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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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Piai A, Gonnelli L, Felli IC, Pierattelli R, Kazimierczuk K, Grudziąż K, Koźmiński W, Zawadzka-Kazimierczuk A. Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 64:239-53. [PMID: 26891900 PMCID: PMC4824835 DOI: 10.1007/s10858-016-0024-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/11/2016] [Indexed: 05/07/2023]
Abstract
Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using automatic strategies for their assignment is very attractive. In this article we present a new version of the automatic assignment program TSAR dedicated to intrinsically disordered proteins. In particular, we demonstrate how the automatic procedure can be improved by incorporating methods for amino acid recognition and information on chemical shifts in selected amino acids. The approach was tested in silico on 16 disordered proteins and experimentally on α-synuclein, with remarkably good results.
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Affiliation(s)
- Alessandro Piai
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Leonardo Gonnelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Isabella C Felli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | | | - Katarzyna Grudziąż
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Anna Zawadzka-Kazimierczuk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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Hošek T, Gil-Caballero S, Pierattelli R, Brutscher B, Felli IC. Longitudinal relaxation properties of (1)H(N) and (1)H(α) determined by direct-detected (13)C NMR experiments to study intrinsically disordered proteins (IDPs). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 254:19-26. [PMID: 25771525 DOI: 10.1016/j.jmr.2015.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 06/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) are functional proteins containing large fragments characterized by high local mobility. Bioinformatic studies have suggested that a significant fraction (more than 30%) of eukaryotic proteins has disordered regions of more than 50 amino acids in length. Hence, NMR methods for the characterization of local compactness and solvent accessibility in such highly disordered proteins are of high importance. Among the available approaches, the HET-SOFAST/BEST experiments (Schanda et al., 2006, Rennella et al., 2014) provide semi-quantitative information by monitoring longitudinal (1)H relaxation of amide protons under different initial conditions. However, when approaching physiological sample conditions, the potential of these amide (1)H detected experiments is reduced due to rapid amide proton solvent exchange. (13)C direct detection methods therefore provide a valuable alternative thanks to a higher chemical shift dispersion and their intrinsic insensitivity toward solvent exchange. Here we present two sets of (13)C-detected experiments, which indirectly measure (1)H(N) and (1)H(α) inversion recovery profiles. The experiments consist of an initial spin inversion-recovery block optimized for selective manipulation of different types of proton spins followed by a CON read-out scheme. The proposed experiments were tested on human α-synuclein and ubiquitin, two representative examples of unfolded and folded proteins.
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Affiliation(s)
- Tomáš Hošek
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | | | - Roberta Pierattelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.
| | - Isabella C Felli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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Li DW, Meng D, Brüschweiler R. Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 254:93-97. [PMID: 25863893 PMCID: PMC4467894 DOI: 10.1016/j.jmr.2015.02.013] [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: 12/13/2014] [Revised: 02/12/2015] [Accepted: 02/14/2015] [Indexed: 06/04/2023]
Abstract
A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of (15)N, (13)C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100-250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation.
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Affiliation(s)
- Da-Wei Li
- Campus Chemical Instrumentation Center, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, United States; Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306, United States
| | - Dan Meng
- Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306, United States
| | - Rafael Brüschweiler
- Campus Chemical Instrumentation Center, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, United States; Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306, United States.
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Felli IC, Pierattelli R. Novel methods based on (13)C detection to study intrinsically disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:115-25. [PMID: 24656084 DOI: 10.1016/j.jmr.2013.10.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 05/23/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by highly flexible solvent exposed backbones and can sample many different conformations. These properties confer them functional advantages, complementary to those of folded proteins, which need to be characterized to expand our view of how protein structural and dynamic features affect function beyond the static picture of a single well defined 3D structure that has influenced so much our way of thinking. NMR spectroscopy provides a unique tool for the atomic resolution characterization of highly flexible macromolecules in general and of IDPs in particular. The peculiar properties of IDPs however have profound effects on spectroscopic parameters. It is thus worth thinking about these aspects to make the best use of the great potential of NMR spectroscopy to contribute to this fascinating field of research. In particular, after many years of dealing with exclusively heteronuclear NMR experiments based on (13)C direct detection, we would like here to address their relevance when studying IDPs.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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Pantoja-Uceda D, Santoro J. A suite of amino acid residue type classification pulse sequences for 13C-detected NMR of proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:190-196. [PMID: 23892405 DOI: 10.1016/j.jmr.2013.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 06/24/2013] [Accepted: 06/28/2013] [Indexed: 06/02/2023]
Abstract
A suite of (13)C-detected NMR pulse sequences to edit the correlation peaks of the CACO and CON spectra according to the amino acid residue type is presented. The pulse sequences exploit the topology of the C(β) carbon and led to the sorting of the CACO or CON signals into several classes depending on the nature of the generating residue. A set of four or eight correlation spectra is recorded where the sign of the cross peaks changes from one spectrum to another according to the amino acid type of the corresponding residue in the protein sequence. Linear combination of these spectra produces subspectra showing signals from residues having similar C(β) topology. The presence of weak breakthrough peaks does not prevent the proper classification, since this is obtained from the subspectrum in which the correlation peak is more intense. The experiments were tested on a globular protonated protein ((13)C, (15)N labeled Ubiquitin), on a globular deuterated protein ((2)H, (13)C, (15)N labeled Ubiquitin), and on an intrinsically disordered protein ((13)C, (15)N labeled Nupr1).
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Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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