1
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Kegulian NC, Langen R, Moradian-Oldak J. The Dynamic Interactions of a Multitargeting Domain in Ameloblastin Protein with Amelogenin and Membrane. Int J Mol Sci 2023; 24:3484. [PMID: 36834897 PMCID: PMC9966149 DOI: 10.3390/ijms24043484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/28/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
The enamel matrix protein Ameloblastin (Ambn) has critical physiological functions, including regulation of mineral formation, cell differentiation, and cell-matrix adhesion. We investigated localized structural changes in Ambn during its interactions with its targets. We performed biophysical assays and used liposomes as a cell membrane model. The xAB2N and AB2 peptides were rationally designed to encompass regions of Ambn that contained self-assembly and helix-containing membrane-binding motifs. Electron paramagnetic resonance (EPR) on spin-labeled peptides showed localized structural gains in the presence of liposomes, amelogenin (Amel), and Ambn. Vesicle clearance and leakage assays indicated that peptide-membrane interactions were independent from peptide self-association. Tryptophan fluorescence and EPR showed competition between Ambn-Amel and Ambn-membrane interactions. We demonstrate localized structural changes in Ambn upon interaction with different targets via a multitargeting domain, spanning residues 57 to 90 of mouse Ambn. Structural changes of Ambn following its interaction with different targets have relevant implications for the multifunctionality of Ambn in enamel formation.
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Affiliation(s)
- Natalie C. Kegulian
- Center for Craniofacial Molecular Biology, Department of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Ralf Langen
- Department of Neuroscience and Physiology, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Janet Moradian-Oldak
- Center for Craniofacial Molecular Biology, Department of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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2
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Biondi B, Syryamina VN, Rocchio G, Barbon A, Formaggio F, Toniolo C, Raap J, Dzuba SA. Is Cys(MTSL) the Best α-Amino Acid Residue to Electron Spin Labeling of Synthetically Accessible Peptide Molecules with Nitroxides? ACS OMEGA 2022; 7:5154-5165. [PMID: 35187331 PMCID: PMC8851612 DOI: 10.1021/acsomega.1c06227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Electron paramagnetic resonance spectroscopy, particularly its pulse technique double electron-electron resonance (DEER) (also termed PELDOR), is rapidly becoming an extremely useful tool for the experimental determination of side chain-to-side chain distances between free radicals in molecules fundamental for life, such as polypeptides. Among appropriate probes, the most popular are undoubtedly nitroxide electron spin labels. In this context, suitable biosynthetically derived, helical regions of proteins, along with synthetic peptides with amphiphilic properties and antibacterial activities, are the most extensively investigated compounds. A strict requirement for a precise distance measurement has been identified in a minimal dynamic flexibility of the two nitroxide-bearing α-amino acid side chains. To this end, in this study, we have experimentally compared in detail the side-chain mobility properties of the two currently most widely utilized residues, namely, Cys(MTSL) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, two double-labeled, chemically synthesized 20-mer peptide molecules have been adopted as appropriate templates for our investigation on the determination of the model intramolecular separations. These double-Cys(MTSL) and double-TOAC compounds are both analogues of the almost completely rigid backbone peptide ruler which we have envisaged and 3D structurally analyzed as our original, unlabeled compound. Here, we have clearly found that the TOAC side-chain labels are largely more 3D structurally restricted than the MTSL labels. From this result, we conclude that the TOAC residue offers more precise information than the Cys(MTSL) residue on the side chain-to-side chain distance distribution in synthetically accessible peptide molecules.
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Affiliation(s)
- Barbara Biondi
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Victoria N. Syryamina
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Gabriele Rocchio
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Antonio Barbon
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Jan Raap
- Leiden
Institute of Chemistry, Gorlaeus Laboratories,
Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
- Department
of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation
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3
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Möbius K, Lubitz W, Savitsky A. CIDEP-Enhanced ENDOR of short-lived radicals. Recollections of first joint experiments with Renad Sagdeev. Russ Chem Bull 2022. [DOI: 10.1007/s11172-021-3366-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Tkach I, Diederichsen U, Bennati M. Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:143-157. [PMID: 33640998 PMCID: PMC8071797 DOI: 10.1007/s00249-021-01508-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 12/01/2022]
Abstract
Electron paramagnetic resonance (EPR)-based pulsed dipolar spectroscopy measures the dipolar interaction between paramagnetic centers that are separated by distances in the range of about 1.5-10 nm. Its application to transmembrane (TM) peptides in combination with modern spin labelling techniques provides a valuable tool to study peptide-to-lipid interactions at a molecular level, which permits access to key parameters characterizing the structural adaptation of model peptides incorporated in natural membranes. In this mini-review, we summarize our approach for distance and orientation measurements in lipid environment using novel semi-rigid TOPP [4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-L-phenylglycine] labels specifically designed for incorporation in TM peptides. TOPP labels can report single peak distance distributions with sub-angstrom resolution, thus offering new capabilities for a variety of TM peptide investigations, such as monitoring of various helix conformations or measuring of tilt angles in membranes.
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Affiliation(s)
- Igor Tkach
- Max Planck Institute for Biophysical Chemistry, RG Electron-Spin Resonance Spectroscopy, 37077, Göttingen, Germany.
| | - Ulf Diederichsen
- Department of Organic and Biomolecular Chemistry, University of Göttingen, 37077, Göttingen, Germany
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, RG Electron-Spin Resonance Spectroscopy, 37077, Göttingen, Germany
- Department of Organic and Biomolecular Chemistry, University of Göttingen, 37077, Göttingen, Germany
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5
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Uddin MA, Yu H, Wang L, Naveed K, Haq F, Amin BU, Mehmood S, Nazir A, Xing Y, Shen D. Recent progress in
EPR
study of spin labeled polymers and spin probed polymer systems. JOURNAL OF POLYMER SCIENCE 2020. [DOI: 10.1002/pol.20200039] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Md Alim Uddin
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Haojie Yu
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Li Wang
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Kaleem‐ur‐Rahman Naveed
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Fazal Haq
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Bilal Ul Amin
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Sahid Mehmood
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Ahsan Nazir
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Yusheng Xing
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
| | - Di Shen
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological EngineeringZhejiang University Hangzhou Zhejiang China
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6
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Naveed KUR, Wang L, Yu H, Ullah RS, Haroon M, Fahad S, Li J, Elshaarani T, Khan RU, Nazir A. Recent progress in the electron paramagnetic resonance study of polymers. Polym Chem 2018. [DOI: 10.1039/c8py00689j] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This review article provides an overview of the contemporary research based on a tailor-made technique to understand the paramagnetic behavior of different polymer classes.
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Affiliation(s)
| | - Li Wang
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
| | - Haojie Yu
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
| | - Raja Summe Ullah
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
| | - Muhammad Haroon
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
| | - Shah Fahad
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
| | - Jiyang Li
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
| | - Tarig Elshaarani
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
| | - Rizwan Ullah Khan
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
| | - Ahsan Nazir
- College of Chemical and Biological Engineering
- Zhejiang University
- Zhejiang
- China
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7
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Hellmich UA, McIlwain B, Doshi R. Where do we go from here? Membrane protein research beyond the structure-function horizon. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:801-803. [PMID: 29277439 DOI: 10.1016/j.bbamem.2017.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ute A Hellmich
- Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | | | - Rupak Doshi
- InhibRx LLP, 11099 N Torrey Pines Rd., Suite 280, La Jolla, San Diego, CA 92037, USA; Department of Electrical Engineering and Computer Science, University of California, Irvine, 2213 Engineering Hall, Irvine, CA 92697-2625, USA.
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8
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Möbius K, Lubitz W, Savitsky A. Jim Hyde and the ENDOR Connection: A Personal Account. APPLIED MAGNETIC RESONANCE 2017; 48:1149-1183. [PMID: 29151676 PMCID: PMC5668355 DOI: 10.1007/s00723-017-0959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Indexed: 06/07/2023]
Abstract
In this minireview, we report on our year-long EPR work, such as electron-nuclear double resonance (ENDOR), pulse electron double resonance (PELDOR) and ELDOR-detected NMR (EDNMR) at X-band and W-band microwave frequencies and magnetic fields. This report is dedicated to James S. Hyde and honors his pioneering contributions to the measurement of spin interactions in large (bio)molecules. From these interactions, detailed information is revealed on structure and dynamics of macromolecules embedded in liquid-solution or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultra-fast electronics for signal data handling and processing have pushed the limits of EPR spectroscopy and its multi-frequency extensions to new horizons concerning sensitivity of detection, selectivity of molecular interactions and time resolution. Among the most important advances is the upgrading of EPR to high magnetic fields, very much in analogy to what happened in NMR. The ongoing progress in EPR spectroscopy is exemplified by reviewing various multi-frequency electron-nuclear double-resonance experiments on organic radicals, light-generated donor-acceptor radical pairs in photosynthesis, and site-specifically nitroxide spin-labeled bacteriorhodopsin, the light-driven proton pump, as well as EDNMR and ENDOR on nitroxides. Signal and resolution enhancements are particularly spectacular for ENDOR, EDNMR and PELDOR on frozen-solution samples at high Zeeman fields. They provide orientation selection for disordered samples approaching single-crystal resolution at canonical g-tensor orientations-even for molecules with small g-anisotropies. Dramatic improvements of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Thus, unique structural and dynamic information is revealed that can hardly be obtained by other analytical techniques. Micromolar concentrations of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems-offering exciting applications for physicists, chemists, biochemists and molecular biologists.
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Affiliation(s)
- Klaus Möbius
- Department of Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
- Max-Planck-Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Anton Savitsky
- Max-Planck-Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
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9
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Harris TV, Szilagyi RK. Protein environmental effects on iron-sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres. J Comput Chem 2016; 37:1681-96. [DOI: 10.1002/jcc.24384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Travis V. Harris
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry and Biochemistry, Montana State University; Bozeman Montana 59717
| | - Robert K. Szilagyi
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry and Biochemistry, Montana State University; Bozeman Montana 59717
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10
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Konov KB, Leonov DV, Isaev NP, Fedotov KY, Voronkova VK, Dzuba SA. Membrane–Sugar Interactions Probed by Pulsed Electron Paramagnetic Resonance of Spin Labels. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b06864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Konstantin B. Konov
- Zavoisky
Physical-Technical Institute, Russian Academy of Sciences, Kazan 420029, Russia
| | - Dmitry V. Leonov
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Nikolay P. Isaev
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Kirill Yu. Fedotov
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Violeta K. Voronkova
- Zavoisky
Physical-Technical Institute, Russian Academy of Sciences, Kazan 420029, Russia
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
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11
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Dong G, Wang H, Cong J, Wang C, Guo J, Zhang T, Yang J, Yang G, Wu K. Calibration ruler for CW-EPR distance measurement using diradical molecule of rigid structure. Acta Biochim Biophys Sin (Shanghai) 2015; 47:342-8. [PMID: 25841441 DOI: 10.1093/abbs/gmv021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/04/2015] [Indexed: 11/13/2022] Open
Abstract
Many experimental factors and uncontrollable factors may introduce errors in the distance measurement by continuous wave electron paramagnetic resonance. To deal with this problem, several C60 nitroxide diradical adducts with rigid structure and definite molecular dimension were used as distance calibration rulers. Based on the improvement of distance calculation program via adding simulation programs of experimental spectra and dipolar broadening function, respectively, the distance calibration method was developed under different conditions such as different solvent, solution concentration, measuring temperature, and microwave power. As a result, stable distance calibration rulers were established within the range of 8-13 Å. The distance calibration effect was evaluated resulting in a corresponding distance measurement precision of 0.84 Å. The results suggested that the influence of non-dipolar spectral broadening factors could be overcome, and the established experimental and calculation methods were suitable to a wide range of situations. The developed method will ensure more accurate and objective distance measurement in biomacromolecular analysis.
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Affiliation(s)
- Guofu Dong
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hongyao Wang
- College of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbo Cong
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Changzhen Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Junwang Guo
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Tong Zhang
- College of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingkui Yang
- College of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoshan Yang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ke Wu
- Beijing Institute of Radiation Medicine, Beijing 100850, China
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12
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Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
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Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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