, directly detects anisotropic NMR parameters such as dipolar couplings (DC) and anisotropic chemical shifts (CS), providing orientational constraints to determine the architecture (i.e., topology) of membrane proteins relative to the lipid membrane. Defining the orientation of membrane proteins and their interactions with lipid membranes is of paramount importance since lipid-protein interactions can shape membrane protein conformations and ultimately define their functional states.In this Account, we report selected studies from our group integrating MAS and OS-ssNMR techniques to give a comprehensive view of the biological processes occurring at cellular membranes. We focus on the main experiments for both techniques, with an emphasis on new implementation to increase both sensitivity and spectral resolution. We also describe how the structural constraints derived from both isotropic and anisotropic NMR parameters are integrated into dynamic structural modeling using replica-averaged orientational-restrained molecular dynamics simulations (RAOR-MD). We showcase small membrane proteins that are involved in Ca2+ transport and regulate cardiac and skeletal muscle contractility: phospholamban (PLN, 6 kDa), sarcolipin (SLN, 4 kDa), and DWORF (4 kDa). We summarize our results for the structures of these polypeptides free and in complex with the sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA, 110 kDa). Additionally, we illustrate the progress toward the determination of the structural topology of a six transmembrane protein associated with succinate and acetate transport (SatP, hexamer 120 kDa). From these examples, the integrated MAS and OS-ssNMR approach, in combination with modern computational methods, emerges as a way to overcome the challenges posed by studying large membrane protein systems.
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Sharma K, Madhu PK, Agarwal V, Mote KR. Simultaneous recording of intra- and inter-residue linking experiments for backbone assignments in proteins at MAS frequencies higher than 60 kHz. JOURNAL OF BIOMOLECULAR NMR 2020; 74:229-237. [PMID: 31894471 DOI: 10.1007/s10858-019-00292-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Obtaining site-specific assignments for the NMR spectra of proteins in the solid state is a significant bottleneck in deciphering their biophysics. This is primarily due to the time-intensive nature of the experiments. Additionally, the low resolution in the [Formula: see text]-dimension requires multiple complementary experiments to be recorded to lift degeneracies in assignments. We present here an approach, gleaned from the techniques used in multiple-acquisition experiments, which allows the recording of forward and backward residue-linking experiments in a single experimental block. Spectra from six additional pathways are also recovered from the same experimental block, without increasing the probe duty cycle. These experiments give intra- and inter residue connectivities for the backbone [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] resonances and should alone be sufficient to assign these nuclei in proteins at MAS frequencies > 60 kHz. The validity of this approach is tested with experiments on a standard tripeptide N-formyl methionyl-leucine-phenylalanine (f-MLF) at a MAS frequency of 62.5 kHz, which is also used as a test-case for determining the sensitivity of each of the experiments. We expect this approach to have an immediate impact on the way assignments are obtained at MAS frequencies [Formula: see text].
Collapse
Affiliation(s)
- Kshama Sharma
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally, Serlingampally Mandal, Rangareddy District, Hyderabad, 500107, India
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally, Serlingampally Mandal, Rangareddy District, Hyderabad, 500107, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally, Serlingampally Mandal, Rangareddy District, Hyderabad, 500107, India.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally, Serlingampally Mandal, Rangareddy District, Hyderabad, 500107, India.
| |
Collapse
|
11
|
Stanek J, Schubeis T, Paluch P, Güntert P, Andreas LB, Pintacuda G. Automated Backbone NMR Resonance Assignment of Large Proteins Using Redundant Linking from a Single Simultaneous Acquisition. J Am Chem Soc 2020; 142:5793-5799. [DOI: 10.1021/jacs.0c00251] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jan Stanek
- Centre de RMN à Très Hauts Champs (FRE 2034 CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, Villeurbanne 69100, France
- Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02089, Poland
| | - Tobias Schubeis
- Centre de RMN à Très Hauts Champs (FRE 2034 CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, Villeurbanne 69100, France
| | - Piotr Paluch
- Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02089, Poland
| | - Peter Güntert
- Physical Chemistry, Eidgenössische Technische Hochschule Zurich, Hochschule Zürich, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji 192-0397, Japan
| | - Loren B. Andreas
- Centre de RMN à Très Hauts Champs (FRE 2034 CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, Villeurbanne 69100, France
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen D-37077, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs (FRE 2034 CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, Villeurbanne 69100, France
| |
Collapse
|
12
|
Gopinath T, Veglia G. Proton-detected polarization optimized experiments (POE) using ultrafast magic angle spinning solid-state NMR: Multi-acquisition of membrane protein spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 310:106664. [PMID: 31837552 PMCID: PMC7003683 DOI: 10.1016/j.jmr.2019.106664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 05/05/2023]
Abstract
Proton-detected solid-state NMR (ssNMR) spectroscopy has dramatically improved the sensitivity and resolution of fast magic angle spinning (MAS) methods. While relatively straightforward for fibers and crystalline samples, the routine application of these techniques to membrane protein samples is still challenging. This is due to the low sensitivity of these samples, which require high lipid:protein ratios to maintain the structural and functional integrity of membrane proteins. We previously introduced a family of novel polarization optimized experiments (POE) that enable to make the best of nuclear polarization and obtain multiple-acquisitions from a single pulse sequence and one receiver. Here, we present the 1H-detected versions of POE using ultrafast MAS ssNMR. Specifically, we implemented proton detection into our three main POE strategies, H-DUMAS, H-MEIOSIS, and H-MAeSTOSO, achieving the acquisition of up to ten different experiments using a single pulse sequence. We tested these experiments on a model compound N-Acetyl-Val-Leu dipeptide and applied to a six transmembrane acetate transporter, SatP, reconstituted in lipid membranes. These new methods will speed up the spectroscopy of challenging biomacromolecules such as membrane proteins.
Collapse
Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Gopinath T, Wang S, Lee J, Aihara H, Veglia G. Hybridization of TEDOR and NCX MAS solid-state NMR experiments for simultaneous acquisition of heteronuclear correlation spectra and distance measurements. JOURNAL OF BIOMOLECULAR NMR 2019; 73:141-153. [PMID: 30805819 PMCID: PMC6526076 DOI: 10.1007/s10858-019-00237-5] [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: 12/19/2018] [Accepted: 02/12/2019] [Indexed: 05/05/2023]
Abstract
Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is a major technique for the characterization of the structural dynamics of biopolymers at atomic resolution. However, the intrinsic low sensitivity of this technique poses significant limitations to its routine application in structural biology. Here we achieve substantial savings in experimental time using a new subclass of Polarization Optimized Experiments (POEs) that concatenate TEDOR and SPECIFIC-CP transfers into a single pulse sequence. Specifically, we designed new 2D and 3D experiments (2D TEDOR-NCX, 3D TEDOR-NCOCX, and 3D TEDOR-NCACX) to obtain distance measurements and heteronuclear chemical shift correlations for resonance assignments using only one experiment. We successfully tested these experiments on N-Acetyl-Val-Leu dipeptide, microcrystalline U-13C,15N ubiquitin, and single- and multi-span membrane proteins reconstituted in lipid membranes. These pulse sequences can be implemented on any ssNMR spectrometer equipped with standard solid-state hardware using only one receiver. Since these new POEs speed up data acquisition considerably, we anticipate their broad application to fibrillar, microcrystalline, and membrane-bound proteins.
Collapse
Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - John Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Hideki Aihara
- 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.
| |
Collapse
|
16
|
Nolis P, Parella T. Practical aspects of the simultaneous collection of COSY and TOCSY spectra. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:S85-S94. [PMID: 30676668 DOI: 10.1002/mrc.4835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
The practical aspects of some NMR experiments designed for the simultaneous acquisition of 2D COSY and 2D TOCSY spectra are presented and discussed. Several techniques involving afterglow-based, coherence transfer pathway (CTP)-based, and NMR by Ordered Acquisition using 1 H-detection (NOAH)-based strategies for the collection of different free-induction signal decays (FIDs) within the same scan are evaluated and compared. These methods offer a faster recording of these spectra in small-molecule NMR when sensitivity is not a limiting factor, with a reduction in spectrometer time about 45-60% when compared with the conventional sequential acquisition of the parent experiments. It is also shown how the optimized design of an extended three-FID approach yields one COSY and two TOCSY spectra simultaneously by combining CTP and NOAH principles in the same experiment, affording substantial sensitivity enhancements per time unit.
Collapse
Affiliation(s)
- Pau Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| |
Collapse
|
17
|
Gopinath T, Veglia G. Probing membrane protein ground and conformationally excited states using dipolar- and J-coupling mediated MAS solid state NMR experiments. Methods 2018; 148:115-122. [PMID: 30012515 PMCID: PMC6428079 DOI: 10.1016/j.ymeth.2018.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/25/2022] Open
Abstract
The intrinsic conformational plasticity of membrane proteins directly influences the magnitude of the orientational-dependent NMR interactions such as dipolar couplings (DC) and chemical shift anisotropy (CSA). As a result, the conventional cross-polarization (CP)-based techniques mainly capture the more rigid regions of membrane proteins, while the most dynamic regions are essentially invisible. Nonetheless, dynamic regions can be detected using experiments in which polarization transfer takes place via J-coupling interactions. Here, we review our recent efforts to develop single and dual acquisition pulse sequences with either 1H or 13C detection that utilize both DC and J-coupling mediated transfer to detect both rigid and mobile regions of membrane proteins in native-like lipid environments. We show the application of these new methods for studying the conformational equilibrium of a single-pass membrane protein, phospholamban, which regulates the calcium transport across the sarcoplasmic reticulum (SR) membrane by interacting with the SR Ca2+-ATPase. We anticipate that these methods will be ideal to portray the complex dynamics of membrane proteins in their native environments.
Collapse
Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
| |
Collapse
|
18
|
Abstract
Biomolecular solid-state NMR experiments have traditionally been collected through detection of 13C or 15N nuclei. Since these nuclei have relatively low sensitivity stemming from their smaller gyromagnetic ratios relative to 1H, the time required to collect multi-dimensional datasets serves as a limitation to resonance assignment and structure determination. One improvement in the field has been to employ simultaneous or parallel acquisition techniques with the goal of acquiring more than one dataset at a time and therefore speeding up the overall data collection process. Central to these experiments is the cross-polarization (CP) element, which serves as a way to transfer magnetization between nuclei via magnetic dipolar couplings. In this chapter, we show how residual signal remaining after CP is a polarization source that can be used to acquire additional datasets. The setup of this class of experiments, referred to as Afterglow spectroscopy, is described and demonstrated using a membrane protein transporter involved in multidrug resistance.
Collapse
Affiliation(s)
- Gili Abramov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Nathaniel J Traaseth
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA.
| |
Collapse
|
19
|
Gopinath T, Veglia G. Experimental Aspects of Polarization Optimized Experiments (POE) for Magic Angle Spinning Solid-State NMR of Microcrystalline and Membrane-Bound Proteins. Methods Mol Biol 2018; 1688:37-53. [PMID: 29151203 DOI: 10.1007/978-1-4939-7386-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Conventional NMR pulse sequences record one spectrum per experiment, while spending most of the time waiting for the spin system to return to the equilibrium. As a result, a full set of multidimensional NMR experiments for biological macromolecules may take up to several months to complete. Here, we present a practical guide for setting up a new class of MAS solid-state NMR experiments (POE or polarization optimized experiments) that enable the simultaneous acquisition of multiple spectra of proteins, accelerating data acquisition. POE exploit the long-lived 15N polarization of isotopically labeled proteins and enable one to obtain up to eight spectra, by concatenating classical NMR pulse sequences. This new strategy propels data throughput of solid-state NMR spectroscopy of fibers, microcrystalline preparations, as well as membrane proteins.
Collapse
Affiliation(s)
- T Gopinath
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
20
|
Gopinath T, Nelson SED, Veglia G. 1H-detected MAS solid-state NMR experiments enable the simultaneous mapping of rigid and dynamic domains of membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 285:101-107. [PMID: 29173803 PMCID: PMC5764182 DOI: 10.1016/j.jmr.2017.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 05/05/2023]
Abstract
Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is emerging as a unique method for the atomic resolution structure determination of native membrane proteins in lipid bilayers. Although 13C-detected ssNMR experiments continue to play a major role, recent technological developments have made it possible to carry out 1H-detected experiments, boosting both sensitivity and resolution. Here, we describe a new set of 1H-detected hybrid pulse sequences that combine through-bond and through-space correlation elements into single experiments, enabling the simultaneous detection of rigid and dynamic domains of membrane proteins. As proof-of-principle, we applied these new pulse sequences to the membrane protein phospholamban (PLN) reconstituted in lipid bilayers under moderate MAS conditions. The cross-polarization (CP) based elements enabled the detection of the relatively immobile residues of PLN in the transmembrane domain using through-space correlations; whereas the most dynamic region, which is in equilibrium between folded and unfolded states, was mapped by through-bond INEPT-based elements. These new 1H-detected experiments will enable one to detect not only the most populated (ground) states of biomacromolecules, but also sparsely populated high-energy (excited) states for a complete characterization of protein free energy landscapes.
Collapse
Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Sarah E D Nelson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
| |
Collapse
|
21
|
Sharma K, Madhu PK, Mote KR. A suite of pulse sequences based on multiple sequential acquisitions at one and two radiofrequency channels for solid-state magic-angle spinning NMR studies of proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 65:127-141. [PMID: 27364976 DOI: 10.1007/s10858-016-0043-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/14/2016] [Indexed: 05/04/2023]
Abstract
One of the fundamental challenges in the application of solid-state NMR is its limited sensitivity, yet a majority of experiments do not make efficient use of the limited polarization available. The loss in polarization in a single acquisition experiment is mandated by the need to select out a single coherence pathway. In contrast, sequential acquisition strategies can encode more than one pathway in the same experiment or recover unused polarization to supplement a standard experiment. In this article, we present pulse sequences that implement sequential acquisition strategies on one and two radiofrequency channels with a combination of proton and carbon detection to record multiple experiments under magic-angle spinning. We show that complementary 2D experiments such as [Formula: see text] and [Formula: see text] or DARR and [Formula: see text], and 3D experiments such as [Formula: see text] and [Formula: see text], or [Formula: see text] and [Formula: see text] can be combined in a single experiment to ensure time savings of at least 40 %. These experiments can be done under fast or slow-moderate magic-angle spinning frequencies aided by windowed [Formula: see text] acquisition and homonulcear decoupling. The pulse sequence suite is further expanded by including pathways that allow the recovery of residual polarization, the so-called 'afterglow' pathways, to encode a number of pulse sequences to aid in assignments and chemical-shift mapping.
Collapse
Affiliation(s)
- Kshama Sharma
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 21, Brundavan Colony, Narsingi, Hyderabad, 500 075, India
| | - Perunthiruthy K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 21, Brundavan Colony, Narsingi, Hyderabad, 500 075, India.
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 21, Brundavan Colony, Narsingi, Hyderabad, 500 075, India.
| |
Collapse
|
22
|
Gopinath T, Veglia G. Orphan spin polarization: A catalyst for high-throughput solid-state NMR spectroscopy of proteins. ANNUAL REPORTS ON NMR SPECTROSCOPY 2016; 89:103-121. [PMID: 31631914 PMCID: PMC6800253 DOI: 10.1016/bs.arnmr.2016.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Magic angle spinning solid-state NMR (MAS ssNMR) spectroscopy is a powerful method for structure determination of biomacromolecules that are recalcitrant to crystallization (membrane proteins and fibrils). Conventional multidimensional ssNMR methods acquire one experiment at a time. This approach is time consuming and discards orphan (unused) spin operators. Relatively low sensitivity and poor resolution of protein samples require long acquisition times for multidimensional ssNMR experiments. Here, we describe our recent progress in the development of multiple acquisition solid-state NMR methods for protein structure determination. A family of experiments called Polarization Optimized Experiments (POE) were designed, in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. Three strategies namely, DUMAS, MEIOSIS, and MAeSTOSO were used for the concatenation of various 2D and 3D experiments. These methods open up new avenues for reducing the acquisition times of multidimensional experiments for biomolecular ssNMR spectroscopy.
Collapse
Affiliation(s)
- T. Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics- University of Minnesota, Minneapolis, MN 55455
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics- University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry– University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
23
|
Gopinath T, Veglia G. Multiple acquisitions via sequential transfer of orphan spin polarization (MAeSTOSO): How far can we push residual spin polarization in solid-state NMR? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 267:1-8. [PMID: 27039168 PMCID: PMC4862926 DOI: 10.1016/j.jmr.2016.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/22/2016] [Accepted: 03/07/2016] [Indexed: 05/05/2023]
Abstract
Conventional multidimensional magic angle spinning (MAS) solid-state NMR (ssNMR) experiments detect the signal arising from the decay of a single coherence transfer pathway (FID), resulting in one spectrum per acquisition time. Recently, we introduced two new strategies, namely DUMAS (DUal acquisition Magic Angle Spinning) and MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), that enable the simultaneous acquisitions of multidimensional ssNMR experiments using multiple coherence transfer pathways. Here, we combined the main elements of DUMAS and MEIOSIS to harness both orphan spin operators and residual polarization and increase the number of simultaneous acquisitions. We show that it is possible to acquire up to eight two-dimensional experiments using four acquisition periods per each scan. This new suite of pulse sequences, called MAeSTOSO for Multiple Acquisitions via Sequential Transfer of Orphan Spin pOlarization, relies on residual polarization of both (13)C and (15)N pathways and combines low- and high-sensitivity experiments into a single pulse sequence using one receiver and commercial ssNMR probes. The acquisition of multiple experiments does not affect the sensitivity of the main experiment; rather it recovers the lost coherences that are discarded, resulting in a significant gain in experimental time. Both merits and limitations of this approach are discussed.
Collapse
Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
| |
Collapse
|
24
|
Gopinath T, Mote KR, Veglia G. Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples. JOURNAL OF BIOMOLECULAR NMR 2015; 62:53-61. [PMID: 25749871 PMCID: PMC4981477 DOI: 10.1007/s10858-015-9916-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/03/2015] [Indexed: 05/20/2023]
Abstract
We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.
Collapse
Affiliation(s)
| | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry and University of Minnesota, Minneapolis, MN 55455
- Corresponding Author. Gianluigi Veglia, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, Phone: (612) 625-0758, Fax: (612) 625-2163,
| |
Collapse
|
25
|
Gopinath T, Veglia G. Multiple acquisition of magic angle spinning solid-state NMR experiments using one receiver: application to microcrystalline and membrane protein preparations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:143-53. [PMID: 25797011 PMCID: PMC4399235 DOI: 10.1016/j.jmr.2015.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 01/02/2015] [Accepted: 01/04/2015] [Indexed: 05/05/2023]
Abstract
Solid-state NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POE allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this perspective, we describe the first generation of POE, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic nuclear polarization (DNP), to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes.
Collapse
Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
| |
Collapse
|
26
|
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
| |
Collapse
|
27
|
Löhr F, Laguerre A, Bock C, Reckel S, Connolly PJ, Abdul-Manan N, Tumulka F, Abele R, Moore JM, Dötsch V. Time-shared experiments for efficient assignment of triple-selectively labeled proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 248:81-95. [PMID: 25442777 PMCID: PMC4254601 DOI: 10.1016/j.jmr.2014.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/10/2014] [Accepted: 09/16/2014] [Indexed: 05/20/2023]
Abstract
Combinatorial triple-selective labeling facilitates the NMR assignment process for proteins that are subject to signal overlap and insufficient signal-to-noise in standard triple-resonance experiments. Aiming at maximum amino-acid type and sequence-specific information, the method represents a trade-off between the number of selectively labeled samples that have to be prepared and the number of spectra to be recorded per sample. In order to address the demand of long measurement times, we here propose pulse sequences in which individual phase-shifted transients are stored separately and recombined later to produce several 2D HN(CX) type spectra that are usually acquired sequentially. Sign encoding by the phases of (13)C 90° pulses allows to either select or discriminate against (13)C' or (13)C(α) spins coupled to (15)N. As a result, (1)H-(15)N correlation maps of the various isotopomeric species present in triple-selectively labeled proteins are deconvoluted which in turn reduces problems due to spectral overlap. The new methods are demonstrated with four different membrane proteins with rotational correlation times ranging from 18 to 52 ns.
Collapse
Affiliation(s)
- Frank Löhr
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Christoph Bock
- Institute of Biochemistry, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Sina Reckel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | | | | | - Franz Tumulka
- Institute of Biochemistry, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Rupert Abele
- Institute of Biochemistry, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | | | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
Mote KR, Gopinath T, Veglia G. Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2013; 57:91-102. [PMID: 23963722 PMCID: PMC3883141 DOI: 10.1007/s10858-013-9766-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/26/2013] [Indexed: 05/11/2023]
Abstract
The low sensitivity inherent to both the static and magic angle spinning techniques of solid-state NMR (ssNMR) spectroscopy has thus far limited the routine application of multidimensional experiments to determine the structure of membrane proteins in lipid bilayers. Here, we demonstrate the advantage of using a recently developed class of experiments, polarization optimized experiments, for both static and MAS spectroscopy to achieve higher sensitivity and substantial time-savings for 2D and 3D experiments. We used sarcolipin, a single pass membrane protein, reconstituted in oriented bicelles (for oriented ssNMR) and multilamellar vesicles (for MAS ssNMR) as a benchmark. The restraints derived by these experiments are then combined into a hybrid energy function to allow simultaneous determination of structure and topology. The resulting structural ensemble converged to a helical conformation with a backbone RMSD ~0.44 Å, a tilt angle of 24° ± 1°, and an azimuthal angle of 55° ± 6°. This work represents a crucial first step toward obtaining high-resolution structures of large membrane proteins using combined multidimensional oriented solid-state NMR and magic angle spinning solid-state NMR.
Collapse
Affiliation(s)
- Kaustubh R. Mote
- Department of Chemistry University of Minnesota, Minneapolis, MN 55455, USA
| | - T. Gopinath
- Department of Biochemistry, Molecular Biology & Biophysics University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Chemistry University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology & Biophysics University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
30
|
Ramamoorthy A, Xu J. 2D 1H/1H RFDR and NOESY NMR experiments on a membrane-bound antimicrobial peptide under magic angle spinning. J Phys Chem B 2013; 117:6693-700. [PMID: 23672643 DOI: 10.1021/jp4034003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
There is significant interest in solving high-resolution dynamic structures of membrane-associated peptides using solid-state NMR spectroscopy. Previous solid-state NMR studies have provided valuable insights into the functional properties of an exciting class of biomacromolecules such as antimicrobial peptides and amyloid peptides. However, it has been a major challenge to apply solid-state NMR techniques to study peptides or proteins that are not labeled with specific isotopes such as (13)C, (15)N, and/or (2)H. This study utilizes 2D (1)H/(1)H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) pulse sequences under magic angle spinning to study a membrane-bound antimicrobial peptide MSI-78 (or also known as pexiganan). We demonstrate that proton resonances can be assigned and structural constraints, NOE and (1)H-(1)H dipolar couplings, can be measured without the need for any isotopic enrichment. The buildup curves, showing the dependence of the cross peak intensity against the mixing time, obtained from 2D (1)H/(1)H NOESY and RFDR experiments are compared. Our results reveal that the RFDR-recovered (1)H-(1)H dipolar couplings associated with alpha and side chain protons are larger than that with the amide-protons. This study provides a means to measure residual (1)H-(1)H dipolar couplings for the investigation of structure, dynamics, and aggregation of peptides using a suitable model membrane like micelles or bicelles.
Collapse
Affiliation(s)
- Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA.
| | | |
Collapse
|