1
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Ben‐Ishay Y, Barak Y, Feintuch A, Ouari O, Pierro A, Mileo E, Su X, Goldfarb D. Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy. Protein Sci 2024; 33:e4903. [PMID: 38358137 PMCID: PMC10868451 DOI: 10.1002/pro.4903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.
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Affiliation(s)
- Yasmin Ben‐Ishay
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Barak
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Akiva Feintuch
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Olivier Ouari
- CNRS, ICR, Institut de Chimie RadicalaireAix‐Marseille UniversitéMarseilleFrance
| | - Annalisa Pierro
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
- Present address:
Konstanz Research School Chemical Biology, Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Elisabetta Mileo
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
| | - Xun‐Cheng Su
- State Key Laboratory of Elemento‐organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of Chemistry, Nankai UniversityTianjinChina
| | - Daniella Goldfarb
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
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2
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Bogetti X, Saxena S. Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics. Chempluschem 2024; 89:e202300506. [PMID: 37801003 DOI: 10.1002/cplu.202300506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/07/2023]
Abstract
Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this Review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations and sample rotameric preferences of label sidechains. For molecular motions longer than milliseconds, enhanced sampling strategies and de novo prediction software incorporating or validated by EPR measurements are able to efficiently refine or predict protein conformations, respectively. To sample large-amplitude conformational transition, a coarse-grained or an atomistic weighted ensemble (WE) strategy can be guided with EPR insights. Looking forward, we anticipate an integrative strategy for efficient sampling of alternate conformations by de novo predictions, followed by validations by systematic EPR measurements and MD simulations. Continuous pathways between alternate states can be further sampled by WE-MD including all intermediate states.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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3
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Kao TY, Chiang YW. DEERefiner-assisted structural refinement using pulsed dipolar spectroscopy: a study on multidrug transporter LmrP. Phys Chem Chem Phys 2023; 25:24508-24517. [PMID: 37656008 DOI: 10.1039/d3cp02569a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Pulsed dipolar spectroscopy, such as double electron-electron resonance (DEER), has been underutilized in protein structure determination, despite its ability to provide valuable spatial information. In this study, we present DEERefiner, a user-friendly MATLAB-based GUI program that enables the modeling of protein structures by combining an initial structure and DEER distance restraints. We illustrate the effectiveness of DEERefiner by successfully modeling the ligand-dependent conformational changes of the proton-drug antiporter LmrP to an extracellular-open-like conformation with an impressive precision of 0.76 Å. Additionally, DEERefiner was able to uncover a previously hypothesized but experimentally unresolved proton-dependent conformation of LmrP, characterized as an extracellular-closed/partially intracellular-open conformation, with a precision of 1.16 Å. Our work not only highlights the ability of DEER spectroscopy to model protein structures but also reveals the potential of DEERefiner to advance the field by providing an accessible and applicable tool for precise protein structure modeling, thereby paving the way for deeper insights into protein function.
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Affiliation(s)
- Te-Yu Kao
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan.
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan.
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4
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Tessmer MH, Stoll S. A novel approach to modeling side chain ensembles of the bifunctional spin label RX. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542139. [PMID: 37292623 PMCID: PMC10245940 DOI: 10.1101/2023.05.24.542139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We introduce a novel approach to modeling side chain ensembles of bifunctional spin labels. This approach utilizes rotamer libraries to generate side chain conformational ensembles. Because the bifunctional label is constrained by two attachment sites, the label is split into two monofunctional rotamers which are first attached to their respective sites, then rejoined by a local optimization in dihedral space. We validate this method against a set of previously published experimental data using the bifunctional spin label, RX. This method is relatively fast and can readily be used for both experimental analysis and protein modeling, providing significant advantages over modeling bifunctional labels with molecular dynamics simulations. Use of bifunctional labels for site directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy dramatically reduces label mobility, which can significantly improve resolution of small changes in protein backbone structure and dynamics. Coupling the use of bifunctional labels with side chain modeling methods allows for improved quantitative application of experimental SDSL EPR data to protein modeling.
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Affiliation(s)
- Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, WA 98103, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98103, United States
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5
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Role of membrane mimetics on biophysical EPR studies of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184138. [PMID: 36764474 DOI: 10.1016/j.bbamem.2023.184138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Biological membranes are essential in providing the stability of membrane proteins in a functional state. Functionally stable homogeneous sample is required for biophysical electron paramagnetic resonance (EPR) studies of membrane proteins for obtaining pertinent structural dynamics of the protein. Significant progresses have been made for the optimization of the suitable membrane environments required for biophysical EPR measurements. However, no universal membrane mimetic system is available that can solubilize all membrane proteins suitable for biophysical EPR studies while maintaining the functional integrity. Great efforts are needed to optimize the sample condition to obtain better EPR data quality of membrane proteins that can provide meaningful information on structural dynamics. In this mini-review, we will discuss important aspects of membrane mimetics for biophysical EPR measurements and current progress with some of the recent examples.
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6
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Tessmer MH, Stoll S. chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling. PLoS Comput Biol 2023; 19:e1010834. [PMID: 37000838 PMCID: PMC10096462 DOI: 10.1371/journal.pcbi.1010834] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/12/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron-electron resonance (DEER). It is based on in silico attachment of rotamer ensemble representations of spin labels to protein structures. chiLife enables the development of custom protein analysis and modeling pipelines using SDSL EPR experimental data. It allows the user to add custom spin labels, scoring functions and spin label modeling methods. chiLife is designed with integration into third-party software in mind, to take advantage of the diverse and rapidly expanding set of molecular modeling tools available with a Python interface. This article describes the main design principles of chiLife and presents a series of examples.
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Affiliation(s)
- Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
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7
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Tessmer MH, Canarie ER, Stoll S. Comparative evaluation of spin-label modeling methods for protein structural studies. Biophys J 2022; 121:3508-3519. [PMID: 35957530 PMCID: PMC9515001 DOI: 10.1016/j.bpj.2022.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a powerful technique for the investigation of protein structure and dynamics. Accurate spin-label modeling methods are essential to make full quantitative use of site-directed spin-labeling electron paramagnetic resonance data for protein modeling and model validation. Using a set of double electron-electron resonance data from seven different site pairs on maltodextrin/maltose-binding protein under two different conditions using five different spin labels, we compare the ability of two widely used spin-label modeling methods, based on accessible volume sampling and rotamer libraries, to predict experimental distance distributions. We present a spin-label modeling approach inspired by canonical side-chain modeling methods and compare modeling accuracy with the established methods.
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Affiliation(s)
- Maxx H Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington
| | | | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington.
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8
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Seal M, Weil-Ktorza O, Despotović D, Tawfik DS, Levy Y, Metanis N, Longo LM, Goldfarb D. Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains. J Am Chem Soc 2022; 144:14150-14160. [PMID: 35904499 PMCID: PMC9376946 DOI: 10.1021/jacs.2c03819] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance spectroscopy (EPR) to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron-electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif revealed the presence of dimers, even in the absence of RNA. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. DEER measurements of spin-diluted, doubly labeled peptides in solution indicated transient α-helical character. The distance distributions between spin labels in the dimer and the signatures of α-helical folding are consistent with the symmetric (HhH)2-Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures via common evolutionary processes, such as duplication and fusion.
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Affiliation(s)
- Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orit Weil-Ktorza
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Dragana Despotović
- Department of Biomolecular Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dan S Tawfik
- Department of Biomolecular Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Casali Center for Applied Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Liam M Longo
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, Washington 98104, United States
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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9
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Peter MF, Gebhardt C, Mächtel R, Muñoz GGM, Glaenzer J, Narducci A, Thomas GH, Cordes T, Hagelueken G. Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET. Nat Commun 2022; 13:4396. [PMID: 35906222 PMCID: PMC9338047 DOI: 10.1038/s41467-022-31945-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity, and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modelling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gabriel G Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Janin Glaenzer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, UK
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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10
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Jeschke G, Esteban-Hofer L. Integrative ensemble modeling of proteins and their complexes with distance distribution restraints. Methods Enzymol 2022; 666:145-169. [PMID: 35465919 DOI: 10.1016/bs.mie.2022.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Many proteins and protein complexes exhibit regions that are intrinsically disordered. Whereas an arsenal of techniques exists to characterize structured proteins or protein regions, characterization of the vast conformational space occupied by intrinsically disordered regions remains a challenging task due the ensemble-averaging nature of many techniques that provide mean value restraints. More representative information can be gained in the form of distribution restraints, such as EPR-derived distance distributions. Previously we developed the ensemble modeling tool MMM, where we partition the macromolecule into structured and unstructured domains and utilize an integrative structural approach with a focus on EPR-derived distance restraints. Here we present the successor program of MMM: MMMx. All the modeling functionality was ported to MMMx and is now accessed by a uniform script format, allowing to combine the different modules at will to modeling pipelines. During the conception of MMMx many of the tools were improved or updated. We discuss the general functionality of MMMx and its modules, and illustrate some of the modeling tools by application examples.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Department of Chemistry and Applied Biosciences, Zürich, Switzerland.
| | - Laura Esteban-Hofer
- ETH Zürich, Department of Chemistry and Applied Biosciences, Zürich, Switzerland
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11
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Tracking protein domain movements by EPR distance determination and multilateration. Methods Enzymol 2022; 666:121-144. [DOI: 10.1016/bs.mie.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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del Alamo D, Jagessar KL, Meiler J, Mchaourab HS. Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints. PLoS Comput Biol 2021; 17:e1009107. [PMID: 34133419 PMCID: PMC8238229 DOI: 10.1371/journal.pcbi.1009107] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/28/2021] [Accepted: 05/24/2021] [Indexed: 12/20/2022] Open
Abstract
We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.
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Affiliation(s)
- Diego del Alamo
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin L. Jagessar
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Hassane S. Mchaourab
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
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13
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Bahrenberg T, Yardeni EH, Feintuch A, Bibi E, Goldfarb D. Substrate binding in the multidrug transporter MdfA in detergent solution and in lipid nanodiscs. Biophys J 2021; 120:1984-1993. [PMID: 33771471 PMCID: PMC8204392 DOI: 10.1016/j.bpj.2021.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/07/2021] [Accepted: 03/15/2021] [Indexed: 10/21/2022] Open
Abstract
MdfA from Escherichia coli is a prototypical secondary multi-drug (Mdr) transporter that exchanges drugs for protons. MdfA-mediated drug efflux is driven by the proton gradient and enabled by conformational changes that accompany the recruitment of drugs and their release. In this work, we applied distance measurements by W-band double electron-electron resonance (DEER) spectroscopy to explore the binding of mito-TEMPO, a nitroxide-labeled substrate analog, to Gd(III)-labeled MdfA. The choice of Gd(III)-nitroxide DEER enabled measurements in the presence of excess of mito-TEMPO, which has a relatively low affinity to MdfA. Distance measurements between mito-TEMPO and MdfA labeled at the periplasmic edges of either of three selected transmembrane helices (TM3101, TM5168, and TM9310) revealed rather similar distance distributions in detergent micelles (n-dodecyl-β-d-maltopyranoside, DDM)) and in lipid nanodiscs (ND). By grafting the predicted positions of the Gd(III) tag on the inward-facing (If) crystal structure, we looked for binding positions that reproduced the maxima of the distance distributions. The results show that the location of the mito-TEMPO nitroxide in DDM-solubilized or ND-reconstituted MdfA is similar (only 0.4 nm apart). In both cases, we located the nitroxide moiety near the ligand binding pocket in the If structure. However, according to the DEER-derived position, the substrate clashes with TM11, suggesting that for mito-TEMPO-bound MdfA, TM11 should move relative to the If structure. Additional DEER studies with MdfA labeled with Gd(III) at two sites revealed that TM9 also dislocates upon substrate binding. Together with our previous reports, this study demonstrates the utility of Gd(III)-Gd(III) and Gd(III)-nitroxide DEER measurements for studying the conformational behavior of transporters.
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Affiliation(s)
- Thorsten Bahrenberg
- Departments of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Eliane Hadas Yardeni
- Departments of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Akiva Feintuch
- Departments of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Eitan Bibi
- Departments of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Daniella Goldfarb
- Departments of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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14
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Abdullin D, Schiemann O. Localization of metal ions in biomolecules by means of pulsed dipolar EPR spectroscopy. Dalton Trans 2021; 50:808-815. [PMID: 33416053 DOI: 10.1039/d0dt03596c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ions are important for the folding, structure, and function of biomolecules. Thus, knowing where their binding sites are located in proteins or oligonucleotides is a critical objective. X-ray crystallography and nuclear magnetic resonance are powerful methods in this respect, but both have their limitations. Here, a complementary method is highlighted in which paramagnetic metal ions are localized by means of trilateration using a combination of site-directed spin labeling and pulsed dipolar electron paramagnetic resonance spectroscopy. The working principle, the requirements, and the limitations of the method are critically discussed. Several applications of the method are outlined and compared with each other.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany.
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15
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Lan YJ, Yeh PS, Kao TY, Lo YC, Sue SC, Chen YW, Hwang DW, Chiang YW. Anti-apoptotic BCL-2 regulation by changes in dynamics of its long unstructured loop. Commun Biol 2020; 3:668. [PMID: 33184407 PMCID: PMC7665024 DOI: 10.1038/s42003-020-01390-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
BCL-2, a key protein in inhibiting apoptosis, has a 65-residue-long highly flexible loop domain (FLD) located on the opposite side of its ligand-binding groove. In vivo phosphorylation of the FLD enhances the affinity of BCL-2 for pro-apoptotic ligands, and consequently anti-apoptotic activity. However, it remains unknown as to how the faraway, unstructured FLD modulates the affinity. Here we investigate the protein-ligand interactions by fluorescence techniques and monitor protein dynamics by DEER and NMR spectroscopy tools. We show that phosphomimetic mutations on the FLD lead to a reduction in structural flexibility, hence promoting ligand access to the groove. The bound pro-apoptotic ligands can be displaced by the BCL-2-selective inhibitor ABT-199 efficiently, and thus released to trigger apoptosis. We show that changes in structural flexibility on an unstructured loop can activate an allosteric protein that is otherwise structurally inactive.
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Affiliation(s)
- Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Pei-Shan Yeh
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Te-Yu Kao
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Yuan-Chao Lo
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Wen Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Dennis W Hwang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan.
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16
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Wuebben C, Vicino MF, Mueller M, Schiemann O. Do the P1 and P2 hairpins of the Guanidine-II riboswitch interact? Nucleic Acids Res 2020; 48:10518-10526. [PMID: 32857846 PMCID: PMC7544219 DOI: 10.1093/nar/gkaa703] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 01/09/2023] Open
Abstract
Riboswitches regulate genes by adopting different structures in responds to metabolite binding. The guanidine-II riboswitch is the smallest representative of the ykkC class with the mechanism of its function being centred on the idea that its two stem loops P1 and P2 form a kissing hairpin interaction upon binding of guanidinium (Gdm+). This mechanism is based on in-line probing experiments with the full-length riboswitch and crystal structures of the truncated stem loops P1 and P2. However, the crystal structures reveal only the formation of the homodimers P1 | P1 and P2 | P2 but not of the proposed heterodimer P1 | P2. Here, site-directed spin labeling (SDSL) in combination with Pulsed Electron–Electron Double Resonance (PELDOR or DEER) is used to study their structures in solution and how they change upon binding of Gdm+. It is found that both hairpins adopt different structures in solution and that binding of Gdm+ does indeed lead to the formation of the heterodimer but alongside the homodimers in a statistical 1:2:1 fashion. These results do thus support the proposed switching mechanism.
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Affiliation(s)
- Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Maria F Vicino
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Marcel Mueller
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
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17
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Siti Halimatul Munawaroh H, Gumilar GG, Nurjanah F, Yuliani G, Aisyah S, Kurnia D, Wulandari AP, Kurniawan I, Ningrum A, Koyande AK, Show PL. In-vitro molecular docking analysis of microalgae extracted phycocyanin as an anti-diabetic candidate. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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PEGylation-based strategy to identify pathways involved in the activation of apoptotic BAX protein. Biochim Biophys Acta Gen Subj 2020; 1864:129541. [PMID: 31987956 DOI: 10.1016/j.bbagen.2020.129541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 10/25/2022]
Abstract
BACKGROUND BAX activation is a crucial step for commitment to apoptosis. Several activators, such as BimBH3-based therapeutic peptides and cleaved Bid (cBid) protein, can trigger BAX-mediated apoptosis, but it is unclear whether they proceed through the same pathway. METHODS Here we utilize PEGylation-based approach, which is shown to efficiently shield individual binding grooves in BAX from activators, to investigate and reveal that the activators take different routes to induce BAX-mediated apoptosis. Various spectroscopic/biochemical tools, including electron spin resonance, circular dichroism, fluorescence recovery after photobleaching, and label-transfer assay, were employed to reveal details in the processes. RESULTS We observe a key mutant BAX 164-PEG that acts differently in response to cBid and BimBH3 stimuli. While BimBH3 directly interacts with the trigger groove (TG) to induce the conformational changes in BAX that includes the release of α9 from the canonical groove (CG) and oligomerization, cBid engages with CG and works with mitochondrial lipids to fully activate BAX. CONCLUSION PEGylation-based approach is proven useful to shield individual binding grooves of BAX from apoptotic stimuli. Groove engagement in CG of BAX is required for a full cBid-induced BAX activation. This study has identified differences in the pathways involved during the initiation of BAX activation by full-length cBid protein versus synthetic BimBH3-based peptides. GENERAL SIGNIFICANCE Our finding is potentially valuable for therapeutic application as the pore-forming activity of 164-PEG is independent from the cBid-mediated apoptotic pathways, but can be administrated by the synthetic short peptides.
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19
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Spicher S, Abdullin D, Grimme S, Schiemann O. Modeling of spin–spin distance distributions for nitroxide labeled biomacromolecules. Phys Chem Chem Phys 2020; 22:24282-24290. [DOI: 10.1039/d0cp04920d] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Combining CREST and MD simulations based on GFN-FF for the automated computation of distance distributions for nitroxide labeled (metallo-) proteins.
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Affiliation(s)
- Sebastian Spicher
- Mulliken Center for Theoretical Chemistry
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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20
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Wuebben C, Blume S, Abdullin D, Brajtenbach D, Haege F, Kath-Schorr S, Schiemann O. Site-Directed Spin Labeling of RNA with a Gem-Diethylisoindoline Spin Label: PELDOR, Relaxation, and Reduction Stability. Molecules 2019; 24:E4482. [PMID: 31817785 PMCID: PMC6943706 DOI: 10.3390/molecules24244482] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 01/08/2023] Open
Abstract
Ribonucleic acid function is governed by its structure, dynamics, and interaction with other biomolecules and influenced by the local environment. Thus, methods are needed that enable one to study RNA under conditions as natural as possible, possibly within cells. Site-directed spin-labeling of RNA with nitroxides in combination with, for example, pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy has been shown to provide such information. However, for in-cell measurements, the usually used gem-dimethyl nitroxides are less suited, because they are quickly reduced under in-cell conditions. In contrast, gem-diethyl nitroxides turned out to be more stable, but labeling protocols for binding these to RNA have been sparsely reported. Therefore, we describe here the bioconjugation of an azide functionalized gem-diethyl isoindoline nitroxide to RNA using a copper (I)-catalyzed azide-alkyne cycloaddition ("click"-chemistry). The labeling protocol provides high yields and site selectivity. The analysis of the orientation selective PELDOR data show that the gem-diethyl and gem-dimethyl labels adopt similar conformations. Interestingly, in deuterated buffer, both labels attached to RNA yield TM relaxation times that are considerably longer than observed for the same type of label attached to proteins, enabling PELDOR time windows of up to 20 microseconds. Together with the increased stability in reducing environments, this label is very promising for in-cell Electron Paramagnetic Resonance (EPR) studies.
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Affiliation(s)
- Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Simon Blume
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Dominik Brajtenbach
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Florian Haege
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
| | - Stephanie Kath-Schorr
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany;
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany; (C.W.); (S.B.); (D.A.); (D.B.); (F.H.)
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21
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Peter MF, Tuukkanen AT, Heubach CA, Selsam A, Duthie FG, Svergun DI, Schiemann O, Hagelueken G. Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology. Structure 2019; 27:1416-1426.e3. [DOI: 10.1016/j.str.2019.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/08/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
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22
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Goldfarb D. Pulse EPR in biological systems - Beyond the expert's courtyard. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:102-108. [PMID: 31337564 DOI: 10.1016/j.jmr.2019.07.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/07/2019] [Accepted: 07/08/2019] [Indexed: 05/14/2023]
Abstract
Application of EPR to biological systems includes many techniques and applications. In this short perspective, which dares to look into the future, I focus on pulse EPR, which is my field of expertise. Generally, pulse EPR techniques can be divided into two main groups: (1) hyperfine spectroscopy, which explores electron-nuclear interactions, and (2) pulse-dipolar (PD) EPR spectroscopy, which is based on electron-electron spin interactions. Here I focus on PD-EPR because it has a better chance of becoming a widely applied, easy-to-use table-top method to study the structural and dynamic aspects of bio-molecules. I will briefly introduce this technique, its current state of the art, the challenges it is facing, and finally I will describe futuristic scenarios of low-cost PD-EPR approaches that can cross the diffusion barrier from the core of experts to the bulk of the scientific community.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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23
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Lai Y, Kuo Y, Chiang Y. Identifying Protein Conformational Dynamics Using Spin‐label ESR. Chem Asian J 2019; 14:3981-3991. [DOI: 10.1002/asia.201900855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Yei‐Chen Lai
- Department of Chemistry National Tsing Hua University Hsinchu 30013 Taiwan
- Department of Chemistry&Biochemistry University of California Santa Barbara CA 93106-9510 USA
| | - Yun‐Hsuan Kuo
- Department of Chemistry National Tsing Hua University Hsinchu 30013 Taiwan
| | - Yun‐Wei Chiang
- Department of Chemistry National Tsing Hua University Hsinchu 30013 Taiwan
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24
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Abdullin D, Matsuoka H, Yulikov M, Fleck N, Klein C, Spicher S, Hagelueken G, Grimme S, Lützen A, Schiemann O. Pulsed EPR Dipolar Spectroscopy under the Breakdown of the High-Field Approximation: The High-Spin Iron(III) Case. Chemistry 2019; 25:8820-8828. [PMID: 31017706 DOI: 10.1002/chem.201900977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Indexed: 12/11/2022]
Abstract
Pulsed EPR dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling and thus the distance between electron-spin centers. To date, PDS measurements to metal centers were limited to ions that adhere to the high-field approximation. Here, the PDS methodology is extended to cases where the high-field approximation breaks down on the example of the high-spin Fe3+ /nitroxide spin-pair. First, the theory developed by Maryasov et al. (Appl. Magn. Reson. 2006, 30, 683-702) was adapted to derive equations for the dipolar coupling constant, which revealed that the dipolar spectrum does not only depend on the length and orientation of the interspin distance vector with respect to the applied magnetic field but also on its orientation to the effective g-tensor of the Fe3+ ion. Then, it is shown on a model system and a heme protein that a PDS method called relaxation-induced dipolar modulation enhancement (RIDME) is well-suited to measuring such spectra and that the experimentally obtained dipolar spectra are in full agreement with the derived equations. Finally, a RIDME data analysis procedure was developed, which facilitates the determination of distance and angular distributions from the RIDME data. Thus, this study enables the application of PDS to for example, the highly relevant class of high-spin Fe3+ heme proteins.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany.,Current address: Graduate School of Science, Osaka City University, Osaka, Japan
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nico Fleck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Christoph Klein
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany.,Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Arne Lützen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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25
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Gamble Jarvi A, Cunningham TF, Saxena S. Efficient localization of a native metal ion within a protein by Cu2+-based EPR distance measurements. Phys Chem Chem Phys 2019; 21:10238-10243. [DOI: 10.1039/c8cp07143h] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A native paramagnetic metal binding site in a protein is located with less than 2 Å resolution by a combination of double histidine (dHis) based Cu2+ labeling and long range distance measurements by EPR.
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Affiliation(s)
| | | | - Sunil Saxena
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
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26
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Li CC, Hung CL, Yeh PS, Li CE, Chiang YW. Doubly spin-labeled nanodiscs to improve structural determination of membrane proteins by ESR. RSC Adv 2019; 9:9014-9021. [PMID: 35517660 PMCID: PMC9062051 DOI: 10.1039/c9ra00896a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 03/14/2019] [Indexed: 11/30/2022] Open
Abstract
Pulsed dipolar spectroscopy (PDS) is a powerful tool to explore conformational changes of membrane proteins (MPs). However, the MPs suffer from relatively weak dipolar signals due to their complex nature in membrane environments, which consequently reduces the interspin distance resolution obtainable by PDS. Here we report the use of nanodiscs (NDs) to improve the distance resolution. Two genetically engineered membrane scaffold protein mutants are introduced, each of which is shown to form double-labeled ND efficiently and with high homogeneity. The resultant interspin distance distribution is featured by a small distribution width, suggesting high resolution. When PDS is performed on a binary mixture of the double-labeled ND devoid of MPs and the un-labeled ND with incorporated double-labeled MPs, the overall amplitude of dipolar signals is increased, leading to a critical enhancement of the distance resolution. A theoretical foundation is provided to validate the analysis. With this approach, the determination of MP structures can be studied at high resolution in NDs. Spin-labeled nanodiscs improve DEER distance measurement of membrane proteins.![]()
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Affiliation(s)
- Chieh-Chin Li
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Chien-Lun Hung
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Pei-Shan Yeh
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Chi-En Li
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
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27
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Kerzhner M, Matsuoka H, Wuebben C, Famulok M, Schiemann O. High-Yield Spin Labeling of Long RNAs for Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2018; 57:2923-2931. [PMID: 29715006 DOI: 10.1021/acs.biochem.8b00040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Site-directed spin labeling is a powerful tool for investigating the conformation and dynamics of biomacromolecules such as RNA. Here we introduce a spin labeling strategy based on click chemistry in solution that, in combination with enzymatic ligation, allows highly efficient labeling of complex and long RNAs with short reaction times and suppressed RNA degradation. With this approach, a 34-nucleotide aptamer domain of the preQ1 riboswitch and an 81-nucleotide TPP riboswitch aptamer could be labeled with two labels in several positions. We then show that conformations of the preQ1 aptamer and its dynamics can be monitored in the absence and presence of Mg2+ and a preQ1 ligand by continuous wave electron paramagnetic resonance spectroscopy at room temperature and pulsed electron-electron double resonance spectroscopy (PELDOR or DEER) in the frozen state.
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Affiliation(s)
- Mark Kerzhner
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie University of Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
| | - Michael Famulok
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie University of Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany.,Max Planck Fellowship Chemical Biology Group , Stiftung caesar , Ludwig-Erhard-Allee 2 , 53175 Bonn , Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
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28
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The contribution of modern EPR to structural biology. Emerg Top Life Sci 2018; 2:9-18. [PMID: 33525779 PMCID: PMC7288997 DOI: 10.1042/etls20170143] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 02/08/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron–electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.
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29
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Hung CL, Lin YY, Chang HH, Chiang YW. Accessing local structural disruption of Bid protein during thermal denaturation by absorption-mode ESR spectroscopy. RSC Adv 2018; 8:34656-34669. [PMID: 35548640 PMCID: PMC9087001 DOI: 10.1039/c8ra06740f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 10/04/2018] [Indexed: 01/19/2023] Open
Abstract
The apoptotic function of Bid does not depend on its native structure.
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Affiliation(s)
- Chien-Lun Hung
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Yu-Ying Lin
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Hsin-Ho Chang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
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30
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Jeschke G. MMM: A toolbox for integrative structure modeling. Protein Sci 2017; 27:76-85. [PMID: 28799219 DOI: 10.1002/pro.3269] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 01/17/2023]
Abstract
Structural characterization of proteins and their complexes may require integration of restraints from various experimental techniques. MMM (Multiscale Modeling of Macromolecules) is a Matlab-based open-source modeling toolbox for this purpose with a particular emphasis on distance distribution restraints obtained from electron paramagnetic resonance experiments on spin-labelled proteins and nucleic acids and their combination with atomistic structures of domains or whole protomers, small-angle scattering data, secondary structure information, homology information, and elastic network models. MMM does not only integrate various types of restraints, but also various existing modeling tools by providing a common graphical user interface to them. The types of restraints that can support such modeling and the available model types are illustrated by recent application examples.
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Affiliation(s)
- Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, CH-8093, Switzerland
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31
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Engelhard C, Diensthuber RP, Möglich A, Bittl R. Blue-light reception through quaternary transitions. Sci Rep 2017; 7:1385. [PMID: 28469162 PMCID: PMC5431215 DOI: 10.1038/s41598-017-01497-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/28/2017] [Indexed: 11/10/2022] Open
Abstract
Sensory photoreceptors absorb light via their photosensor modules and trigger downstream physiological adaptations via their effector modules. Light reception accordingly depends on precisely orchestrated interactions between these modules, the molecular details of which often remain elusive. Using electron-electron double resonance (ELDOR) spectroscopy and site-directed spin labelling, we chart the structural transitions facilitating blue-light reception in the engineered light-oxygen-voltage (LOV) histidine kinase YF1 which represents a paradigm for numerous natural signal receptors. Structural modelling based on pair-wise distance constraints derived from ELDOR pinpoint light-induced rotation and splaying apart of the two LOV photosensors in the dimeric photoreceptor. Resultant molecular strain likely relaxes as left-handed supercoiling of the coiled-coil linker connecting sensor and effector units. ELDOR data on a photoreceptor variant with an inverted signal response indicate a drastically altered dimer interface but light-induced structural transitions in the linker that are similar to those in YF1. Taken together, we provide mechanistic insight into the signal trajectories of LOV photoreceptors and histidine kinases that inform molecular simulations and the engineering of novel receptors.
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Affiliation(s)
- Christopher Engelhard
- Fachbereich Physik, Institut für Experimentalphysik, Freie Universität Berlin, 14195, Berlin, Germany
| | - Ralph P Diensthuber
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany. .,Lehrstuhl für Biochemie and Research Center for Bio-Macromolecules, Universität Bayreuth, 95440, Bayreuth, Germany.
| | - Robert Bittl
- Fachbereich Physik, Institut für Experimentalphysik, Freie Universität Berlin, 14195, Berlin, Germany.
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32
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Balo AR, Feyrer H, Ernst OP. Toward Precise Interpretation of DEER-Based Distance Distributions: Insights from Structural Characterization of V1 Spin-Labeled Side Chains. Biochemistry 2016; 55:5256-63. [PMID: 27532325 DOI: 10.1021/acs.biochem.6b00608] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pulsed electron paramagnetic resonance experiments can measure individual distances between two spin-labeled side chains in proteins in the range of ∼1.5-8 nm. However, the flexibility of traditional spin-labeled side chains leads to diffuse spin density loci and thus distance distributions with relatively broad peaks, thereby complicating the interpretation of protein conformational states. Here we analyzed the spin-labeled V1 side chain, which is internally anchored and hence less flexible. Crystal structures of V1-labeled T4 lysozyme constructs carrying the V1 side chain on α-helical segments suggest that V1 side chains adopt only a few discrete rotamers. In most cases, only one rotamer is observed at a given site, explaining the frequently observed narrow distance distribution for doubly V1-labeled proteins. We used the present data to derive guidelines that may allow distance interpretation of other V1-labeled proteins for higher-precision structural modeling.
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Affiliation(s)
- Aidin R Balo
- Department of Biochemistry and ‡Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Hannes Feyrer
- Department of Biochemistry and ‡Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Oliver P Ernst
- Department of Biochemistry and ‡Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
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33
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Kerzhner M, Abdullin D, Więcek J, Matsuoka H, Hagelueken G, Schiemann O, Famulok M. Post-synthetic Spin-Labeling of RNA through Click Chemistry for PELDOR Measurements. Chemistry 2016; 22:12113-21. [PMID: 27412453 DOI: 10.1002/chem.201601897] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 01/24/2023]
Abstract
Site-directed spin labeling of RNA based on click chemistry is used in combination with pulsed electron-electron double resonance (PELDOR) to benchmark a nitroxide spin label, called here dŲ. We compare this approach with another established method that employs the rigid spin label Çm for RNA labeling. By using CD spectroscopy, thermal denaturation measurements, CW-EPR as well as PELDOR we analyzed and compared the influence of dŲ and Çm on a self-complementary RNA duplex. Our results demonstrate that the conformational diversity of dŲ is significantly reduced near the freezing temperature of a phosphate buffer, resulting in strongly orientation-selective PELDOR time traces of the dŲ-labeled RNA duplex.
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Affiliation(s)
- Mark Kerzhner
- Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Dinar Abdullin
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Jennifer Więcek
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Hideto Matsuoka
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.
| | - Michael Famulok
- Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany. .,Max-Planck Fellow Group Chemical Biology, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
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34
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Evans EGB, Pushie MJ, Markham KA, Lee HW, Millhauser GL. Interaction between Prion Protein's Copper-Bound Octarepeat Domain and a Charged C-Terminal Pocket Suggests a Mechanism for N-Terminal Regulation. Structure 2016; 24:1057-67. [PMID: 27265848 DOI: 10.1016/j.str.2016.04.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 11/29/2022]
Abstract
Copper plays a critical role in prion protein (PrP) physiology. Cu(2+) binds with high affinity to the PrP N-terminal octarepeat (OR) domain, and intracellular copper promotes PrP expression. The molecular details of copper coordination within the OR are now well characterized. Here we examine how Cu(2+) influences the interaction between the PrP N-terminal domain and the C-terminal globular domain. Using nuclear magnetic resonance and copper-nitroxide pulsed double electron-electron resonance, with molecular dynamics refinement, we localize the position of Cu(2+) in its high-affinity OR-bound state. Our results reveal an interdomain cis interaction that is stabilized by a conserved, negatively charged pocket of the globular domain. Interestingly, this interaction surface overlaps an epitope recognized by the POM1 antibody, the binding of which drives rapid cerebellar degeneration mediated by the PrP N terminus. The resulting structure suggests that the globular domain regulates the N-terminal domain by binding the Cu(2+)-occupied OR within a complementary pocket.
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Affiliation(s)
- Eric G B Evans
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - M Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Kate A Markham
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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35
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Demay-Drouhard P, Ching HYV, Akhmetzyanov D, Guillot R, Tabares LC, Bertrand HC, Policar C. A Bis-Manganese(II)-DOTA Complex for Pulsed Dipolar Spectroscopy. Chemphyschem 2016; 17:2066-78. [DOI: 10.1002/cphc.201600234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
| | - H. Y. Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC); Department of Biochemistry, Biophysics and Structural Biology; Université Paris-Saclay, CEA, CNRS UMR 9198; Gif-sur-Yvette F-91198 France
| | - Dmitry Akhmetzyanov
- Goethe-University Frankfurt am Main; Institute of Physical and Theoretical Chemistry and; Center for Biomolecular Magnetic Resonance; Max von Laue Str. 7 60438 Frankfurt am Main Germany
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux O'Orsay; Université Paris-Sud, UMR CNRS 8182, Université Paris-Saclay; 91405 Orsay France
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC); Department of Biochemistry, Biophysics and Structural Biology; Université Paris-Saclay, CEA, CNRS UMR 9198; Gif-sur-Yvette F-91198 France
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
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36
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Jhong SR, Li CY, Sung TC, Lan YJ, Chang KJ, Chiang YW. Evidence for an Induced-Fit Process Underlying the Activation of Apoptotic BAX by an Intrinsically Disordered BimBH3 Peptide. J Phys Chem B 2016; 120:2751-60. [PMID: 26913490 DOI: 10.1021/acs.jpcb.6b00909] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Apoptotic BAX protein functions as a critical gateway to mitochondria-mediated apoptosis. A diversity of stimuli has been implicated in initiating BAX activation, but the triggering mechanism remains elusive. Here we study the interaction of BAX with an intrinsically disordered BH3 motif of Bim protein (BimBH3) using ESR techniques. Upon incubation with BAX, BimBH3 binds to BAX at helices 1/6 trigger site to initiate conformational changes of BAX, which in turn promotes the formation of BAX oligomers. The study strategy is twofold: while BAX oligomerization was monitored through spectral changes of spin-labeled BAX, the binding kinetics was studied by observing time-dependent changes of spin-labeled BimBH3. Meanwhile, conformational transition between the unstructured and structured BimBH3 was measured. We show that helical propensity of the BimBH3 is increased upon binding to BAX but is then reduced after being released from the activated BAX; the release is due to the BimBH3-induced conformational change of BAX that is a prerequisite for the oligomer assembling. Intermediate states are identified, offering a key snapshot of the coupled folding and binding process. Our results provide a quantitative mechanistic description of the BAX activation and reveal new insights into the mechanism underlying the interactions between BAX and BH3-mimetic peptide.
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Affiliation(s)
- Siao-Ru Jhong
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Ching-Yu Li
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Tai-Ching Sung
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Kuo-Jung Chang
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
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37
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Stevens MA, McKay JE, Robinson JLS, El Mkami H, Smith GM, Norman DG. The use of the Rx spin label in orientation measurement on proteins, by EPR. Phys Chem Chem Phys 2016; 18:5799-806. [PMID: 26426572 PMCID: PMC4756314 DOI: 10.1039/c5cp04753f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/25/2015] [Indexed: 12/15/2022]
Abstract
The bipedal spin label Rx is more restricted in its conformation and dynamics than its monopodal counterpart R1. To systematically investigate the utility of the Rx label, we have attempted to comprehensively survey the attachment of Rx to protein secondary structures. We have examined the formation, structure and dynamics of the spin label in relation to the underlying protein in order to determine feasibility and optimum conditions for distance and orientation measurement by pulsed EPR. The labeled proteins have been studied using molecular dynamics, CW EPR, pulsed EPR distance measurement at X-band and orientation measurement at W-band. The utility of different modes and positions of attachment have been compared and contrasted.
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Affiliation(s)
- M A Stevens
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - J E McKay
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - J L S Robinson
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - H El Mkami
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - G M Smith
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - D G Norman
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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38
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Abdullin D, Hagelueken G, Schiemann O. Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography. Phys Chem Chem Phys 2016; 18:10428-37. [DOI: 10.1039/c6cp01307d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PELDOR is used to unravel the position and orientation of MTSSL in six singly-labelled azurin mutants. A comparison with X-ray structures of the mutants shows good agreement with respect to the position and orientation of the nitroxide group.
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Affiliation(s)
- D. Abdullin
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - G. Hagelueken
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - O. Schiemann
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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39
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Sung TC, Li CY, Lai YC, Hung CL, Shih O, Yeh YQ, Jeng US, Chiang YW. Solution Structure of Apoptotic BAX Oligomer: Oligomerization Likely Precedes Membrane Insertion. Structure 2015; 23:1878-1888. [PMID: 26299946 DOI: 10.1016/j.str.2015.07.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/06/2015] [Accepted: 07/28/2015] [Indexed: 12/23/2022]
Abstract
Proapoptotic BAX protein is largely cytosolic in healthy cells, but it oligomerizes and translocates to mitochondria upon receiving apoptotic stimuli. A long-standing challenge has been the inability to capture any structural information beyond the onset of activation. Here, we present solution structures of an activated BAX oligomer by means of spectroscopic and scattering methods, providing details about the monomer-monomer interfaces in the oligomer and how the oligomer is assembled from homodimers. We show that this soluble oligomer undergoes a direct conversion into membrane-inserted oligomer, which has the ability of inducing apoptosis and structurally resembles a membrane-embedded oligomer formed from BAX monomers in lipid environment. Structural differences between the soluble and the membrane-inserted oligomers are manifested in the C-terminal helices. Our data suggest an alternative pathway of apoptosis in which BAX oligomer formation occurs prior to membrane insertion.
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Affiliation(s)
- Tai-Ching Sung
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ching-Yu Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yei-Chen Lai
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chien-Lun Hung
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
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40
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Hagelueken G, Duthie FG, Florin N, Schubert E, Schiemann O. Expression, purification and spin labelling of the ferrous iron transporter FeoB from Escherichia coli BL21 for EPR studies. Protein Expr Purif 2015; 114:30-6. [PMID: 26067172 DOI: 10.1016/j.pep.2015.05.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/29/2015] [Accepted: 05/30/2015] [Indexed: 01/06/2023]
Abstract
The ferrous iron transporter FeoB is an important factor in the iron metabolism of various bacteria. As a membrane bound GTPase it also represents an interesting evolutionary link between prokaryotic and eukaryotic membrane signalling pathways. To date, structural information for FeoB is limited to the cytosolic GTPase domain and structural features such as the oligomeric state of the transporter in the membrane, and thereby the nature of the transport pore are a matter of constant debate. Recently, EPR distance measurements have become an important tool to investigate such questions in frozen solution. As a prerequisite for these experiments, we designed protocols to express and purify both the cytosolic domain of FeoB (NFeoB) and full-length FeoB from Escherichia coli BL21 in purity, quantity and quality needed for EPR studies. Since FeoB from E. coli contains 12 native cysteines, we incorporated the unnatural amino acid para-acetylphenylalanine (pAcF) into the protein. We spin labelled the mutant protein using the HO4120 spin label and performed preliminary EPR experiments using cw-X-band EPR spectroscopy. Our results provide new insights concerning the oligomeric state of full-length FeoB.
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Affiliation(s)
- Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany.
| | - Fraser G Duthie
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Nicole Florin
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Erik Schubert
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany
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41
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Abdullin D, Duthie F, Meyer A, Müller ES, Hagelueken G, Schiemann O. Comparison of PELDOR and RIDME for Distance Measurements between Nitroxides and Low-Spin Fe(III) Ions. J Phys Chem B 2015; 119:13534-42. [DOI: 10.1021/acs.jpcb.5b02118] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Fraser Duthie
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Andreas Meyer
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Elisa S. Müller
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
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42
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Vincent Ching HY, Demay-Drouhard P, Bertrand HC, Policar C, Tabares LC, Un S. Nanometric distance measurements between Mn(ii)DOTA centers. Phys Chem Chem Phys 2015; 17:23368-77. [DOI: 10.1039/c5cp03487f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The distance between two Mn(ii)DOTA complexes attached to the ends of polyproline helices of varying lengths was measured by 94 GHz PELDOR spectroscopy with good accuracy demonstrating their effectiveness as spin-labels.
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Affiliation(s)
- H. Y. Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Sun Un
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
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43
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44
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45
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Abdullin D, Florin N, Hagelueken G, Schiemann O. EPR-based approach for the localization of paramagnetic metal ions in biomolecules. Angew Chem Int Ed Engl 2014; 54:1827-31. [PMID: 25522037 DOI: 10.1002/anie.201410396] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 11/10/2022]
Abstract
Metal ions play an important role in the catalysis and folding of proteins and oligonucleotides. Their localization within the three-dimensional fold of such biomolecules is therefore an important goal in understanding structure-function relationships. A trilateration approach for the localization of metal ions by means of long-range distance measurements based on electron paramagnetic resonance (EPR) is introduced. The approach is tested on the Cu(2+) center of azurin, and factors affecting the precision of the method are discussed.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn (Germany) http://www.schiemann.uni-bonn.de
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46
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Abdullin D, Florin N, Hagelueken G, Schiemann O. EPR-Based Approach for the Localization of Paramagnetic Metal Ions in Biomolecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410396] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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47
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Ward R, Pliotas C, Branigan E, Hacker C, Rasmussen A, Hagelueken G, Booth IR, Miller S, Lucocq J, Naismith JH, Schiemann O. Probing the structure of the mechanosensitive channel of small conductance in lipid bilayers with pulsed electron-electron double resonance. Biophys J 2014; 106:834-42. [PMID: 24559986 PMCID: PMC3944623 DOI: 10.1016/j.bpj.2014.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/16/2023] Open
Abstract
Mechanosensitive channel proteins are important safety valves against osmotic shock in bacteria, and are involved in sensing touch and sound waves in higher organisms. The mechanosensitive channel of small conductance (MscS) has been extensively studied. Pulsed electron-electron double resonance (PELDOR or DEER) of detergent-solubilized protein confirms that as seen in the crystal structure, the outer ring of transmembrane helices do not pack against the pore-forming helices, creating an apparent void. The relevance of this void to the functional form of MscS in the bilayer is the subject of debate. Here, we report PELDOR measurements of MscS reconstituted into two lipid bilayer systems: nanodiscs and bicelles. The distance measurements from multiple mutants derived from the PELDOR data are consistent with the detergent-solution arrangement of the protein. We conclude, therefore, that the relative positioning of the transmembrane helices is preserved in mimics of the cell bilayer, and that the apparent voids are not an artifact of detergent solution but a property of the protein that will have to be accounted for in any molecular mechanism of gating.
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Affiliation(s)
- Richard Ward
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Christos Pliotas
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Emma Branigan
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Christian Hacker
- School of Medicine, University of St. Andrews, St. Andrews, Scotland
| | - Akiko Rasmussen
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Ian R Booth
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Samantha Miller
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - John Lucocq
- School of Medicine, University of St. Andrews, St. Andrews, Scotland
| | - James H Naismith
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland.
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany; Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland.
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48
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Florin N, Schiemann O, Hagelueken G. High-resolution crystal structure of spin labelled (T21R1) azurin from Pseudomonas aeruginosa: a challenging structural benchmark for in silico spin labelling algorithms. BMC STRUCTURAL BIOLOGY 2014; 14:16. [PMID: 24884565 PMCID: PMC4055355 DOI: 10.1186/1472-6807-14-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/08/2014] [Indexed: 01/23/2023]
Abstract
Background EPR-based distance measurements between spin labels in proteins have become a valuable tool in structural biology. The direct translation of the experimental distances into structural information is however often impaired by the intrinsic flexibility of the spin labelled side chains. Different algorithms exist that predict the approximate conformation of the spin label either by using pre-computed rotamer libraries of the labelled side chain (rotamer approach) or by simply determining its accessible volume (accessible volume approach). Surprisingly, comparisons with many experimental distances have shown that both approaches deliver the same distance prediction accuracy of about 3 Å. Results Here, instead of comparing predicted and experimental distances, we test the ability of both approaches to predict the actual conformations of spin labels found in a new high-resolution crystal structure of spin labelled azurin (T21R1). Inside the crystal, the label is found in two very different environments which serve as a challenging test for the in silico approaches. Conclusions Our results illustrate why simple and more sophisticated programs lead to the same prediciton error. Thus, a more precise treatment of the complete environment of the label and also its interactions with the environment will be needed to increase the accuracy of in silico spin labelling algorithms.
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Affiliation(s)
| | | | - Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr, 12, Bonn, NRW 53115, Germany.
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49
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Edwards SJ, Moth CW, Kim S, Brandon S, Zhou Z, Cobb CE, Hustedt EJ, Beth AH, Smith JA, Lybrand TP. Automated structure refinement for a protein heterodimer complex using limited EPR spectroscopic data and a rigid-body docking algorithm: a three-dimensional model for an ankyrin-CDB3 complex. J Phys Chem B 2014; 118:4717-26. [PMID: 24758720 PMCID: PMC4018176 DOI: 10.1021/jp4099705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
We report here specialized functions
incorporated recently in the
rigid-body docking software toolkit TagDock to utilize electron paramagnetic
resonance derived (EPR-derived) interresidue distance measurements
and spin-label accessibility data. The TagDock package extensions
include a custom methanethiosulfonate spin label rotamer library to
enable explicit, all-atom spin-label side-chain modeling and scripts
to evaluate spin-label surface accessibility. These software enhancements
enable us to better utilize the biophysical data routinely available
from various spin-labeling experiments. To illustrate the power and
utility of these tools, we report the refinement of an ankyrin:CDB3
complex model that exhibits much improved agreement with the EPR distance
measurements, compared to model structures published previously.
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Affiliation(s)
- Sarah J Edwards
- Department of Chemistry, ‡Department of Molecular Physiology & Biophysics, §Department of Biochemistry, ∥Department of Pharmacology, ⊥Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37235, United States
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