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Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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2
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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3
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1H NMR of paramagnetic Dy3+ complex with DTPA-amide p-xylylene-cyclophane; possible probing action toward d-histidine and histamine. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Purslow JA, Khatiwada B, Bayro MJ, Venditti V. NMR Methods for Structural Characterization of Protein-Protein Complexes. Front Mol Biosci 2020; 7:9. [PMID: 32047754 PMCID: PMC6997237 DOI: 10.3389/fmolb.2020.00009] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/10/2020] [Indexed: 01/21/2023] Open
Abstract
Protein-protein interactions and the complexes thus formed are critical elements in a wide variety of cellular events that require an atomic-level description to understand them in detail. Such complexes typically constitute challenging systems to characterize and drive the development of innovative biophysical methods. NMR spectroscopy techniques can be applied to extract atomic resolution information on the binding interfaces, intermolecular affinity, and binding-induced conformational changes in protein-protein complexes formed in solution, in the cell membrane, and in large macromolecular assemblies. Here we discuss experimental techniques for the characterization of protein-protein complexes in both solution NMR and solid-state NMR spectroscopy. The approaches include solvent paramagnetic relaxation enhancement and chemical shift perturbations (CSPs) for the identification of binding interfaces, and the application of intermolecular nuclear Overhauser effect spectroscopy and residual dipolar couplings to obtain structural constraints of protein-protein complexes in solution. Complementary methods in solid-state NMR are described, with emphasis on the versatility provided by heteronuclear dipolar recoupling to extract intermolecular constraints in differentially labeled protein complexes. The methods described are of particular relevance to the analysis of membrane proteins, such as those involved in signal transduction pathways, since they can potentially be characterized by both solution and solid-state NMR techniques, and thus outline key developments in this frontier of structural biology.
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Affiliation(s)
- Jeffrey A Purslow
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | | | - Marvin J Bayro
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA, United States.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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5
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Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
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Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
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6
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Interaction of Na+ and K+ ions with DTPA-amide dioxa-pentaaza-cyclophanes: effect of electrostatic field in macrocyclic cavity on UV absorption spectra and protonation. J INCL PHENOM MACRO 2018. [DOI: 10.1007/s10847-018-0864-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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7
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Pinto LF, Correa J, Zhao L, Riguera R, Fernandez-Megia E. Fast NMR Screening of Macromolecular Complexes by a Paramagnetic Spin Relaxation Filter. ACS OMEGA 2018; 3:2974-2983. [PMID: 31458565 PMCID: PMC6641404 DOI: 10.1021/acsomega.7b02074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/28/2018] [Indexed: 05/09/2023]
Abstract
The paramagnetic spin relaxation filter is described for the rapid NMR screening of intermolecular interactions between ligands and macromolecular anionic receptors with large transverse relaxation enhancements (R 2p). The addition of micromolar concentrations of Gd3+ to the mixture produces the immediate broadening/suppression of the NMR signals of interacting species while leaving unaffected those of noncompetitive binders (one-dimensional and two-dimensional experiments). The method is highly sensitive, unveiling interactions that are too weak to generate changes in chemical shifts or relaxation times. It is operationally very simple and hence, it is amenable to ready implementation by nonspecialists. Examples of application such as detecting the formation of interpolymer complexes, cyclodextrin host-guest interactions, and the screening of DNA ligands are included that demonstrate the reliability and broad applicability of the method.
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Affiliation(s)
| | | | - Libo Zhao
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Ricardo Riguera
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Eduardo Fernandez-Megia
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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8
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Niccolai N, Morandi E, Gardini S, Costabile V, Spadaccini R, Crescenzi O, Picone D, Spiga O, Bernini A. Hot spot mapping of protein surfaces with TEMPOL: Bovine pancreatic RNase A as a model system. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:201-207. [PMID: 27890678 DOI: 10.1016/j.bbapap.2016.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/03/2016] [Accepted: 11/22/2016] [Indexed: 10/20/2022]
Abstract
TEMPOL spin-label has been used to identify surface exposure of protein nuclei from NMR analysis of the induced paramagnetic relaxation enhancements (PRE). The absence of linear dependence between atom depths and observed PRE reveals that specific mechanisms drive the approach of the paramagnet to the protein surface. RNase A represents a unique protein system to explore the fine details of the information offered by TEMPOL induced PRE, due to the abundance of previous results, obtained in solution and in the crystal, dealing with surface dynamics behavior of this protein. MD simulations in explicit solvent have been performed, also in the presence of TEMPOL, in order to delineate the role of intermolecular hydrogen bonds (HB) on PRE extents. Comparison of our results with the ones obtained from multiple solvent crystal structure (MSCS) studies yields information on the specificities that these two techniques have for characterizing protein-ligand interactions, a fundamental step in the development of reliable surface druggability predictors.
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Affiliation(s)
- Neri Niccolai
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Edoardo Morandi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Simone Gardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Valentino Costabile
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Roberta Spadaccini
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy.
| | - Orlando Crescenzi
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia, 80126 Napoli, Italy.
| | - Delia Picone
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia, 80126 Napoli, Italy.
| | - Ottavia Spiga
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Andrea Bernini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
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9
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Khantwal CM, Abraham SJ, Han W, Jiang T, Chavan TS, Cheng RC, Elvington SM, Liu CW, Mathews II, Stein RA, Mchaourab HS, Tajkhorshid E, Maduke M. Revealing an outward-facing open conformational state in a CLC Cl(-)/H(+) exchange transporter. eLife 2016; 5. [PMID: 26799336 PMCID: PMC4769167 DOI: 10.7554/elife.11189] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/14/2016] [Indexed: 11/22/2022] Open
Abstract
CLC secondary active transporters exchange Cl- for H+. Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Gluex) upon its protonation. Using 19F NMR, we show that as [H+] is increased to protonate Gluex and enrich the outward-facing state, a residue ~20 Å away from Gluex, near the subunit interface, moves from buried to solvent-exposed. Consistent with functional relevance of this motion, constriction via inter-subunit cross-linking reduces transport. Molecular dynamics simulations indicate that the cross-link dampens extracellular gate-opening motions. In support of this model, mutations that decrease steric contact between Helix N (part of the extracellular gate) and Helix P (at the subunit interface) remove the inhibitory effect of the cross-link. Together, these results demonstrate the formation of a previously uncharacterized 'outward-facing open' state, and highlight the relevance of global structural changes in CLC function. DOI:http://dx.doi.org/10.7554/eLife.11189.001 Cells have transporter proteins on their surface to carry molecules in and out of the cell. For example, the CLC family of transporters move two chloride ions in one direction at the same time as moving one hydrogen ion in the opposite direction. To be able to move these ions in opposite directions, transporters have to cycle through a series of shapes in which the ions can only access alternate sides of the membrane. First, the transporter adopts an 'outward-facing' shape when the ions first bind to the transporter, then it switches into the 'occluded' shape to move the ions through the membrane. Finally, the transporter takes on the 'inward-facing' shape to release the ions on the other side of the membrane. However, structural studies of CLCs suggest that the structures of these proteins do not change much while they are moving ions, which suggests that they might work in a different way. Khantwal, Abraham et al. have now used techniques called “nuclear magnetic resonance” and "double electron-electron resonance" to investigate how a CLC from a bacterium moves ions. The experiments suggest that when the transporter adopts the outward-facing shape, points on the protein known as Y419 and D417 shift their positions. Chemically linking two regions of the CLC prevented this movement and inhibited the transport of chloride ions across the membrane. Khantwal, Abraham et al. then used a computer simulation to model how the protein changes shape in more detail. This model predicts that two regions of the transporter undergo major rearrangements resulting in a gate-opening motion that widens a passage to allow the chloride ions to bind to the protein. Khantwal, Abraham et al.’s findings will prompt future studies to reveal the other shapes and how CLCs transition between them. DOI:http://dx.doi.org/10.7554/eLife.11189.002
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Affiliation(s)
- Chandra M Khantwal
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Sherwin J Abraham
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Wei Han
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Tao Jiang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Tanmay S Chavan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Ricky C Cheng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Shelley M Elvington
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Corey W Liu
- Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
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11
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Yañez SD, Jatomea O, Velázquez EF, Santacruz H, Navarro RE, Inoue M. Ion-pairing of anionic DTPA-based cyclophanes with diaminoalkanes and methylated amino acids, lysine and arginine, in their dicationic form. J INCL PHENOM MACRO 2014. [DOI: 10.1007/s10847-014-0398-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Koers EJ, van der Cruijsen EAW, Rosay M, Weingarth M, Prokofyev A, Sauvée C, Ouari O, van der Zwan J, Pongs O, Tordo P, Maas WE, Baldus M. NMR-based structural biology enhanced by dynamic nuclear polarization at high magnetic field. JOURNAL OF BIOMOLECULAR NMR 2014; 60:157-68. [PMID: 25284462 DOI: 10.1007/s10858-014-9865-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/23/2014] [Indexed: 05/04/2023]
Abstract
Dynamic nuclear polarization (DNP) has become a powerful method to enhance spectroscopic sensitivity in the context of magnetic resonance imaging and nuclear magnetic resonance spectroscopy. We show that, compared to DNP at lower field (400 MHz/263 GHz), high field DNP (800 MHz/527 GHz) can significantly enhance spectral resolution and allows exploitation of the paramagnetic relaxation properties of DNP polarizing agents as direct structural probes under magic angle spinning conditions. Applied to a membrane-embedded K(+) channel, this approach allowed us to refine the membrane-embedded channel structure and revealed conformational substates that are present during two different stages of the channel gating cycle. High-field DNP thus offers atomic insight into the role of molecular plasticity during the course of biomolecular function in a complex cellular environment.
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Affiliation(s)
- Eline J Koers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
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13
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Bernini A, Henrici De Angelis L, Morandi E, Spiga O, Santucci A, Assfalg M, Molinari H, Pillozzi S, Arcangeli A, Niccolai N. Searching for protein binding sites from Molecular Dynamics simulations and paramagnetic fragment-based NMR studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:561-6. [PMID: 24373878 DOI: 10.1016/j.bbapap.2013.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/16/2013] [Accepted: 12/18/2013] [Indexed: 11/30/2022]
Abstract
Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces. Disruptors of protein-protein interactions can be designed provided that the sterical features of binding pockets, including the transient ones, can be defined. Molecular Dynamics, MD, simulations have been used as a reliable framework for identifying transient pocket openings on the protein surface. Accessible surface area and intramolecular H-bond involvement of protein backbone amides are proposed as descriptors for characterizing binding pocket occurrence and evolution along MD trajectories. TEMPOL induced paramagnetic perturbations on (1)H-(15)N HSQC signals of protein backbone amides have been analyzed as a fragment-based search for surface hotspots, in order to validate MD predicted pockets. This procedure has been applied to CXCL12, a small chemokine responsible for tumor progression and proliferation. From combined analysis of MD data and paramagnetic profiles, two CXCL12 sites suitable for the binding of small molecules were identified. One of these sites is the already well characterized CXCL12 region involved in the binding to CXCR4 receptor. The other one is a transient pocket predicted by Molecular Dynamics simulations, which could not be observed from static analysis of CXCL12 PDB structures. The present results indicate how TEMPOL, instrumental in identifying this transient pocket, can be a powerful tool to delineate minor conformations which can be highly relevant in dynamic discovery of antitumoral drugs.
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Affiliation(s)
- Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | | | - Edoardo Morandi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; SienaBioGrafiX Srl, 53100 Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Serena Pillozzi
- Dipartimento di Medicina Sperimentale e Clinica, University of Florence, 50134 Florence, Italy
| | - Annarosa Arcangeli
- Dipartimento di Medicina Sperimentale e Clinica, University of Florence, 50134 Florence, Italy
| | - Neri Niccolai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; SienaBioGrafiX Srl, 53100 Siena, Italy.
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14
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Hocking HG, Zangger K, Madl T. Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes. Chemphyschem 2013; 14:3082-94. [PMID: 23836693 PMCID: PMC4171756 DOI: 10.1002/cphc.201300219] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 12/20/2022]
Abstract
Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes.
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Affiliation(s)
- Henry G Hocking
- Chair of Biomolecular NMR, Department Chemie, Technische Universität München, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg (Germany)
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15
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Bernini A, Spiga O, Venditti V, Prischi F, Botta M, Croce G, Tong APL, Wong WT, Niccolai N. The use of a ditopic Gd(III) paramagnetic probe for investigating α-bungarotoxin surface accessibility. J Inorg Biochem 2012; 112:25-31. [DOI: 10.1016/j.jinorgbio.2012.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 03/02/2012] [Accepted: 03/03/2012] [Indexed: 01/06/2023]
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Hohlweg W, Kosol S, Zangger K. Determining the orientation and localization of membrane-bound peptides. Curr Protein Pept Sci 2012; 13:267-79. [PMID: 22044140 PMCID: PMC3394173 DOI: 10.2174/138920312800785049] [Citation(s) in RCA: 18] [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: 12/07/2010] [Revised: 10/01/2011] [Accepted: 10/10/2011] [Indexed: 01/06/2023]
Abstract
Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance.
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Affiliation(s)
| | | | - Klaus Zangger
- Institute of Chemistry / Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Soberanes Y, Arvízu-Santamaría AG, Machi L, Navarro RE, Inoue M. Fluorescent aza-cyclophanes derived from diethylenetriaminepentaacetic acid (DTPA), and their complexation with Gd(III). Polyhedron 2012. [DOI: 10.1016/j.poly.2012.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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18
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Spadaccini R, Ercole C, Gentile MA, Sanfelice D, Boelens R, Wechselberger R, Batta G, Bernini A, Niccolai N, Picone D. NMR studies on structure and dynamics of the monomeric derivative of BS-RNase: new insights for 3D domain swapping. PLoS One 2012; 7:e29076. [PMID: 22253705 PMCID: PMC3257227 DOI: 10.1371/journal.pone.0029076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/20/2011] [Indexed: 11/18/2022] Open
Abstract
Three-dimensional domain swapping is a common phenomenon in pancreatic-like ribonucleases. In the aggregated state, these proteins acquire new biological functions, including selective cytotoxicity against tumour cells. RNase A is able to dislocate both N- and C-termini, but usually this process requires denaturing conditions. In contrast, bovine seminal ribonuclease (BS-RNase), which is a homo-dimeric protein sharing 80% of sequence identity with RNase A, occurs natively as a mixture of swapped and unswapped isoforms. The presence of two disulfides bridging the subunits, indeed, ensures a dimeric structure also to the unswapped molecule. In vitro, the two BS-RNase isoforms interconvert under physiological conditions. Since the tendency to swap is often related to the instability of the monomeric proteins, in these paper we have analysed in detail the stability in solution of the monomeric derivative of BS-RNase (mBS) by a combination of NMR studies and Molecular Dynamics Simulations. The refinement of NMR structure and relaxation data indicate a close similarity with RNase A, without any evidence of aggregation or partial opening. The high compactness of mBS structure is confirmed also by H/D exchange, urea denaturation, and TEMPOL mapping of the protein surface. The present extensive structural and dynamic investigation of (monomeric) mBS did not show any experimental evidence that could explain the known differences in swapping between BS-RNase and RNase A. Hence, we conclude that the swapping in BS-RNase must be influenced by the distinct features of the dimers, suggesting a prominent role for the interchain disulfide bridges.
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Affiliation(s)
- Roberta Spadaccini
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Benevento, Italy
| | - Carmine Ercole
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Maria A. Gentile
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Domenico Sanfelice
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Rolf Boelens
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Rainer Wechselberger
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Gyula Batta
- Institute of Chemistry, University of Debrecen, Debrecen, Hungary
| | - Andrea Bernini
- Dipartimento di Biotecnologie, Università degli Studi di Siena, Siena, Italy
| | - Neri Niccolai
- Dipartimento di Biotecnologie, Università degli Studi di Siena, Siena, Italy
| | - Delia Picone
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- * E-mail:
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19
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Abstract
Stable nitroxyl radicals are important tools in chemistry, biophysics, biology, and materials science. Their stability and the sensitivity of their EPR spectra to the local environment make them valuable molecular probes. This review seeks to give an overview of the developments in the field of nitroxide spin probes and their various applications, with the main focus on the pH-sensitive imidazoline nitroxide family.
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Affiliation(s)
- Evelyn Zottler
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Georg Gescheidt
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
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20
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Mangels C, Kellner R, Einsiedel J, Weiglmeier PR, Rosch P, Gmeiner P, Schwarzinger S. The therapeutically anti-prion active antibody-fragment scFv-W226: paramagnetic relaxation-enhanced NMR spectroscopy aided structure elucidation of the paratope-epitope interface. J Biomol Struct Dyn 2010; 28:13-22. [PMID: 20476792 DOI: 10.1080/07391102.2010.10507340] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antibodies have become indispensable reagents with numerous applications in biological and biotechnical analysis, in diagnostics as well as in therapy. In all cases, selective interaction with an epitope is crucial and depends on the conformation of the paratope. While epitopes are routinely mapped at high throughput, methods revealing structural insights on a rather short timescale are rare. We here demonstrate paramagnetic relaxation-enhanced (PRE) NMR spectroscopy to be a powerful tool unraveling structural information about epitope-orientation in a groove spanned by the complementary determining regions. In particular, we utilize the spin label TOAC, which is fused to the peptidic epitope using standard solid-phase chemistry and which is characterized by a reduced mobility compared to, e.g., spin labels attached to the side-chain functionalities of cysteine or lysine residues. We apply the method to determine the orientation of helix 1 of the prion protein, which is the epitope for the therapeutically anti-prion active scF(v) fragment W226.
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Affiliation(s)
- Christian Mangels
- Department of Biopolymers, Universitat Bayreuth, Universitatsstrasse 30, 95440 Bayreuth, Germany
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21
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Kellner R, Mangels C, Schweimer K, Prasch SJ, Weiglmeier PR, Rösch P, Schwarzinger S. SEMPRE: spectral editing mediated by paramagnetic relaxation enhancement. J Am Chem Soc 2010; 131:18016-7. [PMID: 19947644 DOI: 10.1021/ja905412z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Paramagnetic relaxation enhancement (PRE) has become a useful and widely applied tool in biomolecular NMR spectroscopy. In particular investigations of large complexes or transient contacts benefit from PRE effects. Frequently such studies involve modification of the biomacromolecules under study. We here present a method for editing NMR spectra by utilizing a soluble gadolinium complex that broadens nuclear spins being at or close to the macromolecule-solvent interface. NOE signals in NOESY spectra are selectively attenuated if surface exposed nuclear spins are involved. HSQC-type spectra with paramagnetic agent contain only signals of the interior of the protein, while the corresponding difference spectra harbor signals allocated to surface spins. Thus, the number of signals can be reduced helping to minimize spectral overlap in large proteins. The method reveals additional information about the localization of spins being helpful for structure determination of large complexes.
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Affiliation(s)
- Ruth Kellner
- Lehrstuhl Biopolymere, Universitat Bayreuth, Bayreuth, Germany
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22
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An NMR method for the determination of protein binding interfaces using TEMPOL-induced chemical shift perturbations. Biochim Biophys Acta Gen Subj 2009; 1790:1368-76. [PMID: 19520148 DOI: 10.1016/j.bbagen.2009.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/28/2009] [Accepted: 06/01/2009] [Indexed: 11/20/2022]
Abstract
BACKGROUND The determination of protein-protein interfaces is of crucial importance to understand protein function and to guide the design of compounds. To identify protein-protein interface by NMR spectroscopy, 13C NMR paramagnetic shifts induced by freely diffusing 4-hydroxy-2, 2, 6, 6-tetramethyl-piperidine-1-oxyl (TEMPOL) are promising, because TEMPOL affects distinct 13C NMR chemical shifts of the solvent accessible nuclei belonging to proteins of interest, while 13C nuclei within the interior of the proteins may be distinguished by a lack of such shifts. METHOD We measured the 13C NMR paramagnetic shifts induced by TEMPOL by recording 13C-(13)C TOCSY spectra for ubiquitin in the free state and the complex state with yeast ubiquitin hydrolase1 (YUH1). RESULTS Upon complexation of ubiquitin with YUH1, 13C NMR paramagnetic shifts associated with the protein binding interface were reduced by 0.05 ppm or more. The identified interfacial atoms agreed with the prior X-ray crystallographic data. CONCLUSIONS The TEMPOL-induced 13C chemical shift perturbation is useful to determine precise protein-protein interfaces. GENERAL SIGNIFICANCE The present method is a useful method to determine protein-protein interface by NMR, because it has advantages in easy sample preparations, simple data analyses, and wide applicabilities.
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23
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Bernini A, Venditti V, Spiga O, Ciutti A, Prischi F, Consonni R, Zetta L, Arosio I, Fusi P, Guagliardi A, Niccolai N. NMR studies on the surface accessibility of the archaeal protein Sso7d by using TEMPOL and Gd(III)(DTPA-BMA) as paramagnetic probes. Biophys Chem 2008; 137:71-5. [DOI: 10.1016/j.bpc.2008.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 07/08/2008] [Accepted: 07/08/2008] [Indexed: 11/27/2022]
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24
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Venditti V, Niccolai N, Butcher SE. Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL. Nucleic Acids Res 2007; 36:e20. [PMID: 18056080 PMCID: PMC2275091 DOI: 10.1093/nar/gkm1062] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible surface of RNA using NMR and the small paramagnetic molecule TEMPOL. We investigated two RNAs with known structures, one that is extremely stable and one that is dynamic. For helical regions, the TEMPOL probing data correlate well with the predicted RNA surface, and the method is able to distinguish subtle variations in atom depths, such as the relative accessibility of pyrimidine versus purine aromatic carbon atoms. Dynamic motions are also detected by TEMPOL probing, and the method accurately reports a previously characterized pH-dependent conformational transition involving formation of a protonated C-A pair and base flipping. Some loop regions are observed to exhibit anomalously high accessibility, reflective of motions that are not evident within the ensemble of NMR structures. We conclude that TEMPOL probing can provide valuable insights into the surface accessibility and dynamics of RNA, and can also be used as an independent means of validating RNA structure and dynamics in solution.
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Affiliation(s)
- Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, via Fiorentina 1, 53100 Siena, Italy
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25
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Respondek M, Madl T, Göbl C, Golser R, Zangger K. Mapping the orientation of helices in micelle-bound peptides by paramagnetic relaxation waves. J Am Chem Soc 2007; 129:5228-34. [PMID: 17397158 DOI: 10.1021/ja069004f] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many antimicrobial peptides form alpha-helices when bound to a membrane. In addition, around 80% of residues in membrane-bound proteins are found in alpha-helical regions. The orientation and location of such helical peptides and proteins in the membrane are key factors determining their function and activity. Here we present a new solution state NMR method for obtaining the orientation of helical peptides in a membrane-mimetic environment (micelle-bound) without any chemical perturbation of the peptide-micelle system. By monitoring proton longitudinal relaxation rates upon addition of the freely water-soluble and inert paramagnetic probe Gd(DTPA-BMA) to an alpha-helical peptide, a wavelike pattern with a periodicity of 3.6 residues per turn is observed. The tilt and azimuth (rotation) angle of the helix determine the shape of this paramagnetic relaxation wave and can be obtained by least-square fitting of measured relaxation enhancements. Results are presented for the 15-residue antimicrobial peptide CM15 which forms an amphipathic helix almost parallel to the surface of the micelle. Thus, a few fast experiments enable the identification of helical regions and determination of the helix orientation within the micelle without the need for covalent modification, isotopic labeling, or sophisticated equipment. This approach opens a path toward the topology determination of alpha-helical membrane-proteins without the need for a complete NOE-based structure determination.
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Affiliation(s)
- Michal Respondek
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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