1
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Zumpfe K, Berbon M, Habenstein B, Loquet A, Smith AA. Analytical Framework to Understand the Origins of Methyl Side-Chain Dynamics in Protein Assemblies. J Am Chem Soc 2024; 146:8164-8178. [PMID: 38476076 PMCID: PMC10979401 DOI: 10.1021/jacs.3c12620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Side-chain motions play an important role in understanding protein structure, dynamics, protein-protein, and protein-ligand interactions. However, our understanding of protein side-chain dynamics is currently limited by the lack of analytical tools. Here, we present a novel analytical framework employing experimental nuclear magnetic resonance (NMR) relaxation measurements at atomic resolution combined with molecular dynamics (MD) simulation to characterize with a high level of detail the methyl side-chain dynamics in insoluble protein assemblies, using amyloid fibrils formed by the prion HET-s. We use MD simulation to interpret experimental results, where rotameric hops, including methyl group rotation and χ1/χ2 rotations, cannot be completely described with a single correlation time but rather sample a broad distribution of correlation times, resulting from continuously changing local structure in the fibril. Backbone motion similarly samples a broad range of correlation times, from ∼100 ps to μs, although resulting from mostly different dynamic processes; nonetheless, we find that the backbone is not fully decoupled from the side-chain motion, where changes in side-chain dynamics influence backbone motion and vice versa. While the complexity of side-chain motion in protein assemblies makes it very challenging to obtain perfect agreement between experiment and simulation, our analytical framework improves the interpretation of experimental dynamics measurements for complex protein assemblies.
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Affiliation(s)
- Kai Zumpfe
- Institute
for Medical Physics and Biophysics, Leipzig
University, Härtelstraße
16-18, 04107 Leipzig, Germany
| | - Mélanie Berbon
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Birgit Habenstein
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Antoine Loquet
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Albert A. Smith
- Institute
for Medical Physics and Biophysics, Leipzig
University, Härtelstraße
16-18, 04107 Leipzig, Germany
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2
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Kotschy J, Söldner B, Singh H, Vasa SK, Linser R. Microsecond Timescale Conformational Dynamics of a Small-Molecule Ligand within the Active Site of a Protein. Angew Chem Int Ed Engl 2024; 63:e202313947. [PMID: 37974542 DOI: 10.1002/anie.202313947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
The possible internal dynamics of non-isotope-labeled small-molecule ligands inside a target protein is inherently difficult to capture. Whereas high crystallographic temperature factors can denote either static disorder or motion, even moieties with very low B-factors can be subject to vivid motion between symmetry-related sites. Here we report the experimental identification of internal μs timescale dynamics of a high-affinity, natural-abundance ligand tightly bound to the enzyme human carbonic anhydrase II (hCAII) even within a crystalline lattice. The rotamer jumps of the ligand's benzene group manifest themselves both, in solution and fast magic-angle spinning solid-state NMR 1 H R1ρ relaxation dispersion, for which we obtain further mechanistic insights from molecular-dynamics (MD) simulations. The experimental confirmation of rotameric jumps in bound ligands within proteins in solution or the crystalline state may improve understanding of host-guest interactions in biology and supra-molecular chemistry and may facilitate medicinal chemistry for future drug campaigns.
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Affiliation(s)
- Julia Kotschy
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Benedikt Söldner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Himanshu Singh
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
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3
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Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Curr Opin Struct Biol 2023; 82:102660. [PMID: 37536064 DOI: 10.1016/j.sbi.2023.102660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies.
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Affiliation(s)
- Federico Napoli
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria. https://twitter.com/iomichiamofede
| | - Lea Marie Becker
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria. https://twitter.com/bckrlea
| | - Paul Schanda
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria.
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4
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Elena-Real CA, Urbanek A, Imbert L, Morató A, Fournet A, Allemand F, Sibille N, Boisbouvier J, Bernadó P. Site-Specific Introduction of Alanines for the Nuclear Magnetic Resonance Investigation of Low-Complexity Regions and Large Biomolecular Assemblies. ACS Chem Biol 2023; 18:2039-2049. [PMID: 37582223 DOI: 10.1021/acschembio.3c00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Nuclear magnetic resonance (NMR) studies of large biomolecular machines and highly repetitive proteins remain challenging due to the difficulty of assigning frequencies to individual nuclei. Here, we present an efficient strategy to address this challenge by engineering a Pyrococcus horikoshii tRNA/alanyl-tRNA synthetase pair that enables the incorporation of up to three isotopically labeled alanine residues in a site-specific manner using in vitro protein expression. The general applicability of this approach for NMR assignment has been demonstrated by introducing isotopically labeled alanines into four distinct proteins: huntingtin exon-1, HMA8 ATPase, the 300 kDa molecular chaperone ClpP, and the alanine-rich Phox2B transcription factor. For large protein assemblies, our labeling approach enabled unambiguous assignments while avoiding potential artifacts induced by site-specific mutations. When applied to Phox2B, which contains two poly-alanine tracts of nine and twenty alanines, we observed that the helical stability is strongly dependent on the homorepeat length. The capacity to selectively introduce alanines with distinct labeling patterns is a powerful tool to probe structure and dynamics of challenging biomolecular systems.
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Affiliation(s)
- Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Annika Urbanek
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Lionel Imbert
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Anna Morató
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Jérôme Boisbouvier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
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5
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Danmaliki GI, Yu S, Braun S, Zhao YY, Moore J, Fahlman RP, West FG, Hwang PM. Cost-effective selective deuteration of aromatic amino acid residues produces long-lived solution 1H NMR magnetization in proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107499. [PMID: 37307676 DOI: 10.1016/j.jmr.2023.107499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023]
Abstract
Solution NMR studies of large proteins are hampered by rapid signal decay due to short-range dipolar 1H-1H and 1H-13C interactions. These are attenuated by rapid rotation in methyl groups and by deuteration (2H), so selective 1H,13C-isotope labelling of methyl groups in otherwise perdeuterated proteins, combined with methyl transverse relaxation optimized spectroscopy (methyl-TROSY), is now standard for solution NMR of large protein systems > 25 kDa. For non-methyl positions, long-lived magnetization can be introduced as isolated 1H-12C groups. We have developed a cost-effective chemical synthesis for producing selectively deuterated phenylpyruvate and hydroxyphenylpyruvate. Feeding these amino acid precursors to E. coli in D2O, along with selectively deuterated anthranilate and unlabeled histidine, results in isolated and long-lived 1H magnetization in the aromatic rings of Phe (HD, HZ), Tyr (HD), Trp (HH2, HE3) and His (HD2 and HE1). We are additionally able to obtain stereoselective deuteration of Asp, Asn, and Lys amino acid residues using unlabeled glucose and fumarate as carbon sources and oxalate and malonate as metabolic inhibitors. Combining these approaches produces isolated 1H-12C groups in Phe, Tyr, Trp, His, Asp, Asn, and Lys in a perdeuterated background, which is compatible with standard 1H-13C labeling of methyl groups in Ala, Ile, Leu, Val, Thr, Met. We show that isotope labeling of Ala is improved using the transaminase inhibitor L-cycloserine, and labeling of Thr is improved through addition of Cys and Met, which are known inhibitors of homoserine dehydrogenase. We demonstrate the creation of long-lived 1H NMR signals in most amino acid residues using our model system, the WW domain of human Pin1, as well as the bacterial outer membrane protein PagP.
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Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Shaohui Yu
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Shelly Braun
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Yuan Y Zhao
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jack Moore
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Frederick G West
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.
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6
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Lends A, Birlirakis N, Cai X, Daskalov A, Shenoy J, Abdul-Shukkoor MB, Berbon M, Ferrage F, Liu Y, Loquet A, Tan KO. Efficient 18.8 T MAS-DNP NMR reveals hidden side chains in amyloid fibrils. JOURNAL OF BIOMOLECULAR NMR 2023:10.1007/s10858-023-00416-5. [PMID: 37289306 DOI: 10.1007/s10858-023-00416-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Amyloid fibrils are large and insoluble protein assemblies composed of a rigid core associated with a cross-β arrangement rich in β-sheet structural elements. It has been widely observed in solid-state NMR experiments that semi-rigid protein segments or side chains do not yield easily observable NMR signals at room temperature. The reasons for the missing peaks may be due to the presence of unfavorable dynamics that interfere with NMR experiments, which result in very weak or unobservable NMR signals. Therefore, for amyloid fibrils, semi-rigid and dynamically disordered segments flanking the amyloid core are very challenging to study. Here, we show that high-field dynamic nuclear polarization (DNP), an NMR hyperpolarization technique typically performed at low temperatures, can circumvent this issue because (i) the low-temperature environment (~ 100 K) slows down the protein dynamics to escape unfavorable detection regime, (ii) DNP improves the overall NMR sensitivity including those of flexible side chains, and (iii) efficient cross-effect DNP biradicals (SNAPol-1) optimized for high-field DNP (≥ 18.8 T) are employed to offer high sensitivity and resolution suitable for biomolecular NMR applications. By combining these factors, we have successfully established an impressive enhancement factor of ε ~ 50 on amyloid fibrils using an 18.8 T/ 800 MHz magnet. We have compared the DNP efficiencies of M-TinyPol, NATriPol-3, and SNAPol-1 biradicals on amyloid fibrils. We found that SNAPol-1 (with ε ~ 50) outperformed the other two radicals. The MAS DNP experiments revealed signals of flexible side chains previously inaccessible at conventional room-temperature experiments. These results demonstrate the potential of MAS-DNP NMR as a valuable tool for structural investigations of amyloid fibrils, particularly for side chains and dynamically disordered segments otherwise hidden at room temperature.
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Affiliation(s)
- Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Nicolas Birlirakis
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Asen Daskalov
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Jayakrishna Shenoy
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Muhammed Bilal Abdul-Shukkoor
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Mélanie Berbon
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
| | - Kong Ooi Tan
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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7
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Nishikino T, Miyanoiri Y. Site-Specific Isotope Labeling of FliG for Studying Structural Dynamics Using Nuclear Magnetic Resonance Spectroscopy. Methods Mol Biol 2023; 2646:57-70. [PMID: 36842106 DOI: 10.1007/978-1-0716-3060-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
To understand flagella-driven motility of bacteria, it is important to understand the structure and dynamics of the flagellar motor machinery. We have conducted structural dynamics analyses using solution nuclear magnetic resonance (NMR) to elucidate the detailed functions of flagellar motor proteins. Here, we introduce the analysis of the FliG protein, which is a flagellar motor protein, focusing on the preparation method of the original stable isotope-labeled protein.
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Affiliation(s)
- Tatsuro Nishikino
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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8
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Akke M, Weininger U. NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins. J Phys Chem B 2023; 127:591-599. [PMID: 36640108 PMCID: PMC9884080 DOI: 10.1021/acs.jpcb.2c07258] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale "breathing" motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.
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Affiliation(s)
- Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden,(M.A.)
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06129 Halle (Saale), Germany,(U.W.)
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9
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Ahlawat S, Mopidevi SMV, Taware PP, Raran-Kurussi S, Mote KR, Agarwal V. Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS. J Struct Biol X 2022; 7:100082. [PMID: 36618437 PMCID: PMC9817166 DOI: 10.1016/j.yjsbx.2022.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/18/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022] Open
Abstract
The assignment of aromatic side-chain spins has always been more challenging than assigning backbone and aliphatic spins. Selective labeling combined with mutagenesis has been the approach for assigning aromatic spins. This manuscript reports a method for assigning aromatic spins in a fully protonated protein by connecting them to the backbone atoms using a low-power TOBSY sequence. The pulse sequence employs residual polarization and sequential acquisitions techniques to record HN- and HC-detected spectra in a single experiment. The unambiguous assignment of aromatic spins also enables the characterization of 1H-1H distance restraints involving aromatic spins. Broadband (RFDR) and selective (BASS-SD) recoupling sequences were used to generate HN-ΗC, HC-HN and HC-HC restraints involving the side-chain proton spins of aromatic residues. This approach has been demonstrated on a fully protonated U-[13C,15N] labeled GB1 sample at 95-100 kHz MAS.
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10
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Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. J Struct Biol X 2022; 7:100079. [PMID: 36578472 PMCID: PMC9791609 DOI: 10.1016/j.yjsbx.2022.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.
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11
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How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation. Curr Opin Struct Biol 2022; 77:102459. [PMID: 36148743 DOI: 10.1016/j.sbi.2022.102459] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022]
Abstract
Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from 15N relaxation and side-chain dynamics from 13C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.
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12
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Dreydoppel M, Akke M, Weininger U. Characterizing Fast Conformational Exchange of Aromatic Rings Using Residual Dipolar Couplings: Distinguishing Jumplike Flips from Other Exchange Mechanisms. J Phys Chem B 2022; 126:7950-7956. [PMID: 36180044 PMCID: PMC9574926 DOI: 10.1021/acs.jpcb.2c05097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Aromatic ring flips are a hallmark of protein dynamics.
They are
experimentally studied by NMR spectroscopy, where recent advances
have led to improved characterization across a wide range of time
scales. Results on different proteins have been interpreted as continuous
diffusive ring rotations or jumplike flips, leading to diverging views
of the protein interior as being fluidlike or solidlike, respectively.
It is challenging to distinguish between these mechanisms and other
types of conformational exchange because chemical-shift-mediated line
broadening provides only conclusive evidence for ring flips only if
the system can be moved from the slow- to intermediate/fast-exchange
regime. Moreover, whenever the chemical shift difference between the
two symmetry-related sites is close to zero, it is not generally possible
to determine the exchange time scale. Here we resolve these issues
by measuring residual dipolar coupling (RDC)-mediated exchange contributions
using NMR relaxation dispersion experiments on proteins dissolved
in dilute liquid crystalline media. Excellent agreement is found between
the experimental difference in RDC between the two symmetry-related
sites and the value calculated from high-resolution X-ray structures,
demonstrating that dynamics measured for F52 in the B1 domain of protein
G reports on distinct, jumplike flips rather than other types of conformational
exchange.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120Halle (Saale), Germany
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-22100Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120Halle (Saale), Germany
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13
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Keeler EG, McDermott AE. Rotating Frame Relaxation in Magic Angle Spinning Solid State NMR, a Promising Tool for Characterizing Biopolymer Motion. Chem Rev 2022; 122:14940-14953. [PMID: 36099021 PMCID: PMC10122933 DOI: 10.1021/acs.chemrev.2c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Magic angle spinning NMR rotating frame relaxation measurements provide a unique experimental window into biomolecules dynamics, as is illustrated by numerous recent applications. We discuss experimental strategies for this class of experiments, with a particular focus on systems where motion-driven modulation of the chemical shift interaction is the main mechanism for relaxation. We also explore and describe common strategies for interpreting the data sets to extract motion time scale, activation energy, and angle or order parameters from rotating frame relaxation data. Using model free analysis and numerical simulations, including time domain treatment, we explore conditions under which it is possible to obtain accurate and precise information about the time scales of motions. Overall, with rapid technical advances in solid state NMR, there is a bright future for this class of studies.
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Affiliation(s)
- Eric G Keeler
- New York Structural Biology Center, New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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14
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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15
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Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nat Commun 2022; 13:1927. [PMID: 35395851 PMCID: PMC8993905 DOI: 10.1038/s41467-022-29423-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/14/2022] [Indexed: 02/07/2023] Open
Abstract
Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,ICSN, CNRS UPR2301, Univ. Paris-Saclay, Gif-sur-Yvette, France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,Celonic AG, Eulerstrasse 55, 4051, Basel, Switzerland
| | - Duccio Malinverni
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,i3S, Instituto de Investigacao e Inovacao em Saude, Universidade do Porto, Porto, Portugal
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Iva Sučec
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Juan Pablo Bustamante
- Instituto de Bioingenieria y Bioinformatica, IBB (CONICET-UNER), Oro Verde, Entre Rios, Argentina
| | - Alessandro Barducci
- Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France. .,Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
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16
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Mariño Pérez L, Ielasi FS, Bessa LM, Maurin D, Kragelj J, Blackledge M, Salvi N, Bouvignies G, Palencia A, Jensen MR. Visualizing protein breathing motions associated with aromatic ring flipping. Nature 2022; 602:695-700. [PMID: 35173330 PMCID: PMC8866124 DOI: 10.1038/s41586-022-04417-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/07/2022] [Indexed: 01/11/2023]
Abstract
Aromatic residues cluster in the core of folded proteins, where they stabilize the structure through multiple interactions. Nuclear magnetic resonance (NMR) studies in the 1970s showed that aromatic side chains can undergo ring flips-that is, 180° rotations-despite their role in maintaining the protein fold1-3. It was suggested that large-scale 'breathing' motions of the surrounding protein environment would be necessary to accommodate these ring flipping events1. However, the structural details of these motions have remained unclear. Here we uncover the structural rearrangements that accompany ring flipping of a buried tyrosine residue in an SH3 domain. Using NMR, we show that the tyrosine side chain flips to a low-populated, minor state and, through a proteome-wide sequence analysis, we design mutants that stabilize this state, which allows us to capture its high-resolution structure by X-ray crystallography. A void volume is generated around the tyrosine ring during the structural transition between the major and minor state, and this allows fast flipping to take place. Our results provide structural insights into the protein breathing motions that are associated with ring flipping. More generally, our study has implications for protein design and structure prediction by showing how the local protein environment influences amino acid side chain conformations and vice versa.
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Affiliation(s)
- Laura Mariño Pérez
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Departament de Química, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Francesco S Ielasi
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Luiza M Bessa
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Damien Maurin
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Jaka Kragelj
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Nicola Salvi
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules (LBM), Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France.
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17
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Klein A, Rovó P, Sakhrani VV, Wang Y, Holmes JB, Liu V, Skowronek P, Kukuk L, Vasa SK, Güntert P, Mueller LJ, Linser R. Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR. Proc Natl Acad Sci U S A 2022; 119:e2114690119. [PMID: 35058365 PMCID: PMC8795498 DOI: 10.1073/pnas.2114690119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/13/2021] [Indexed: 02/07/2023] Open
Abstract
NMR chemical shifts provide detailed information on the chemical properties of molecules, thereby complementing structural data from techniques like X-ray crystallography and electron microscopy. Detailed analysis of protein NMR data, however, often hinges on comprehensive, site-specific assignment of backbone resonances, which becomes a bottleneck for molecular weights beyond 40 to 45 kDa. Here, we show that assignments for the (2x)72-kDa protein tryptophan synthase (665 amino acids per asymmetric unit) can be achieved via higher-dimensional, proton-detected, solid-state NMR using a single, 1-mg, uniformly labeled, microcrystalline sample. This framework grants access to atom-specific characterization of chemical properties and relaxation for the backbone and side chains, including those residues important for the catalytic turnover. Combined with first-principles calculations, the chemical shifts in the β-subunit active site suggest a connection between active-site chemistry, the electrostatic environment, and catalytically important dynamics of the portal to the β-subunit from solution.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Petra Rovó
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
| | - Varun V Sakhrani
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Yangyang Wang
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Jacob B Holmes
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Viktoriia Liu
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Patricia Skowronek
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
| | - Laura Kukuk
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Rasmus Linser
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany;
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
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18
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Reif B. Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR. Chem Rev 2021; 122:10019-10035. [PMID: 34870415 DOI: 10.1021/acs.chemrev.1c00681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
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Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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19
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Álvarez Z, Kolberg-Edelbrock AN, Sasselli IR, Ortega JA, Qiu R, Syrgiannis Z, Mirau PA, Chen F, Chin SM, Weigand S, Kiskinis E, Stupp SI. Bioactive scaffolds with enhanced supramolecular motion promote recovery from spinal cord injury. Science 2021; 374:848-856. [PMID: 34762454 DOI: 10.1126/science.abh3602] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Z Álvarez
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - A N Kolberg-Edelbrock
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - I R Sasselli
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - J A Ortega
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,The Ken & Ruth Davee Department of Neurology, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - R Qiu
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Z Syrgiannis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - P A Mirau
- Materials and Manufacturing Directorate, Nanostructured and Biological Materials Branch, Air Force Research Laboratories, Wright-Patterson AFB, OH 45433, USA
| | - F Chen
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
| | - S M Chin
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - S Weigand
- DuPont-Northwestern-Dow Collaborative Access Team Synchrotron Research Center, Northwestern University, DND-CAT, Argonne, IL 60439, USA
| | - E Kiskinis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,The Ken & Ruth Davee Department of Neurology, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - S I Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA.,Department of Medicine, Northwestern University, Chicago, IL 60611, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.,Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.,Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
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20
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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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21
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Malär AA, Wili N, Völker LA, Kozlova MI, Cadalbert R, Däpp A, Weber ME, Zehnder J, Jeschke G, Eckert H, Böckmann A, Klose D, Mulkidjanian AY, Meier BH, Wiegand T. Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase. Nat Commun 2021; 12:5293. [PMID: 34489448 PMCID: PMC8421360 DOI: 10.1038/s41467-021-25599-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.
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Affiliation(s)
| | - Nino Wili
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | | | - Maria I Kozlova
- Department of Physics, Osnabrück University, Osnabrück, Germany
| | | | | | | | | | | | - Hellmut Eckert
- Institut für Physikalische Chemie, WWU Münster, Münster, Germany
- Instituto de Física de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Daniel Klose
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Armen Y Mulkidjanian
- Department of Physics, Osnabrück University, Osnabrück, Germany.
- School of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany.
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen, Aachen, Germany.
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22
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Dreydoppel M, Dorn B, Modig K, Akke M, Weininger U. Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations. JACS AU 2021; 1:833-842. [PMID: 34467336 PMCID: PMC8395657 DOI: 10.1021/jacsau.1c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 06/13/2023]
Abstract
Proteins are dynamic entities that intermittently depart from their ground-state structures and undergo conformational transitions as a critical part of their functions. Central to understanding such transitions are the structural rearrangements along the connecting pathway, where the transition state plays a special role. Using NMR relaxation at variable temperature and pressure to measure aromatic ring flips inside a protein core, we obtain information on the structure and thermodynamics of the transition state. We show that the isothermal compressibility coefficient of the transition state is similar to that of short-chain hydrocarbon liquids, implying extensive local unfolding of the protein. Our results further indicate that the required local volume expansions of the protein can occur not only with a net positive activation volume of the protein, as expected from previous studies, but also with zero activation volume by compaction of remote void volume, when averaged over the ensemble of states.
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Affiliation(s)
- Matthias Dreydoppel
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Britta Dorn
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Kristofer Modig
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
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23
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Akbey Ü. Dynamics of uniformly labelled solid proteins between 100 and 300 K: A 2D 2H- 13C MAS NMR approach. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106974. [PMID: 33823335 DOI: 10.1016/j.jmr.2021.106974] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
We describe a 2H based MAS nuclear magnetic resonance (NMR) method to obtain site-specific molecular dynamics of biomolecules. The method utilizes the use of deuterium nucleus as a spin label that is proven to be very useful in dynamics studies of solid biological and functional materials. The aim is to understand overall characteristics of protein backbone and side-chain motions for CD3, CD2 and CD groups, in terms of timescale, type and activation energy of the underlying processes. Variable temperature two-dimensional (2D) 2H-13C correlation MAS NMR spectra were recorded for the uniformly 2H,13C,15N labelled Alanine and microcrystalline SH3 at a broad temperature range, from 320 K down to 100 K. First, the deuterium quadrupolar-coupling constant from specific D-C sites is obtained with the 2D experiment by utilizing carbon chemical shifts. Second, the static quadrupolar patterns are obtained at 100 K. Third, variable temperature approach enabled the observation of quadrupolar pattern over different motional regimes; slow, intermediate and fast. And finally, the apparent activation energies for C-D sites are determined and compared, by evaluating the temperature induced signal intensities. This information led to the determination of the dynamic processes for different D-C sites at a broad range of temperature and motional timescales. This is a first representation of 2D 2H-13C MAS NMR approach applied to fully isotope labelled deuterated protein covering 220 K temperature range.
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Affiliation(s)
- Ümit Akbey
- Weizmann Institute of Science, Department of Chemical and Biological Physics, Perlman Chemical Sciences Building, P.O. Box 26, Rehovot 76100, Israel.
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24
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Bonaccorsi M, Le Marchand T, Pintacuda G. Protein structural dynamics by Magic-Angle Spinning NMR. Curr Opin Struct Biol 2021; 70:34-43. [PMID: 33915352 DOI: 10.1016/j.sbi.2021.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 02/07/2023]
Abstract
Magic-Angle Spinning (MAS) Nuclear Magnetic Resonance (NMR) is a fast-developing technique, capable of complementing solution NMR, X-ray crystallography, and electron microscopy for the biophysical characterization of microcrystalline, poorly crystalline or disordered protein samples, such as enzymes, biomolecular assemblies, membrane-embedded systems or fibrils. Beyond structures, MAS NMR is an ideal tool for the investigation of dynamics, since it is unique in its ability to distinguish static and dynamic disorder, and to characterize not only amplitudes but also timescales of motion. Building on seminal work on model proteins, the technique is now ripe for widespread application in structural biology. This review briefly summarizes the recent evolutions in biomolecular MAS NMR and accounts for the growing number of systems where this spectroscopy has provided a description of conformational dynamics over the very last few years.
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Affiliation(s)
- Marta Bonaccorsi
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Tanguy Le Marchand
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France.
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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Solid-state NMR approaches to investigate large enzymes in complex with substrates and inhibitors. Biochem Soc Trans 2020; 49:131-144. [PMID: 33367567 DOI: 10.1042/bst20200099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022]
Abstract
Enzyme catalysis is omnipresent in the cell. The mechanisms by which highly evolved protein folds enable rapid and specific chemical transformation of substrates belong to the marvels of structural biology. Targeting of enzymes with inhibitors has immediate application in drug discovery, from chemotherapeutics over antibiotics to antivirals. NMR spectroscopy combines multiple assets for the investigation of enzyme function. The non-invasive technique can probe enzyme structure and dynamics and map interactions with substrates, cofactors and inhibitors at the atomic level. With experiments performed at close to native conditions, catalytic transformations can be monitored in real time, giving access to kinetic parameters. The power of NMR in the solid state, in contrast with solution, lies in the absence of fundamental size limitations, which is crucial for enzymes that are either membrane-embedded or assemble into large soluble complexes exceeding hundreds of kilodaltons in molecular weight. Here we review recent progress in solid-state NMR methodology, which has taken big leaps in the past years due to steady improvements in hardware design, notably magic angle spinning, and connect it to parallel biochemical advances that enable isotope labelling of increasingly complex enzymes. We first discuss general concepts and requirements of the method and then highlight the state-of-the-art in sample preparation, structure determination, dynamics and interaction studies. We focus on examples where solid-state NMR has been instrumental in elucidating enzyme mechanism, alone or in integrative studies.
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Rovó P. Recent advances in solid-state relaxation dispersion techniques. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 108:101665. [PMID: 32574905 DOI: 10.1016/j.ssnmr.2020.101665] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
This review describes two rotating-frame (R1ρ) relaxation dispersion methods, namely the Bloch-McConnell Relaxation Dispersion and the Near-rotary Resonance Relaxation Dispersion, which enable the study of microsecond time-scale conformational fluctuations in the solid state using magic-angle-spinning nuclear magnetic resonance spectroscopy. The goal is to provide the reader with key ideas, experimental descriptions, and practical considerations associated with R1ρ measurements that are needed for analyzing relaxation dispersion and quantifying conformational exchange. While the focus is on protein motion, many presented concepts can be equally well adapted to study the microsecond time-scale dynamics of other bio- (e.g. lipids, polysaccharides, nucleic acids), organic (e.g. pharmaceutical compounds), or inorganic molecules (e.g., metal organic frameworks). This article summarizes the essential contributions made by recent theoretical and experimental solid-state NMR studies to our understanding of protein motion. Here we discuss recent advances in fast MAS applications that enable the observation and atomic level characterization of sparsely populated conformational states which are otherwise inaccessible for other experimental methods. Such high-energy states are often associated with protein functions such as molecular recognition, ligand binding, or enzymatic catalysis, as well as with disease-related properties such as misfolding and amyloid formation.
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Affiliation(s)
- Petra Rovó
- Department of Chemistry, Ludwig Maximilian University Munich, Butenandtstr. 5-13, 81377, Munich, Germany; Center for NanoScience (CeNS), Schellingstr. 4, 80799, Munich, Germany.
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Recent developments in isotope-aided NMR methods for supramolecular protein complexes –SAIL aromatic TROSY. Biochim Biophys Acta Gen Subj 2020; 1864:129439. [DOI: 10.1016/j.bbagen.2019.129439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 11/18/2022]
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Alderson TR, Kay LE. Unveiling invisible protein states with NMR spectroscopy. Curr Opin Struct Biol 2020; 60:39-49. [DOI: 10.1016/j.sbi.2019.10.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
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