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van der Wel PCA. Dihedral Angle Measurements for Structure Determination by Biomolecular Solid-State NMR Spectroscopy. Front Mol Biosci 2021; 8:791090. [PMID: 34938776 PMCID: PMC8685456 DOI: 10.3389/fmolb.2021.791090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
In structural studies of immobilized, aggregated and self-assembled biomolecules, solid-state NMR (ssNMR) spectroscopy can provide valuable high-resolution structural information. Among the structural restraints provided by magic angle spinning (MAS) ssNMR the canonical focus is on inter-atomic distance measurements. In the current review, we examine the utility of ssNMR measurements of angular constraints, as a complement to distance-based structure determination. The focus is on direct measurements of angular restraints via the judicious recoupling of multiple anisotropic ssNMR parameters, such as dipolar couplings and chemical shift anisotropies. Recent applications are highlighted, with a focus on studies of nanocrystalline polypeptides, aggregated peptides and proteins, receptor-substrate interactions, and small molecule interactions with amyloid protein fibrils. The review also examines considerations of when and where ssNMR torsion angle experiments are (most) effective, and discusses challenges and opportunities for future applications.
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Affiliation(s)
- Patrick C. A. van der Wel
- Solid-state NMR Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
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Yarava JR, Nishiyama Y, Raghothama S, Ramanathan KV. Conformational investigation of peptides using solid-state NMR spectroscopy-A study of polymorphism of β-turn peptides containing diprolines. Chem Biol Drug Des 2019; 95:394-407. [PMID: 31755652 DOI: 10.1111/cbdd.13649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/02/2019] [Accepted: 11/16/2019] [Indexed: 11/26/2022]
Abstract
The construction of complex protein folds relies on the precise conversion of a linear polypeptide chain into a compact 3-dimensional structure. In this context, study of isolated secondary structural modules containing short stretches of amino acids assumes significance. Additionally, peptides, both natural and synthetic, play a major role as potential drugs. With a view to understand the local conformations adopted by peptides in the solid state, we propose a multinuclear NMR approach utilizing spectra of nuclei in their natural isotopic abundance. Various solid-state NMR experiments have been utilized for assignment of the spectra. Additionally, the gauge-including projector augmented-wave (GIPAW) calculations were used to confirm the assignments. Particularly, the utility of the double-quantum-single-quantum correlation experiments is highlighted for the purpose of assignment and for inferring the conformation across the peptide bond. The methodology is illustrated for the case of designed peptides containing diproline residues occurring at the β-turns for identifying their cis-trans conformational polymorphism. The proposed method promises to be of use in the study of conformations of small- to medium-sized peptides such as antimicrobial peptides and in the study of polymorphism leading to applications in drug development protocols.
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Affiliation(s)
- Jayasubba Reddy Yarava
- NMR Research Centre, Indian Institute of Science, Bangalore, India.,Department of Physics, Indian Institute of Science, Bangalore, India
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Musashino, Akishima, Japan.,RIKEN-JEOL Collaboration Center, Tsurumi, Yokohama, Japan
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Yarava JR, Sonti R, Kantharaju K, Raghothama S, Ramanathan KV. Solid-state NMR at natural isotopic abundance for the determination of conformational polymorphism - the case of designed β-turn peptides containing di-prolines. Chem Commun (Camb) 2017; 53:1317-1320. [PMID: 28074945 DOI: 10.1039/c6cc08676d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The proton double quantum-carbon single quantum correlation experiment has been applied to designed peptides in the solid state in natural isotopic abundance. Analogous to nOe studies in solution, through-space double-quantum connectivities have been exploited to obtain the cis-trans conformational polymorphism of diproline residues occurring at β-turns in the peptides.
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Affiliation(s)
- Jayasubba Reddy Yarava
- Department of Physics, Indian Institute of Science, Bangalore-560012, India and NMR Research Center, Indian Institute of Science, Bangalore-560012, India. and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fedérale de Lausanne, Switzerland
| | - Rajesh Sonti
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India. and Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India and Biozentrum, Structural Biology, Universität Basel, Basel, Switzerland
| | - K Kantharaju
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India and Department of Chemistry, Rani Channamma University, Belgavi, India
| | - S Raghothama
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India.
| | - K V Ramanathan
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India.
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Jenkins JE, Sampath S, Butler E, Kim J, Henning RW, Holland GP, Yarger JL. Characterizing the secondary protein structure of black widow dragline silk using solid-state NMR and X-ray diffraction. Biomacromolecules 2013; 14:3472-83. [PMID: 24024617 PMCID: PMC3914425 DOI: 10.1021/bm400791u] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked β-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) (13)C-(13)C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about the amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and, hence, to the amino acids that make up the motifs. Specifically, alanine is incorporated in β-sheet (poly(Alan) and poly(Gly-Ala)), 3(1)-helix (poly(Gly-Gly-Xaa), and α-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in β-sheet (poly(Gly-Ala)) and 3(1)-helical (poly(Gly-Gly-X(aa))) regions, while serine is present in β-sheet (poly(Gly-Ala-Ser)), 3(1)-helix (poly(Gly-Gly-Ser)), and β-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk.
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Affiliation(s)
- Janelle E. Jenkins
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Sujatha Sampath
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287-1604, USA
- Department of Physics, University of Wisconsin, Milwaukee, WI 53211
| | - Emily Butler
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Jihyun Kim
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Robert W. Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637
| | - Gregory P. Holland
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Jeffery L. Yarger
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287-1604, USA
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Potapov A, Yau WM, Tycko R. Dynamic nuclear polarization-enhanced 13C NMR spectroscopy of static biological solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 231:5-14. [PMID: 23562665 PMCID: PMC3660528 DOI: 10.1016/j.jmr.2013.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/12/2013] [Accepted: 02/14/2013] [Indexed: 05/21/2023]
Abstract
We explore the possibility of using dynamic nuclear polarization (DNP) to enhance signals in structural studies of biological solids by solid state NMR without sample spinning. Specifically, we use 2D (13)C-(13)C exchange spectroscopy to probe the peptide backbone torsion angles (φ, ψ) in a series of selectively (13)C-labeled 40-residue β-amyloid (Aβ(1-40)) samples, in both fibrillar and non-fibrillar states. Experiments are carried out at 9.39 T and 8 K, using a static double-resonance NMR probe and low-power microwave irradiation at 264 GHz. In frozen solutions of Aβ(1-40) fibrils doped with DOTOPA-TEMPO, we observe DNP signal enhancement factors of 16-21. We show that the orientation- and frequency-dependent spin polarization exchange between sequential backbone carbonyl (13)C labels can be simulated accurately using a simple expression for the exchange rate, after experimentally determined homogeneous (13)C lineshapes are incorporated in the simulations. The experimental 2D (13)C-(13)C exchange spectra place constraints on the φ and ψ angles between the two carbonyl labels. Although the data are not sufficient to determine φ and ψ uniquely, the data do provide non-trivial constraints that could be included in structure calculations. With DNP at low temperatures, 2D (13)C-(13)C exchange spectra can be obtained from a 3.5 mg sample of Aβ(1-40) fibrils in 4 h or less, despite the broad (13)C chemical shift anisotropy line shapes that are observed in static samples.
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Affiliation(s)
- Alexey Potapov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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Asakura T, Suzuki Y, Nakazawa Y, Yazawa K, Holland GP, Yarger JL. Silk structure studied with nuclear magnetic resonance. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 69:23-68. [PMID: 23465642 DOI: 10.1016/j.pnmrs.2012.08.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
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Potapov A, Thurber KR, Yau WM, Tycko R. Dynamic nuclear polarization-enhanced ¹H-¹³C double resonance NMR in static samples below 20 K. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 221:32-40. [PMID: 22743540 PMCID: PMC3727229 DOI: 10.1016/j.jmr.2012.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 05/21/2023]
Abstract
We demonstrate the feasibility of one-dimensional and two-dimensional ¹H-¹³C double resonance NMR experiments with dynamic nuclear polarization (DNP) at 9.4 T and temperatures below 20 K, including both ¹H-¹³C cross-polarization and ¹H decoupling, and discuss the effects of polarizing agent type, polarizing agent concentration, temperature, and solvent deuteration. We describe a two-channel low-temperature DNP/NMR probe, capable of carrying the radio-frequency power load required for ¹H-¹³C cross-polarization and high-power proton decoupling. Experiments at 8 K and 16 K reveal a significant T₂ relaxation of ¹³C, induced by electron spin flips. Carr-Purcell experiments and numerical simulations of Carr-Purcell dephasing curves allow us to determine the effective correlation time of electron flips under our experimental conditions. The dependence of the DNP signal enhancement on electron spin concentration shows a maximum near 80 mM. Although no significant difference in the absolute DNP enhancements for triradical (DOTOPA-TEMPO) and biradical (TOTAPOL) dopants was found, the triradical produced greater DNP build-up rates, which are advantageous for DNP experiments. Additionally the feasibility of structural measurements on ¹³C-labeled biomolecules was demonstrated with a two-dimensional ¹³C-¹³C exchange spectrum of selectively ¹³C-labeled β-amyloid fibrils.
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Affiliation(s)
- Alexey Potapov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892-0520, USA.
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Gowda CM, van Eck ERH, van Buul AM, Schwartz E, van Pruissen GWP, Cornelissen JJLM, Rowan AE, Nolte RJM, Kentgens APM. Direct Backbone Structure Determination of Polyisocyanodipeptide Using Solid-State Nuclear Magnetic Resonance. Macromolecules 2012. [DOI: 10.1021/ma300102e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chandrakala M. Gowda
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ernst R. H. van Eck
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Arend M. van Buul
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Erik Schwartz
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Gijsbrecht W. P. van Pruissen
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Alan E. Rowan
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Roeland J. M. Nolte
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Arno P. M. Kentgens
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Hu KN, Havlin RH, Yau WM, Tycko R. Quantitative determination of site-specific conformational distributions in an unfolded protein by solid-state nuclear magnetic resonance. J Mol Biol 2009; 392:1055-73. [PMID: 19647001 DOI: 10.1016/j.jmb.2009.07.073] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 06/27/2009] [Accepted: 07/25/2009] [Indexed: 10/20/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) techniques are used to investigate the structure of the 35-residue villin headpiece subdomain (HP35) in folded, partially denatured, and fully denatured states. Experiments are carried out in frozen glycerol/water solutions, with chemical denaturation by guanidine hydrochloride (GdnHCl). Without GdnHCl, two-dimensional solid-state (13)C NMR spectra of samples prepared with uniform (13)C labeling of selected residues show relatively sharp cross-peaks at chemical shifts that are consistent with the known three-helix bundle structure of folded HP35. At high GdnHCl concentrations, most cross-peaks broaden and shift, qualitatively indicating disruption of the folded structure and development of static conformational disorder in the frozen denatured state. Conformational distributions at one residue in each helical segment are probed quantitatively with three solid-state NMR techniques that provide independent constraints on backbone varphi and psi torsion angles in samples with sequential pairs of carbonyl (13)C labels. Without GdnHCl, the combined data are well fit by alpha-helical conformations. At [GdnHCl]=4.5 M, corresponding to the approximate denaturation midpoint, the combined data are well fit by a combination of alpha-helical and partially extended conformations at each site, but with a site-dependent population ratio. At [GdnHCl]=7.0 M, corresponding to the fully denatured state, the combined data are well fit by a combination of partially extended and polyproline II conformations, again with a site-dependent population ratio. Two entirely different models for conformational distributions lead to nearly the same best-fit distributions, demonstrating the robustness of these conclusions. This work represents the first quantitative investigation of site-specific conformational distributions in partially folded and unfolded states of a protein by solid-state NMR.
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Affiliation(s)
- Kan-Nian Hu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520, USA
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Holland GP, Jenkins JE, Creager MS, Lewis RV, Yarger JL. Solid-state NMR investigation of major and minor ampullate spider silk in the native and hydrated states. Biomacromolecules 2008; 9:651-7. [PMID: 18171016 DOI: 10.1021/bm700950u] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Silks spun from the major (Ma) and minor (Mi) ampullate glands by the spider Nephila clavipes respond to water differently. Specifically, Ma silk supercontracts (shrinks 40-50% in length) while Mi silk does not contract at all when hydrated with water. In the present study, 1H --> 13C cross polarization magic angle spinning (CP-MAS), 13C MAS NMR collected with dipolar decoupling, and two-dimensional wide-line separation spectra are presented on Mi silk in its native and hydrated state and comparisons are made to Ma silk. This combination of NMR data demonstrates that water plasticizes Mi and Ma silk similarly, with an increase in chain dynamics observed in regions containing Gly, Glu, Ser, Tyr, Leu, and a fraction of Ala when the Mi silk is hydrated. Resonances that correspond to the poly(Ala) and poly(Gly Ala) motifs of Ma and Mi silk are predominately rigid indicating that water does not penetrate these beta-sheet domains.
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Affiliation(s)
- Gregory P Holland
- Magnetic Resonance Research Center, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA.
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Hetterscheid DGH, Hendriksen C, Dzik WI, Smits JMM, van Eck ERH, Rowan AE, Busico V, Vacatello M, Van Axel Castelli V, Segre A, Jellema E, Bloemberg TG, de Bruin B. Rhodium-Mediated Stereoselective Polymerization of “Carbenes”. J Am Chem Soc 2006; 128:9746-52. [PMID: 16866530 DOI: 10.1021/ja058722j] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unprecedented rhodium-catalyzed stereoselective polymerization of "carbenes" from ethyl diazoacetate (EDA) to give high molecular mass poly(ethyl 2-ylidene-acetate) is described. The mononuclear, neutral [(N,O-ligand)M(I)(cod)] (M = Rh, Ir) catalytic precursors for this reaction are characterized by (among others) single-crystal X-ray diffraction. These species mediate formation of a new type of polymers from EDA: carbon-chain polymers functionalized with a polar substituent at each carbon of the polymer backbone. The polymers are obtained as white powders with surprisingly sharp NMR resonances. Solution and solid state NMR data for these new polymers reveal a highly stereoregular polymer, with a high degree of crystallinity. The polymer is likely syndiotactic. Material properties are very different from those of atactic poly(diethyl fumarate) polymer obtained by radical polymerization of diethyl fumarate. Other diazoacetates are also polymerized. Further studies are underway to reveal possible applications of these new materials.
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Affiliation(s)
- Dennis G H Hetterscheid
- Institute for Molecules and Materials (IMM), Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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