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Nimerovsky E, Najbauer EÉ, Becker S, Andreas LB. Great Offset Difference Internuclear Selective Transfer. J Phys Chem Lett 2023; 14:3939-3945. [PMID: 37078685 PMCID: PMC10150390 DOI: 10.1021/acs.jpclett.3c00194] [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: 01/20/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Carbon-carbon dipolar recoupling sequences are frequently used building blocks in routine magic-angle spinning NMR experiments. While broadband homonuclear first-order dipolar recoupling sequences mainly excite intra-residue correlations, selective methods can detect inter-residue transfers and long-range correlations. Here, we present the great offset difference internuclear selective transfer (GODIST) pulse sequence optimized for selective carbonyl or aliphatic recoupling at fast magic-angle spinning, here, 55 kHz. We observe a 3- to 5-fold increase in intensities compared with broadband RFDR recoupling for perdeuterated microcrystalline SH3 and for the membrane protein influenza A M2 in lipid bilayers. In 3D (H)COCO(N)H and (H)CO(CO)NH spectra, inter-residue carbonyl-carbonyl correlations up to about 5 Å are observed in uniformly 13C-labeled proteins.
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Affiliation(s)
- Evgeny Nimerovsky
- Department of NMR-based Structural
Biology, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Eszter Éva Najbauer
- Department of NMR-based Structural
Biology, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Stefan Becker
- Department of NMR-based Structural
Biology, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Loren B. Andreas
- Department of NMR-based Structural
Biology, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, Göttingen 37077, Germany
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2
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Nimerovsky E, Najbauer EE, Movellan KT, Xue K, Becker S, Andreas LB. Modest Offset Difference Internuclear Selective Transfer via Homonuclear Dipolar Coupling. J Phys Chem Lett 2022; 13:1540-1546. [PMID: 35133845 PMCID: PMC8859849 DOI: 10.1021/acs.jpclett.1c03871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/02/2022] [Indexed: 05/02/2023]
Abstract
Homonuclear dipolar recoupling is routinely used for magic-angle spinning NMR-based structure determination. In fully protonated samples, only short proton-proton distances are accessible to broadband recoupling approaches because of high proton density. Selective methods allow detection of longer distances by directing polarization to a subset of spins. Here we introduce the selective pulse sequence MODIST, which recouples spins that have a modest chemical shift offset difference, and demonstrate it to selectively record correlations between amide protons. The sequence was selected for good retention of total signal, leading to up to twice the intensity for proton-proton correlations compared with other selective methods. The sequence is effective across a range of spinning conditions and magnetic fields, here tested at 55.555 and 100 kHz magic-angle spinning and at proton Larmor frequencies from 600 to 1200 MHz. For influenza A M2 in lipid bilayers, cross-peaks characteristic of a helical conformation are observed.
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Affiliation(s)
- Evgeny Nimerovsky
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eszter E. Najbauer
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kai Xue
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Loren B. Andreas
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Addison B, Stengel D, Bharadwaj VS, Happs RM, Doeppke C, Wang T, Bomble YJ, Holland GP, Harman-Ware AE. Selective One-Dimensional 13C- 13C Spin-Diffusion Solid-State Nuclear Magnetic Resonance Methods to Probe Spatial Arrangements in Biopolymers Including Plant Cell Walls, Peptides, and Spider Silk. J Phys Chem B 2020; 124:9870-9883. [PMID: 33091304 DOI: 10.1021/acs.jpcb.0c07759] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Two-dimensional (2D) and 3D through-space 13C-13C homonuclear spin-diffusion techniques are powerful solid-state nuclear magnetic resonance (NMR) tools for extracting structural information from 13C-enriched biomolecules, but necessarily long acquisition times restrict their applications. In this work, we explore the broad utility and underutilized power of a chemical shift-selective one-dimensional (1D) version of a 2D 13C-13C spin-diffusion solid-state NMR technique. The method, which is called 1D dipolar-assisted rotational resonance (DARR) difference, is applied to a variety of biomaterials including lignocellulosic plant cell walls, microcrystalline peptide fMLF, and black widow dragline spider silk. 1D 13C-13C spin-diffusion methods described here apply in select cases in which the 1D 13C solid-state NMR spectrum displays chemical shift-resolved moieties. This is analogous to the selective 1D nuclear Overhauser effect spectroscopy (NOESY) experiment utilized in liquid-state NMR as a faster (1D instead of 2D) and often less ambiguous (direct sampling of the time domain data, coupled with increased signal averaging) alternative to 2D NOESY. Selective 1D 13C-13C spin-diffusion methods are more time-efficient than their 2D counterparts such as proton-driven spin diffusion (PDSD) and dipolar-assisted rotational resonance. The additional time gained enables measurements of 13C-13C spin-diffusion buildup curves and extraction of spin-diffusion time constants TSD, yielding detailed structural information. Specifically, selective 1D DARR difference buildup curves applied to 13C-enriched hybrid poplar woody stems confirm strong spatial interaction between lignin and acetylated xylan polymers within poplar plant secondary cell walls, and an interpolymer distance of ∼0.45-0.5 nm was estimated. Additionally, Tyr/Gly long-range correlations were observed on isotopically enriched black widow spider dragline silks.
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Affiliation(s)
- Bennett Addison
- Renewable Resources and Enabling Sciences Center, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Dillan Stengel
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Renee M Happs
- Renewable Resources and Enabling Sciences Center, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Crissa Doeppke
- Renewable Resources and Enabling Sciences Center, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yannick J Bomble
- Biosciences Center, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Gregory P Holland
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - Anne E Harman-Ware
- Renewable Resources and Enabling Sciences Center, 15013 Denver West Parkway, Golden, Colorado 80401, United States
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Jolly MM, Jarvis JA, Carravetta M, Levitt MH, Williamson PTF. Bidirectional band-selective magnetization transfer along the protein backbone doubles the information content of solid-state NMR correlation experiments. JOURNAL OF BIOMOLECULAR NMR 2017; 69:197-205. [PMID: 29116557 PMCID: PMC5736786 DOI: 10.1007/s10858-017-0147-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 10/21/2017] [Indexed: 05/05/2023]
Abstract
Resonance assignment is the first stage towards solving the structure of a protein. This is normally achieved by the employment of separate inter and intra residue experiments. By utilising the mixed rotation and rotary recoupling (MIRROR) condition it is possible to double the information content through the efficient bidirectional transfer of magnetization from the CO to its adjacent Cα and the Cα of the subsequent amino acid. We have incorporated this into a 3D experiment, a 3D-MIRROR-NCOCA, where correlations present in the 3D spectrum permit the sequential assignment of the protein backbone from a single experiment as we have demonstrated on a microcrystalline preparation of GB3. Furthermore, the low-power requirements of the MIRROR recoupling sequence facilitate the development of a low-power 3D-NCOCA experiment. This has enabled us to realise significant reductions in acquisition times, allowing the acquisition of a single 3D-NCOCA spectrum suitable for a full backbone resonance assignment of GB3 in less than 24 h.
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Affiliation(s)
- M M Jolly
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - J A Jarvis
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - M Carravetta
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - M H Levitt
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - P T F Williamson
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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Mithu VS, Sarkar B, Bhowmik D, Das AK, Chandrakesan M, Maiti S, Madhu PK. Curcumin alters the salt bridge-containing turn region in amyloid β(1-42) aggregates. J Biol Chem 2014; 289:11122-11131. [PMID: 24599958 DOI: 10.1074/jbc.m113.519447] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Amyloid β (Aβ) fibrillar deposits in the brain are a hallmark of Alzheimer disease (AD). Curcumin, a common ingredient of Asian spices, is known to disrupt Aβ fibril formation and to reduce AD pathology in mouse models. Understanding the structural changes induced by curcumin can potentially lead to AD pharmaceutical agents with inherent bio-compatibility. Here, we use solid-state NMR spectroscopy to investigate the structural modifications of amyloid β(1-42) (Aβ42) aggregates induced by curcumin. We find that curcumin induces major structural changes in the Asp-23-Lys-28 salt bridge region and near the C terminus. Electron microscopy shows that the Aβ42 fibrils are disrupted by curcumin. Surprisingly, some of these alterations are similar to those reported for Zn(2+) ions, another agent known to disrupt the fibrils and alter Aβ42 toxicity. Our results suggest the existence of a structurally related family of quasi-fibrillar conformers of Aβ42, which is stabilized both by curcumin and by Zn(2+.)
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Affiliation(s)
- Venus Singh Mithu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005
| | - Bidyut Sarkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005
| | - Debanjan Bhowmik
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005
| | - Anand Kant Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005
| | - Muralidharan Chandrakesan
- Department of Biochemistry, Seth Gordhandas Sunderdas Medical College and King Edward Memorial Hospital, A. D. Marg, Parel, Mumbai 400012, and
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005,.
| | - Perunthiruthy K Madhu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005,; Tata Institute of Fundamental Research Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsinghi, Hyderabad 500 075, India.
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Huster D. Solid-state NMR spectroscopy to study protein-lipid interactions. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:1146-60. [PMID: 24333800 DOI: 10.1016/j.bbalip.2013.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 12/22/2022]
Abstract
The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K(+) channel KcsA are discussed. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany.
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Chevelkov V, Shi C, Fasshuber HK, Becker S, Lange A. Efficient band-selective homonuclear CO-CA cross-polarization in protonated proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 56:303-11. [PMID: 23925478 DOI: 10.1007/s10858-013-9767-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/30/2013] [Indexed: 05/10/2023]
Abstract
Previously introduced for highly deuterated proteins, band-selective magnetization transfer between CO and CA spins by dipolar-based homonuclear cross polarization is applied here to a protonated protein. Robust and efficient recoupling is achieved when the sum of effective radio-frequency fields on CO and CA resonances equals two times the spinning rate, yielding up to 33% of magnetization transfer efficiency in protonated ubiquitin. The approach is designed for moderate magic-angle spinning rates and high external magnetic fields when the isotropic chemical shift difference of CO and CA considerably exceeds the spinning rate. This method has been implemented in NiCOi-1CAi-1 and CAi(Ni)COi-1CAi-1 two-dimensional interresidual correlation experiments for fast and efficient resonance assignment of ubiquitin by solid-state NMR spectroscopy.
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