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Ledwitch KV, Künze G, McKinney JR, Okwei E, Larochelle K, Pankewitz L, Ganguly S, Darling HL, Coin I, Meiler J. Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction. JOURNAL OF BIOMOLECULAR NMR 2023; 77:69-82. [PMID: 37016190 PMCID: PMC10443207 DOI: 10.1007/s10858-023-00412-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
A single experimental method alone often fails to provide the resolution, accuracy, and coverage needed to model integral membrane proteins (IMPs). Integrating computation with experimental data is a powerful approach to supplement missing structural information with atomic detail. We combine RosettaNMR with experimentally-derived paramagnetic NMR restraints to guide membrane protein structure prediction. We demonstrate this approach using the disulfide bond formation protein B (DsbB), an α-helical IMP. Here, we attached a cyclen-based paramagnetic lanthanide tag to an engineered non-canonical amino acid (ncAA) using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry reaction. Using this tagging strategy, we collected 203 backbone HN pseudocontact shifts (PCSs) for three different labeling sites and used these as input to guide de novo membrane protein structure prediction protocols in Rosetta. We find that this sparse PCS dataset combined with 44 long-range NOEs as restraints in our calculations improves structure prediction of DsbB by enhancements in model accuracy, sampling, and scoring. The inclusion of this PCS dataset improved the Cα-RMSD transmembrane segment values of the best-scoring and best-RMSD models from 9.57 Å and 3.06 Å (no NMR data) to 5.73 Å and 2.18 Å, respectively.
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Affiliation(s)
- Kaitlyn V Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Chemistry, Center for Structural Biology, MRBIII 5154E, Vanderbilt University, Nashville, TN, 37212, USA.
| | - Georg Künze
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103, Leipzig, Germany
| | - Jacob R McKinney
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Elleansar Okwei
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Katherine Larochelle
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Lisa Pankewitz
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Soumya Ganguly
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Heather L Darling
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Science, University of Leipzig, 04103, Leipzig, Germany
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103, Leipzig, Germany
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Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
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Pan Y, Stocks BB, Brown L, Konermann L. Structural Characterization of an Integral Membrane Protein in Its Natural Lipid Environment by Oxidative Methionine Labeling and Mass Spectrometry. Anal Chem 2008; 81:28-35. [DOI: 10.1021/ac8020449] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Pan
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Bradley B. Stocks
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Leonid Brown
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Lars Konermann
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Mason AJ, Turner GJ, Glaubitz C. Conformational heterogeneity of transmembrane residues after the Schiff base reprotonation of bacteriorhodopsin. FEBS J 2005; 272:2152-64. [PMID: 15853800 DOI: 10.1111/j.1742-4658.2005.04633.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
bR, N-like and O-like intermediate states of [15N]methionine-labelled wild type and D85N/T170C bacteriorhodopsin were accumulated in native membranes by controlling the pH of the preparations. 15N cross polarization and magic angle sample spinning (CPMAS) NMR spectroscopy allowed resolution of seven out of nine resonances in the bR-state. It was possible to assign some of the observed resonances by using 13C/15N rotational echo double resonance (REDOR) NMR and Mn2+ quenching as well as D2O exchange, which helps to identify conformational changes after the bacteriorhodopsin Schiff base reprotonation. The significant differences in chemical shifts and linewidths detected for some of the resonances in N- and O-like samples indicate changes in conformation, structural heterogeneity or altered molecular dynamics in parts of the protein.
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Affiliation(s)
- A James Mason
- Centre for Biomolecular Magnetic Resonance and Institut für Biophysikalische Chemie, J.W. Goethe Universität, Frankfurt, Germany
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Mason AJ, Grage SL, Straus SK, Glaubitz C, Watts A. Identifying anisotropic constraints in multiply labeled bacteriorhodopsin by 15N MAOSS NMR: a general approach to structural studies of membrane proteins. Biophys J 2004; 86:1610-7. [PMID: 14990487 PMCID: PMC1303995 DOI: 10.1016/s0006-3495(04)74228-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Structural models of membrane proteins can be refined with sets of multiple orientation constraints derived from structural NMR studies of specifically labeled amino acids. The magic angle oriented sample spinning (MAOSS) NMR approach was used to determine a set of orientational constraints in bacteriorhodopsin (bR) in the purple membrane (PM). This method combines the benefits of magic angle spinning (MAS), i.e., improved sensitivity and resolution, with the ability to measure the orientation of anisotropic interactions, which provide important structural information. The nine methionine residues in bacteriorhodopsin were isotopically (15)N labeled and spectra simplified by deuterium exchange before cross-polarization magic angle spinning (CPMAS) experiments. The orientation of the principal axes of the (15)N chemical shift anisotropy (CSA) tensors was determined with respect to the membrane normal for five of six residual resonances by analysis of relative spinning sideband intensities. The applicability of this approach to large proteins embedded in a membrane environment is discussed in light of these results.
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Affiliation(s)
- A James Mason
- Oxford University Biomembrane Structure Unit, Department of Biochemistry, Oxford OX1 3QU, United Kingdom
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Sanders CR, Oxenoid K. Customizing model membranes and samples for NMR spectroscopic studies of complex membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1508:129-45. [PMID: 11090822 DOI: 10.1016/s0005-2736(00)00308-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Both solution and solid state nuclear magnetic resonance (NMR) techniques for structural determination are advancing rapidly such that it is possible to contemplate bringing these techniques to bear upon integral membrane proteins having multiple transmembrane segments. This review outlines existing and emerging options for model membrane media for use in such studies and surveys the special considerations which must be taken into account when preparing larger membrane proteins for NMR spectroscopic studies.
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Affiliation(s)
- C R Sanders
- Department of Physiology and Biophysics, Case Western Reserve University, 44106-4970, Cleveland, OH, USA.
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Tanio M, Tuzi S, Yamaguchi S, Konishi H, Naito A, Needleman R, Lanyi JK, Saitô H. Evidence of local conformational fluctuations and changes in bacteriorhodopsin, dependent on lipids, detergents and trimeric structure, as studied by 13C NMR. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1375:84-92. [PMID: 9767127 DOI: 10.1016/s0005-2736(98)00151-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We examined how the local conformation and dynamics of [3-13C]Ala-labeled bacteriorhodopsin (bR) are altered as viewed from 13C NMR spectra when the natural membrane lipids are partly or completely replaced with detergents. It turned out that the major conformational features of bR, the alphaII-helices, are generally unchanged in the delipidated or solubilized preparations. Upon partial delipidation or detergent solubilization, however, a significant conformational change occurs, ascribed to local conversion of alphaII-->alphaI-helix (one Ala residue involved), evident from the upfield displacement of the transmembrane helical peak from 16.4 ppm to 14.5 ppm, conformational change (one or two Ala residues) within alphaII-helices from 16.4 to 16.0 ppm, and acquired flexibility in the loop region (especially at the F-G loop) as manifested from suppressed peak-intensities in cross-polarization magic angle spinning (CP-MAS) NMR spectra. On the other hand, formation of monomers as solubilized by Triton X-100, Triton N-101 and n-dodecylmaltoside is characterized by the presence of a peak at 15.5 ppm and a shifted absorption maximum (550 nm). The size of micelles under the first two conditions was small enough to yield 13C NMR signals observable by a solution NMR spectrometer, although 13C CP-MAS NMR signals were also visible from a fraction of large-sized micelles. We found that the 16.9 ppm peak (three Ala residues involved), visible by CP-MAS NMR, was displaced upfield when Schiff base was removed by solubilization with sodium dodecyl sulfate, consistent with our previous finding of bleaching to yield bacterioopsin.
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Affiliation(s)
- M Tanio
- Department of Life Science, Himeji Institute of Technology, Hyogo 678-1297, Japan
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Vinogradova O, Badola P, Czerski L, Sönnichsen FD, Sanders CR. Escherichia coli diacylglycerol kinase: a case study in the application of solution NMR methods to an integral membrane protein. Biophys J 1997; 72:2688-701. [PMID: 9168044 PMCID: PMC1184466 DOI: 10.1016/s0006-3495(97)78912-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Diacylglycerol kinase (DAGK) is a 13-kDa integral membrane protein that spans the lipid bilayer three times and which is active in some micellar systems. In this work DAGK was purified using metal ion chelate chromatography, and its structural properties in micelles and organic solvent mixtures studies were examined, primarily to address the question of whether the structure of DAGK can be determined using solution NMR methods. Cross-linking studies established that DAGK is homotrimeric in decyl maltoside (DM) micelles and mixed micelles. The aggregate detergent-protein molecular mass of DAGK in both octyl glucoside and DM micelles was determined to be in the range of 100-110 kDa-much larger than the sum of the molecular weights of the DAGK trimers and the protein-free micelles. In acidic organic solvent mixtures, DAGK-DM complexes were highly soluble and yielded relatively well-resolved NMR spectra. NMR and circular dichroism studies indicated that in these mixtures the enzyme adopts a kinetically trapped monomeric structure in which it irreversibly binds several detergent molecules and is primarily alpha-helical, but in which its tertiary structure is largely disordered. Although these results provide new information regarding the native oligomeric state of DAGK and the structural properties of complex membrane proteins in micelles and organic solvent mixtures, the results discourage the notion that the structure of DAGK can be readily determined at high resolution with solution NMR methods.
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Affiliation(s)
- O Vinogradova
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106-4970, USA
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