1
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Törner R, Awad R, Gans P, Brutscher B, Boisbouvier J. Spectral editing of intra- and inter-chain methyl-methyl NOEs in protein complexes. JOURNAL OF BIOMOLECULAR NMR 2020; 74:83-94. [PMID: 31897934 DOI: 10.1007/s10858-019-00293-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
Specific isotopic labeling of methyl groups in a perdeuterated protein background enables the detection of long range NOEs in proteins or high molecular weight complexes. We introduce here an approach, combining an optimized isotopic labeling scheme with a specifically tailored NMR pulse sequence, to distinguish between intramolecular and intermolecular NOE connectivities. In hetero-oligomeric complexes, this strategy enables sign encoding of intra-subunit and inter-subunit NOEs. For homo-oligomeric assemblies, our strategy allows the specific detection of intra-chain NOEs in high resolution 3D NOESY spectra. The general principles, possibilities and limitations of this approach are presented. Applications of this approach for the detection of intermolecular NOEs in a hetero-hexamer, and the assignment of methyl 1H and 13C resonances in a homo-tetrameric protein complex are shown.
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Affiliation(s)
- Ricarda Törner
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Rida Awad
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Pierre Gans
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Bernhard Brutscher
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France.
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2
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Sala D, Cerofolini L, Fragai M, Giachetti A, Luchinat C, Rosato A. A protocol to automatically calculate homo-oligomeric protein structures through the integration of evolutionary constraints and NMR ambiguous contacts. Comput Struct Biotechnol J 2019; 18:114-124. [PMID: 31969972 PMCID: PMC6961069 DOI: 10.1016/j.csbj.2019.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/20/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Protein assemblies are involved in many important biological processes. Solid-state NMR (SSNMR) spectroscopy is a technique suitable for the structural characterization of samples with high molecular weight and thus can be applied to such assemblies. A significant bottleneck in terms of both effort and time required is the manual identification of unambiguous intermolecular contacts. This is particularly challenging for homo-oligomeric complexes, where simple uniform labeling may not be effective. We tackled this challenge by exploiting coevolution analysis to extract information on homo-oligomeric interfaces from NMR-derived ambiguous contacts. After removing the evolutionary couplings (ECs) that are already satisfied by the 3D structure of the monomer, the predicted ECs are matched with the automatically generated list of experimental contacts. This approach provides a selection of potential interface residues that is used directly in monomer-monomer docking calculations. We validated the protocol on tetrameric L-asparaginase II and dimeric Sod1.
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Affiliation(s)
- Davide Sala
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Linda Cerofolini
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Andrea Giachetti
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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3
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V S M, Gopinath T, Wang S, Veglia G. T 2* weighted Deconvolution of NMR Spectra: Application to 2D Homonuclear MAS Solid-State NMR of Membrane Proteins. Sci Rep 2019; 9:8225. [PMID: 31160739 PMCID: PMC6546711 DOI: 10.1038/s41598-019-44461-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/01/2019] [Indexed: 11/14/2022] Open
Abstract
2D homonuclear NMR spectroscopy is an essential technique to characterize small and large molecules, such as organic compounds, metabolites, and biomacromolecules at atomic resolution. However, for complex samples 2D homonuclear spectra display poor resolution, making spectral assignment very cumbersome. Here, we propose a new method that exploits the differential T2* relaxation times of individual resonances and resolves the 2D NMR peaks into pseudo-3D spectra, where time is the 3rd dimension. T2* weIghted DEconvolution or TIDE analyzes individual free induction decays (FIDs) and dissects them into sub-FIDs that are transformed into pseudo-3D spectra combining Fourier transformation and covariance NMR. TIDE achieves higher resolution and sensitivity for NMR spectra than classical covariance NMR reducing offset-dependent artifacts. We demonstrate the performance of TIDE for magic angle spinning (MAS) [13C,13C]-DARR NMR spectra of single- and multi-span membrane proteins embedded in lipid bilayers. Since TIDE is applicable to all type of homonuclear correlation experiments for liquid and solid samples, we anticipate that it will be a general method for processing NMR data of biomacromolecules, complex mixtures of metabolites as well as material samples.
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Affiliation(s)
- Manu V S
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
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4
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Larsen EK, Olivieri C, Walker C, V S M, Gao J, Bernlohr DA, Tonelli M, Markley JL, Veglia G. Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy. Molecules 2018; 23:E1937. [PMID: 30081441 PMCID: PMC6205158 DOI: 10.3390/molecules23081937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 11/23/2022] Open
Abstract
Protein-protein interactions (PPIs) regulate a plethora of cellular processes and NMR spectroscopy has been a leading technique for characterizing them at the atomic resolution. Technically, however, PPIs characterization has been challenging due to multiple samples required to characterize the hot spots at the protein interface. In this paper, we review our recently developed methods that greatly simplify PPI studies, which minimize the number of samples required to fully characterize residues involved in the protein-protein binding interface. This original strategy combines asymmetric labeling of two binding partners and the carbonyl-carbon label selective (CCLS) pulse sequence element implemented into the heteronuclear single quantum correlation (¹H-15N HSQC) spectra. The CCLS scheme removes signals of the J-coupled 15N⁻13C resonances and records simultaneously two individual amide fingerprints for each binding partner. We show the application to the measurements of chemical shift correlations, residual dipolar couplings (RDCs), and paramagnetic relaxation enhancements (PRE). These experiments open an avenue for further modifications of existing experiments facilitating the NMR analysis of PPIs.
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Affiliation(s)
- Erik K Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Manu V S
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Madison, WI 53706, USA.
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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5
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Ekanayake EV, Fu R, Cross TA. Structural Influences: Cholesterol, Drug, and Proton Binding to Full-Length Influenza A M2 Protein. Biophys J 2016; 110:1391-9. [PMID: 27028648 DOI: 10.1016/j.bpj.2015.11.3529] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 12/25/2022] Open
Abstract
The structure and functions of the M2 protein from Influenza A are sensitive to pH, cholesterol, and the antiinfluenza drug Amantadine. This is a tetrameric membrane protein of 97 amino-acid residues that has multiple functions, among them as a proton-selective channel and facilitator of viral budding, replacing the need for the ESCRT proteins that other viruses utilize. Here, various amino-acid-specific-labeled samples of the full-length protein were prepared and mixed, so that only interresidue (13)C-(13)C cross peaks between two differently labeled proteins representing interhelical interactions are observed. This channel is activated at slightly acidic pH values in the endosome when the His(37) residues in the middle of the transmembrane domain take on a +2 or +3 charged state. Changes observed here in interhelical distances in the N-terminus can be accounted for by modest structural changes, and no significant changes in structure were detected in the C-terminal portion of the channel upon activation of the channel. Amantadine, which blocks proton conductance by binding in the aqueous pore near the N-terminus, however, significantly modifies the tetrameric structure on the opposite side of the membrane. The interactions between the juxtamembrane amphipathic helix of one monomer and its neighboring monomer observed in the absence of drug are disrupted in its presence. However, the addition of cholesterol prevents this structural disruption. In fact, strong interactions are observed between cholesterol and residues in the amphipathic helix, accounting for cholesterol binding adjacent to a native palmitoylation site and near to an interhelix crevice that is typical of cholesterol binding sites. The resultant stabilization of the amphipathic helix deep in the bilayer interface facilitates the bilayer curvature that is essential for viral budding.
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Affiliation(s)
- E Vindana Ekanayake
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida; National High Magnetic Field Lab, Florida State University, Tallahassee, Florida
| | - Riqiang Fu
- National High Magnetic Field Lab, Florida State University, Tallahassee, Florida
| | - Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida; National High Magnetic Field Lab, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida.
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6
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Anglister J, Srivastava G, Naider F. Detection of intermolecular NOE interactions in large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:40-56. [PMID: 27888839 DOI: 10.1016/j.pnmrs.2016.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 08/04/2016] [Accepted: 08/07/2016] [Indexed: 05/12/2023]
Abstract
Intermolecular NOE interactions are invaluable for structure determination of biomolecular complexes by NMR and they represent the "gold-standard" amongst NMR measurements for characterizing interfaces. These NOEs constitute only a small fraction of the observed NOEs in a complex and are usually weaker than many of the intramolecular NOEs. A number of methods have been developed to remove the intramolecular NOEs that interfere with the identification of intermolecular NOEs. NMR experiments used to observe intermolecular NOE interactions in large protein complexes must cope with the short T2 relaxation time of the protons and heteronuclei in these complexes because they result in severe losses in sensitivity. The isotope-edited/isotope-filtered experiment is a powerful method for extraction of intermolecular NOEs in biomolecular complexes. Its application to large protein complexes is limited because of severe losses in signal-to-noise ratio caused by delays in the pulse sequence necessary for the multiple magnetization transfer steps between protons and heteronuclei. Isotope-edited/isotope-edited experiments, in which one protein is usually labeled with 13C and the other is labeled with 15N, reduce possible artifacts in the filtering experiments and improve somewhat the sensitivity of these experiments. Sensitivity can also be improved by deuteration of the components of the complex in order to replace either or both of the filtering or editing steps. Asymmetric deuteration, where aromatic residues in one protein and non-aromatic amino acids in the other are reverse protonated, can eliminate the editing and the filtering steps altogether, thus maintaining high sensitivity even for large proteins complexes. Difference spectroscopy and the use of 2D NOESY experiments without using editing or filtering steps can significantly increase the signal-to-noise ratio in experiments aimed at observing intermolecular NOEs. The measurement of NOESY spectra of three different preparations of a heterodimeric complex under investigation in which one or neither of the components is uniformly deuterated, and calculation of a double difference spectrum provides information on all intermolecular NOEs of non-exchangeable protons. Recent studies indicate that many protein-protein interactions are actually between a protein and a linear peptide recognition motif of the second protein, and determinants represented by linear peptides contribute significantly to the binding energy. NMR is a very versatile method to study peptide-protein interactions over a wide range of binding affinities and binding kinetics. Protein-peptide interactions in complexes exhibiting tight binding can be studied using single and/or multiple deuteration of the peptide residues and measuring a difference NOESY spectrum. This difference spectrum will show exclusively intra- and intermolecular interactions of the peptide protons that were deuterated. Transferred nuclear Overhauser spectroscopy (TRNOE) extends NMR to determine interactions within and between a weakly-bound rapidly-exchanging peptide and its protein target. TRNOE, together with asymmetric deuteration, is applicable to complexes up to ∼100KDa and is highly sensitive, taking advantage of the long average T2 of the peptide protons. Among the methods described in this review, TRNOE has the best potential to determine intermolecular NOEs for the upper molecular weight limit of proteins that can be studied in detail by NMR.
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Affiliation(s)
- Jacob Anglister
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Gautam Srivastava
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Fred Naider
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, New York 10314, USA; Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA; Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel(1)
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7
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Rossi P, Shi L, Liu G, Barbieri CM, Lee HW, Grant TD, Luft JR, Xiao R, Acton TB, Snell EH, Montelione GT, Baker D, Lange OF, Sgourakis NG. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta. Proteins 2015; 83:309-17. [PMID: 25388768 PMCID: PMC5061451 DOI: 10.1002/prot.24719] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/10/2014] [Accepted: 10/29/2014] [Indexed: 01/26/2023]
Abstract
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology-based methods, protein-protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet-V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution.
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Affiliation(s)
- Paolo Rossi
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Lei Shi
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Gaohua Liu
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Christopher M. Barbieri
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Hsiau-Wei Lee
- Department of Chemistry, Complex Carbohydrate Research Center, and Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center, and Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia 30602
| | - Thomas D. Grant
- Hauptman–Woodward Medical Research Institute, and Northeast Structural Genomics Consortium, Buffalo, New York 14203
- SUNY Buffalo Department of Structural Biology, Buffalo, New York 14203
| | - Joseph R. Luft
- Hauptman–Woodward Medical Research Institute, and Northeast Structural Genomics Consortium, Buffalo, New York 14203
- SUNY Buffalo Department of Structural Biology, Buffalo, New York 14203
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Thomas B. Acton
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, and Northeast Structural Genomics Consortium, Buffalo, New York 14203
- SUNY Buffalo Department of Structural Biology, Buffalo, New York 14203
| | - Gaetano T. Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
- Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195
| | - Oliver F. Lange
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Nikolaos G. Sgourakis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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8
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Asymmetric perturbations of signalling oligomers. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:153-69. [PMID: 24650570 DOI: 10.1016/j.pbiomolbio.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 01/06/2023]
Abstract
This review focuses on rapid and reversible noncovalent interactions for symmetric oligomers of signalling proteins. Symmetry mismatch, transient symmetry breaking and asymmetric perturbations via chemical (ligand binding) and physical (electric or mechanic) effects can initiate the signalling events. Advanced biophysical methods can reveal not only structural symmetries of stable membrane-bound signalling proteins but also asymmetric functional transition states. Relevant techniques amenable to distinguish between symmetric and asymmetric architectures are discussed including those with the capability of capturing low-populated transient conformational states. Typical examples of signalling proteins are overviewed for symmetry breaking in dimers (GPCRs, growth factor receptors, transcription factors); trimers (acid-sensing ion channels); tetramers (voltage-gated cation channels, ionotropic glutamate receptor, CNG and CHN channels); pentameric ligand-gated and mechanosensitive channels; higher order oligomers (gap junction channel, chaperonins, proteasome, virus capsid); as well as primary and secondary transporters. In conclusion, asymmetric perturbations seem to play important functional roles in a broad range of communicating networks.
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9
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Vostrikov VV, Mote KR, Verardi R, Veglia G. Structural dynamics and topology of phosphorylated phospholamban homopentamer reveal its role in the regulation of calcium transport. Structure 2013; 21:2119-30. [PMID: 24207128 DOI: 10.1016/j.str.2013.09.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 01/25/2023]
Abstract
Phospholamban (PLN) inhibits the sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA), thereby regulating cardiac diastole. In membranes, PLN assembles into homopentamers that in both the phosphorylated and nonphosphorylated states have been proposed to form ion-selective channels. Here, we determined the structure of the phosphorylated pentamer using a combination of solution and solid-state nuclear magnetic resonance methods. We found that the pinwheel architecture of the homopentamer is preserved upon phosphorylation, with each monomer having an L-shaped conformation. The TM domains form a hydrophobic pore approximately 24 Å long and 2 Å in diameter, which is inconsistent with canonical Ca²⁺-selective channels. Phosphorylation, however, enhances the conformational dynamics of the cytoplasmic region of PLN, causing partial unwinding of the amphipathic helix. We propose that PLN oligomers act as storage for active monomers, keeping SERCA function within a physiological window.
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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10
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Verardi R, Traaseth NJ, Masterson LR, Vostrikov VV, Veglia G. Isotope labeling for solution and solid-state NMR spectroscopy of membrane proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:35-62. [PMID: 23076578 PMCID: PMC3555569 DOI: 10.1007/978-94-007-4954-2_3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this chapter, we summarize the isotopic labeling strategies used to obtain high-quality solution and solid-state NMR spectra of biological samples, with emphasis on integral membrane proteins (IMPs). While solution NMR is used to study IMPs under fast tumbling conditions, such as in the presence of detergent micelles or isotropic bicelles, solid-state NMR is used to study the structure and orientation of IMPs in lipid vesicles and bilayers. In spite of the tremendous progress in biomolecular NMR spectroscopy, the homogeneity and overall quality of the sample is still a substantial obstacle to overcome. Isotopic labeling is a major avenue to simplify overlapped spectra by either diluting the NMR active nuclei or allowing the resonances to be separated in multiple dimensions. In the following we will discuss isotopic labeling approaches that have been successfully used in the study of IMPs by solution and solid-state NMR spectroscopy.
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Affiliation(s)
- Raffaello Verardi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | | | | | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
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11
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Cavalli A, Montalvao RW, Vendruscolo M. Using Chemical Shifts to Determine Structural Changes in Proteins upon Complex Formation. J Phys Chem B 2011; 115:9491-4. [DOI: 10.1021/jp202647q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Andrea Cavalli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Rinaldo W. Montalvao
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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12
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Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method. Proc Natl Acad Sci U S A 2011; 108:9101-6. [PMID: 21576492 DOI: 10.1073/pnas.1016535108] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Phospholamban (PLN) is a type II membrane protein that inhibits the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA), thereby regulating calcium homeostasis in cardiac muscle. In membranes, PLN forms pentamers that have been proposed to function either as a storage for active monomers or as ion channels. Here, we report the T-state structure of pentameric PLN solved by a hybrid solution and solid-state NMR method. In lipid bilayers, PLN adopts a pinwheel topology with a narrow hydrophobic pore, which excludes ion transport. In the T state, the cytoplasmic amphipathic helices (domains Ia) are absorbed into the lipid bilayer with the transmembrane domains arranged in a left-handed coiled-coil configuration, crossing the bilayer with a tilt angle of approximately 11° with respect to the membrane normal. The tilt angle difference between the monomer and pentamer is approximately 13°, showing that intramembrane helix-helix association forces dominate over the hydrophobic mismatch, driving the overall topology of the transmembrane assembly. Our data reveal that both topology and function of PLN are shaped by the interactions with lipids, which fine-tune the regulation of SERCA.
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13
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Shi L, Traaseth NJ, Verardi R, Gustavsson M, Gao J, Veglia G. Paramagnetic-based NMR restraints lift residual dipolar coupling degeneracy in multidomain detergent-solubilized membrane proteins. J Am Chem Soc 2011; 133:2232-41. [PMID: 21287984 DOI: 10.1021/ja109080t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are widely used as orientation-dependent NMR restraints to improve the resolution of the NMR conformational ensemble of biomacromolecules and define the relative orientation of multidomain proteins and protein complexes. However, the interpretation of RDCs is complicated by the intrinsic degeneracy of analytical solutions and protein dynamics that lead to ill-defined orientations of the structural domains (ghost orientations). Here, we illustrate how restraints from paramagnetic relaxation enhancement (PRE) experiments lift the orientational ambiguity of multidomain membrane proteins solubilized in detergent micelles. We tested this approach on monomeric phospholamban (PLN), a 52-residue membrane protein, which is composed of two helical domains connected by a flexible loop. We show that the combination of classical solution NMR restraints (NOEs and dihedral angles) with RDC and PRE constraints resolves topological ambiguities, improving the convergence of the PLN structural ensemble and giving the depth of insertion of the protein within the micelle. The combination of RDCs with PREs will be necessary for improving the accuracy and precision of membrane protein conformational ensembles, where three-dimensional structures are dictated by interactions with the membrane-mimicking environment rather than compact tertiary folds common in globular proteins.
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Affiliation(s)
- Lei Shi
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Traaseth NJ, Veglia G. Probing excited states and activation energy for the integral membrane protein phospholamban by NMR CPMG relaxation dispersion experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:77-81. [PMID: 19781521 DOI: 10.1016/j.bbamem.2009.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 09/09/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
Abstract
Phospholamban (PLN) is a dynamic single-pass membrane protein that inhibits the flow of Ca(2+) ions into the sarcoplasmic reticulum (SR) of heart muscle by directly binding to and inhibiting the SR Ca(2+)ATPase (SERCA). The PLN monomer is the functionally active form that exists in equilibrium between ordered (T state) and disordered (R state) states. While the T state has been fully characterized using a hybrid solution/solid-state NMR approach, the R state structure has not been fully portrayed. It has, however, been detected by both NMR and EPR experiments in detergent micelles and lipid bilayers. In this work, we quantitatively probed the mus to ms dynamics of the PLN excited states by observing the T state in DPC micelles using CPMG relaxation dispersion NMR spectroscopy under functional conditions for SERCA. The (15)N backbone and (13)C(delta1) Ile-methyl dispersion curves were fit using a two-state equilibrium model, and indicate that residues within domain Ia (residues 1-16), the loop (17-22), and domain Ib (23-30) of PLN undergo mus-ms dynamics (k(ex)=6100+/-800 s(-1) at 17 degrees C). We measured k(ex) at additional temperatures, which allowed for a calculation of activation energy equal to approximately 5 kcal/mol. This energy barrier probably does not correspond to the detachment of the amphipathic domain Ia, but rather the energy needed to unwind domain Ib on the membrane surface, likely an important mechanism by which PLN converts between high and low affinity states for its binding partners.
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Affiliation(s)
- Nathaniel J Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55445, USA
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Shi L, Traaseth NJ, Verardi R, Cembran A, Gao J, Veglia G. A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints. JOURNAL OF BIOMOLECULAR NMR 2009; 44:195-205. [PMID: 19597943 PMCID: PMC2824793 DOI: 10.1007/s10858-009-9328-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 05/15/2009] [Indexed: 05/11/2023]
Abstract
To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, E (z) (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.
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Affiliation(s)
- Lei Shi
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nathaniel J. Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
| | - Raffaello Verardi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
| | - Alessandro Cembran
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA. Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
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Structure and topology of monomeric phospholamban in lipid membranes determined by a hybrid solution and solid-state NMR approach. Proc Natl Acad Sci U S A 2009; 106:10165-70. [PMID: 19509339 DOI: 10.1073/pnas.0904290106] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phospholamban (PLN) is an essential regulator of cardiac muscle contractility. The homopentameric assembly of PLN is the reservoir for active monomers that, upon deoligomerization form 1:1 complexes with the sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA), thus modulating the rate of calcium uptake. In lipid bilayers and micelles, monomeric PLN exists in equilibrium between a bent (or resting) T state and a more dynamic (or active) R state. Here, we report the high-resolution structure and topology of the T state of a monomeric PLN mutant in lipid bilayers, using a hybrid of solution and solid-state NMR restraints together with molecular dynamics simulations in explicit lipid environments. Unlike the previous structural ensemble determined in micelles, this approach gives a complete picture of the PLN monomer structure in a lipid bilayer. This hybrid ensemble exemplifies the tilt, rotation, and depth of membrane insertion, revealing the interaction with the lipids for all protein domains. The N-terminal amphipathic helical domain Ia (residues 1-16) rests on the surface of the lipid membrane with the hydrophobic face of domain Ia embedded in the membrane bilayer interior. The helix comprised of domain Ib (residues 23-30) and transmembrane domain II (residues 31-52) traverses the bilayer with a tilt angle of approximately 24 degrees . The specific interactions between PLN and lipid membranes may represent an additional regulatory element of its inhibitory function. We propose this hybrid method for the simultaneous determination of structure and topology for membrane proteins with compact folds or proteins whose spatial arrangement is dictated by their specific interactions with lipid bilayers.
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Masterson LR, Tonelli M, Markley JL, Veglia G. Simultaneous detection and deconvolution of congested NMR spectra containing three isotopically labeled species. J Am Chem Soc 2008; 130:7818-9. [PMID: 18512910 DOI: 10.1021/ja802701w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a procedure for isolating subspectra corresponding to individual protein or peptide components in a ternary mixture or complex. Each of the three-component species is labeled differently: species A uniformly with 15N, species B uniformly with 15N and 13C, and species C uniformly with 15N but selectively with 13C' or 13Calpha. By using the dual carbon label selective HSQC (DCLS-HSQC) pulse sequence and exploiting differences in 1J 15N-13C coupling patterns to filter selected 15N resonances from detection during a constant time period, a subspectrum from each species can be generated from three spectra acquired from a single sample. Many important biological pathways involve dynamic interactions among members of multicomponent protein assemblies, and this approach offers a powerful way to monitor such processes.
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Affiliation(s)
- Larry R Masterson
- Department of Chemistry and Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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