101
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Glaenzer J, Peter MF, Thomas GH, Hagelueken G. PELDOR Spectroscopy Reveals Two Defined States of a Sialic Acid TRAP Transporter SBP in Solution. Biophys J 2017; 112:109-120. [PMID: 28076802 DOI: 10.1016/j.bpj.2016.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/29/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022] Open
Abstract
The tripartite ATP-independent periplasmic (TRAP) transporters are a widespread class of membrane transporters in bacteria and archaea. Typical substrates for TRAP transporters are organic acids including the sialic acid N-acetylneuraminic acid. The substrate binding proteins (SBP) of TRAP transporters are the best studied component and are responsible for initial high-affinity substrate binding. To better understand the dynamics of the ligand binding process, pulsed electron-electron double resonance (PELDOR, also known as DEER) spectroscopy was applied to study the conformational changes in the N-acetylneuraminic acid-specific SBP VcSiaP. The protein is the SBP of VcSiaPQM, a sialic acid TRAP transporter from Vibrio cholerae. Spin-labeled double-cysteine mutants of VcSiaP were analyzed in the substrate-bound and -free state and the measured distances were compared to available crystal structures. The data were compatible with two clear states only, which are consistent with the open and closed forms seen in TRAP SBP crystal structures. Substrate titration experiments demonstrated the transition of the population from one state to the other with no other observed forms. Mutants of key residues involved in ligand binding and/or proposed to be involved in domain closure were produced and the corresponding PELDOR experiments reveal important insights into the open-closed transition. The results are in excellent agreement with previous in vivo sialylation experiments. The structure of the spin-labeled Q54R1/L173R1 R125A mutant was solved at 2.1 Å resolution, revealing no significant changes in the protein structure. Thus, the loss of domain closure appears to be solely due to loss of binding. In conclusion, these data are consistent with TRAP SBPs undergoing a simple two-state transition from an open-unliganded to closed-liganded state during the transport cycle.
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Affiliation(s)
- Janin Glaenzer
- Institute for Physical & Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Martin F Peter
- Institute for Physical & Theoretical Chemistry, University of Bonn, Bonn, Germany
| | | | - Gregor Hagelueken
- Institute for Physical & Theoretical Chemistry, University of Bonn, Bonn, Germany.
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102
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Yin DM, Hannam JS, Schmitz A, Schiemann O, Hagelueken G, Famulok M. Studying the Conformation of a Receptor Tyrosine Kinase in Solution by Inhibitor-Based Spin Labeling. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dongsheng M. Yin
- Max Planck Fellow Chemical Biology; Center of Advanced European Studies and Research (caesar); Ludwig-Erhard-Allee 2 53175 Bonn Germany
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Jeffrey S. Hannam
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Anton Schmitz
- Max Planck Fellow Chemical Biology; Center of Advanced European Studies and Research (caesar); Ludwig-Erhard-Allee 2 53175 Bonn Germany
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Wegelerstrasse 12 53115 Bonn Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Wegelerstrasse 12 53115 Bonn Germany
| | - Michael Famulok
- Max Planck Fellow Chemical Biology; Center of Advanced European Studies and Research (caesar); Ludwig-Erhard-Allee 2 53175 Bonn Germany
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
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103
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Yin DM, Hannam JS, Schmitz A, Schiemann O, Hagelueken G, Famulok M. Studying the Conformation of a Receptor Tyrosine Kinase in Solution by Inhibitor-Based Spin Labeling. Angew Chem Int Ed Engl 2017. [PMID: 28628261 PMCID: PMC5575716 DOI: 10.1002/anie.201703154] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The synthesis of a spin label based on PD168393, a covalent inhibitor of a major anticancer drug target, the epidermal growth factor receptor (EGFR), is reported. The label facilitates the analysis of the EGFR structure in solution by pulsed electron paramagnetic resonance (EPR) spectroscopy. For various EGFR constructs, including near-full-length EGFR, we determined defined distance distributions between the two spin labels bound to the ATP binding sites of the EGFR dimer. The distances are in excellent agreement with an asymmetric dimer of the EGFR. Based on crystal structures, this dimer had previously been proposed to reflect the active conformation of the receptor but structural data demonstrating its existence in solution have been lacking. More generally, our study provides proof-of-concept that inhibitor-based spin labeling enables the convenient introduction of site-specific spin labels into kinases for which covalent or tight-binding small-molecule modulators are available.
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Affiliation(s)
- Dongsheng M Yin
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.,LIMES Chemical Biology Unit, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Jeffrey S Hannam
- LIMES Chemical Biology Unit, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Anton Schmitz
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.,LIMES Chemical Biology Unit, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn, Germany
| | - Michael Famulok
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.,LIMES Chemical Biology Unit, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
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104
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Studies on the X-Ray and Solution Structure of FeoB from Escherichia coli BL21. Biophys J 2017; 110:2642-2650. [PMID: 27332122 DOI: 10.1016/j.bpj.2016.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/15/2016] [Accepted: 05/06/2016] [Indexed: 12/22/2022] Open
Abstract
The ferrous iron transporter FeoB is an important factor in the iron metabolism of many bacteria. Although several structural studies have been performed on its cytosolic GTPase domain (NFeoB), the full-length structure of FeoB remains elusive. Based on a crystal packing analysis that was performed on crystals of NFeoB, a trimeric structure of the FeoB channel was proposed, where the transport pore runs along the trimer axis. Because this trimer has not been observed in some subsequently solved structures of NFeoB homologs, it remains unclear whether or not the trimer is indeed functionally relevant. Here, pulsed electron-electron double resonance spectroscopy, negative stain electron microscopy, and native mass spectrometry are used to analyze the oligomeric state of different soluble and full-length FeoB constructs. The results show that the full-length protein is predominantly monomeric, whereas dimers and trimers are formed to a small percentage. Furthermore, the solution structure of the switch I region is analyzed by pulsed electron-electron double resonance spectroscopy and a new, to our knowledge, crystal structure of NFeoB from Escherichia coli BL21 is presented.
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105
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Dastvan R, Brouwer EM, Schuetz D, Mirus O, Schleiff E, Prisner TF. Relative Orientation of POTRA Domains from Cyanobacterial Omp85 Studied by Pulsed EPR Spectroscopy. Biophys J 2017; 110:2195-206. [PMID: 27224485 DOI: 10.1016/j.bpj.2016.04.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/31/2016] [Accepted: 04/20/2016] [Indexed: 12/30/2022] Open
Abstract
Many proteins of the outer membrane of Gram-negative bacteria and of the outer envelope of the endosymbiotically derived organelles mitochondria and plastids have a β-barrel fold. Their insertion is assisted by membrane proteins of the Omp85-TpsB superfamily. These proteins are composed of a C-terminal β-barrel and a different number of N-terminal POTRA domains, three in the case of cyanobacterial Omp85. Based on structural studies of Omp85 proteins, including the five POTRA-domain-containing BamA protein of Escherichia coli, it is predicted that anaP2 and anaP3 bear a fixed orientation, whereas anaP1 and anaP2 are connected via a flexible hinge. We challenged this proposal by investigating the conformational space of the N-terminal POTRA domains of Omp85 from the cyanobacterium Anabaena sp. PCC 7120 using pulsed electron-electron double resonance (PELDOR, or DEER) spectroscopy. The pronounced dipolar oscillations observed for most of the double spin-labeled positions indicate a rather rigid orientation of the POTRA domains in frozen liquid solution. Based on the PELDOR distance data, structure refinement of the POTRA domains was performed taking two different approaches: 1) treating the individual POTRA domains as rigid bodies; and 2) using an all-atom refinement of the structure. Both refinement approaches yielded ensembles of model structures that are more restricted compared to the conformational ensemble obtained by molecular dynamics simulations, with only a slightly different orientation of N-terminal POTRA domains anaP1 and anaP2 compared with the x-ray structure. The results are discussed in the context of the native environment of the POTRA domains in the periplasm.
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Affiliation(s)
- Reza Dastvan
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany; Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eva-Maria Brouwer
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Denise Schuetz
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany; Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Oliver Mirus
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Enrico Schleiff
- Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt am Main, Germany; Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany; Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt am Main, Germany.
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106
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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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107
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Yang Y, Yang F, Gong YJ, Chen JL, Goldfarb D, Su XC. A Reactive, Rigid Gd III Labeling Tag for In-Cell EPR Distance Measurements in Proteins. Angew Chem Int Ed Engl 2017; 56:2914-2918. [PMID: 28145030 DOI: 10.1002/anie.201611051] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/02/2016] [Indexed: 01/17/2023]
Abstract
The cellular environment of proteins differs considerably from in vitro conditions under which most studies of protein structures are carried out. Therefore, there is a growing interest in determining dynamics and structures of proteins in the cell. A key factor for in-cell distance measurements by the double electron-electron resonance (DEER) method in proteins is the nature of the used spin label. Here we present a newly designed GdIII spin label, a thiol-specific DOTA-derivative (DO3MA-3BrPy), which features chemical stability and kinetic inertness, high efficiency in protein labelling, a short rigid tether, as well as favorable spectroscopic properties, all are particularly suitable for in-cell distance measurements by the DEER method carried out at W-band frequencies. The high performance of DO3MA-3BrPy-GdIII is demonstrated on doubly labelled ubiquitin D39C/E64C, both in vitro and in HeLa cells. High-quality DEER data could be obtained in HeLa cells up to 12 h after protein delivery at in-cell protein concentrations as low as 5-10 μm.
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Affiliation(s)
- Yin Yang
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
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108
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Yang Y, Yang F, Gong YJ, Chen JL, Goldfarb D, Su XC. A Reactive, Rigid GdIII
Labeling Tag for In-Cell EPR Distance Measurements in Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yin Yang
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot 76100 Israel
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Daniella Goldfarb
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot 76100 Israel
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
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109
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Voskoboynikova N, Mosslehy W, Colbasevici A, Ismagulova TT, Bagrov DV, Akovantseva AA, Timashev PS, Mulkidjanian AY, Bagratashvili VN, Shaitan KV, Kirpichnikov MP, Steinhoff HJ. Characterization of an archaeal photoreceptor/transducer complex from Natronomonas pharaonis assembled within styrene–maleic acid lipid particles. RSC Adv 2017. [DOI: 10.1039/c7ra10756k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The archaeal receptor/transducer complex NpSRII/NpHtrII retains its integrity upon reconstitution in styrene–maleic acid lipid particles.
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Affiliation(s)
| | - W. Mosslehy
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - A. Colbasevici
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - T. T. Ismagulova
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - D. V. Bagrov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - A. A. Akovantseva
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - P. S. Timashev
- Institute for Regenerative Medicine of I. M. Sechenov First Moscow State Medical University
- Moscow
- Russia
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
| | | | - V. N. Bagratashvili
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - K. V. Shaitan
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - M. P. Kirpichnikov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - H.-J. Steinhoff
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
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110
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Kao TY, Tsai CJ, Lan YJ, Chiang YW. The role of conformational heterogeneity in regulating the apoptotic activity of BAX protein. Phys Chem Chem Phys 2017; 19:9584-9591. [DOI: 10.1039/c7cp00401j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Inactive BAX exists in two states. A shift in the equilibrium would initiate apoptosis.
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Affiliation(s)
- Te-Yu Kao
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Chia-Jung Tsai
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Yu-Jing Lan
- 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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111
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Yang Y, Gong YJ, Litvinov A, Liu HK, Yang F, Su XC, Goldfarb D. Generic tags for Mn(ii) and Gd(iii) spin labels for distance measurements in proteins. Phys Chem Chem Phys 2017; 19:26944-26956. [DOI: 10.1039/c7cp04311b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The coordination mode of the metal ion in the spin label affects the distance distribution determined by DEER distance measurements.
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Affiliation(s)
- Yin Yang
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Aleksei Litvinov
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Hong-Kai Liu
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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112
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Jassoy JJ, Berndhäuser A, Duthie F, Kühn SP, Hagelueken G, Schiemann O. Versatile Trityl Spin Labels for Nanometer Distance Measurements on Biomolecules In Vitro and within Cells. Angew Chem Int Ed Engl 2016; 56:177-181. [PMID: 27918126 DOI: 10.1002/anie.201609085] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/03/2016] [Indexed: 01/04/2023]
Abstract
Structure determination of biomacromolecules under in-cell conditions is a relevant yet challenging task. Electron paramagnetic resonance (EPR) distance measurements in combination with site-directed spin labeling (SDSL) are a valuable tool in this endeavor but the usually used nitroxide spin labels are not well-suited for in-cell measurements. In contrast, triarylmethyl (trityl) radicals are highly persistent, exhibit a long relaxation time and a narrow spectral width. Here, the synthesis of a versatile collection of trityl spin labels and their application in in vitro and in-cell trityl-iron distance measurements on a cytochrome P450 protein are described. The trityl labels show similar labeling efficiencies and better signal-to-noise ratios (SNR) as compared to the popular methanethiosulfonate spin label (MTSSL) and enabled a successful in-cell measurement.
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Affiliation(s)
- J Jacques Jassoy
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Andreas Berndhäuser
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Fraser Duthie
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Sebastian P Kühn
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Gregor Hagelueken
- 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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113
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Jassoy JJ, Berndhäuser A, Duthie F, Kühn SP, Hagelueken G, Schiemann O. Versatile Trityl Spin Labels for Nanometer Distance Measurements on Biomolecules In Vitro and within Cells. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609085] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- J. Jacques Jassoy
- Institute of Physical and Theoretical Chemistry University of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Andreas Berndhäuser
- Institute of Physical and Theoretical Chemistry University of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Fraser Duthie
- Institute of Physical and Theoretical Chemistry University of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Sebastian P. Kühn
- Institute of Physical and Theoretical Chemistry University of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Gregor Hagelueken
- 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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114
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Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications. Biochem Soc Trans 2016; 43:1023-32. [PMID: 26517918 DOI: 10.1042/bst20150138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented.
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115
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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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116
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Jones CE, Berliner LJ. Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function. Cell Biochem Biophys 2016; 75:195-202. [PMID: 27342129 DOI: 10.1007/s12013-016-0751-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
Abstract
Copper is one of the most abundant biological metals, and its chemical properties mean that organisms need sophisticated and multilayer mechanisms in place to maintain homoeostasis and avoid deleterious effects. Studying copper proteins requires multiple techniques, but electron paramagnetic resonance (EPR) plays a key role in understanding Cu(II) sites in proteins. When spin-labels such as aminoxyl radicals (commonly referred to as nitroxides) are introduced, then EPR becomes a powerful technique to monitor not only the coordination environment, but also to obtain structural information that is often not readily available from other techniques. This information can contribute to explaining how cuproproteins fold and misfold. The theory and practice of EPR can be daunting to the non-expert; therefore, in this mini review, we explore how nitroxide spin-labelling can be used to help the inorganic biochemist gain greater understanding of cuproprotein structure and function in vitro and how EPR imaging may help improve understanding of copper homoeostasis in vivo.
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Affiliation(s)
- Christopher E Jones
- The School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2759, Australia.
| | - Lawrence J Berliner
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208-0183, USA
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117
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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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118
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Motion C, Lovett JE, Bell S, Cassidy SL, Cruickshank PAS, Bolton DR, Hunter RI, El Mkami H, Van Doorslaer S, Smith GM. DEER Sensitivity between Iron Centers and Nitroxides in Heme-Containing Proteins Improves Dramatically Using Broadband, High-Field EPR. J Phys Chem Lett 2016; 7:1411-5. [PMID: 27035368 PMCID: PMC4863198 DOI: 10.1021/acs.jpclett.6b00456] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/30/2016] [Indexed: 05/22/2023]
Abstract
This work demonstrates the feasibility of making sensitive nanometer distance measurements between Fe(III) heme centers and nitroxide spin labels in proteins using the double electron-electron resonance (DEER) pulsed EPR technique at 94 GHz. Techniques to measure accurately long distances in many classes of heme proteins using DEER are currently strongly limited by sensitivity. In this paper we demonstrate sensitivity gains of more than 30 times compared with previous lower frequency (X-band) DEER measurements on both human neuroglobin and sperm whale myoglobin. This is achieved by taking advantage of recent instrumental advances, employing wideband excitation techniques based on composite pulses and exploiting more favorable relaxation properties of low-spin Fe(III) in high magnetic fields. This gain in sensitivity potentially allows the DEER technique to be routinely used as a sensitive probe of structure and conformation in the large number of heme and many other metalloproteins.
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Affiliation(s)
- Claire
L. Motion
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Janet E. Lovett
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Stacey Bell
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Scott L. Cassidy
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Paul A. S. Cruickshank
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - David R. Bolton
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Robert I. Hunter
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Hassane El Mkami
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | | | - Graham M. Smith
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
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119
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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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120
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Hammond CM, Sundaramoorthy R, Larance M, Lamond A, Stevens MA, El-Mkami H, Norman DG, Owen-Hughes T. The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3-H4 tetramers and Asf1-H3-H4 complexes. Nucleic Acids Res 2016; 44:6157-72. [PMID: 27036862 PMCID: PMC5291247 DOI: 10.1093/nar/gkw209] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/17/2016] [Indexed: 11/14/2022] Open
Abstract
Vps75 is a histone chaperone that has been historically characterized as homodimer by X-ray crystallography. In this study, we present a crystal structure containing two related tetrameric forms of Vps75 within the crystal lattice. We show Vps75 associates with histones in multiple oligomers. In the presence of equimolar H3–H4 and Vps75, the major species is a reconfigured Vps75 tetramer bound to a histone H3–H4 tetramer. However, in the presence of excess histones, a Vps75 dimer bound to a histone H3–H4 tetramer predominates. We show the Vps75–H3–H4 interaction is compatible with the histone chaperone Asf1 and deduce a structural model of the Vps75–Asf1-H3–H4 (VAH) co-chaperone complex using the Pulsed Electron-electron Double Resonance (PELDOR) technique and cross-linking MS/MS distance restraints. The model provides a molecular basis for the involvement of both Vps75 and Asf1 in Rtt109 catalysed histone H3 K9 acetylation. In the absence of Asf1 this model can be used to generate a complex consisting of a reconfigured Vps75 tetramer bound to a H3–H4 tetramer. This provides a structural explanation for many of the complexes detected biochemically and illustrates the ability of Vps75 to interact with dimeric or tetrameric H3–H4 using the same interaction surface.
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Affiliation(s)
- Colin M Hammond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Mark Larance
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Angus Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Michael A Stevens
- Nucleic Acids Structure Research Group, University of Dundee, Dundee DD1 5EH, UK
| | - Hassane El-Mkami
- School of Physics and Astronomy, University of St Andrews, St Andrews, KY16 9SS, UK
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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121
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Cunningham TF, Pornsuwan S, Horne WS, Saxena S. Rotameric preferences of a protein spin label at edge-strand β-sheet sites. Protein Sci 2016; 25:1049-60. [PMID: 26948069 DOI: 10.1002/pro.2918] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022]
Abstract
Protein spin labeling to yield the nitroxide-based R1 side chain is a powerful method to measure protein dynamics and structure by electron spin resonance. However, R1 measurements are complicated by the flexibility of the side chain. While analysis approaches for solvent-exposed α-helical environment have been developed to partially account for flexibility, similar work in β-sheets is lacking. The goal of this study is to provide the first essential steps for understanding the conformational preferences of R1 within edge β-strands using X-ray crystallography and double electron electron resonance (DEER) distance measurements. Crystal structures yielded seven rotamers for a non-hydrogen-bonded site and three rotamers for a hydrogen-bonded site. The observed rotamers indicate contextual differences in R1 conformational preferences compared to other solvent-exposed environments. For the DEER measurements, each strand site was paired with the same α-helical site elsewhere on the protein. The most probable distance observed by DEER is rationalized based on the rotamers observed in the crystal structure. Additionally, the appropriateness of common molecular modeling methods that account for R1 conformational preferences are assessed for the β-sheet environment. These results show that interpretation of R1 behavior in β-sheets is difficult and indicate further development is needed for these computational methods to correctly relate DEER distances to protein structure at edge β-strand sites.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - Soraya Pornsuwan
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
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122
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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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123
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Jeschke G. Ensemble models of proteins and protein domains based on distance distribution restraints. Proteins 2016; 84:544-60. [PMID: 26994550 DOI: 10.1002/prot.25000] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
Conformational ensembles of intrinsically disordered peptide chains are not fully determined by experimental observations. Uncertainty due to lack of experimental restraints and due to intrinsic disorder can be distinguished if distance distributions restraints are available. Such restraints can be obtained from pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy applied to pairs of spin labels. Here, we introduce a Monte Carlo approach for generating conformational ensembles that are consistent with a set of distance distribution restraints, backbone dihedral angle statistics in known protein structures, and optionally, secondary structure propensities or membrane immersion depths. The approach is tested with simulated restraints for a terminal and an internal loop and for a protein with 69 residues by using sets of sparse restraints for underlying well-defined conformations and for published ensembles of a premolten globule-like and a coil-like intrinsically disordered protein.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Zürich, 8093, Switzerland
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124
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Constantinescu-Aruxandei D, Petrovic-Stojanovska B, Schiemann O, Naismith JH, White MF. Taking a molecular motor for a spin: helicase mechanism studied by spin labeling and PELDOR. Nucleic Acids Res 2016; 44:954-68. [PMID: 26657627 PMCID: PMC4737156 DOI: 10.1093/nar/gkv1373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 01/30/2023] Open
Abstract
The complex molecular motions central to the functions of helicases have long attracted attention. Protein crystallography has provided transformative insights into these dynamic conformational changes, however important questions about the true nature of helicase configurations during the catalytic cycle remain. Using pulsed EPR (PELDOR or DEER) to measure interdomain distances in solution, we have examined two representative helicases: PcrA from superfamily 1 and XPD from superfamily 2. The data show that PcrA is a dynamic structure with domain movements that correlate with particular functional states, confirming and extending the information gleaned from crystal structures and other techniques. XPD in contrast is shown to be a rigid protein with almost no conformational changes resulting from nucleotide or DNA binding, which is well described by static crystal structures. Our results highlight the complimentary nature of PELDOR to crystallography and the power of its precision in understanding the conformational changes relevant to helicase function.
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Affiliation(s)
| | | | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
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125
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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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126
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Characterization of the Domain Orientations of E. coli 5'-Nucleotidase by Fitting an Ensemble of Conformers to DEER Distance Distributions. Structure 2015; 24:43-56. [PMID: 26724996 DOI: 10.1016/j.str.2015.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/20/2015] [Accepted: 11/13/2015] [Indexed: 01/04/2023]
Abstract
Escherichia coli 5'-nucleotidase is a two-domain enzyme exhibiting a unique 96° domain motion that is required for catalysis. Here we present an integrated structural biology study that combines DEER distance distributions with structural information from X-ray crystallography and computational biology to describe the population of presumably almost isoenergetic open and closed states in solution. Ensembles of models that best represent the experimental distance distributions are determined by a Monte Carlo search algorithm. As a result, predominantly open conformations are observed in the unliganded state indicating that the majority of enzyme molecules await substrate binding for the catalytic cycle. The addition of a substrate analog yields ensembles with an almost equal mixture of open and closed states. Thus, in the presence of substrate, efficient catalysis is provided by the simultaneous appearance of open conformers (binding substrate or releasing product) and closed conformers (enabling the turnover of the substrate).
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127
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Matei E, Gronenborn AM. 19
F Paramagnetic Relaxation Enhancement: A Valuable Tool for Distance Measurements in Proteins. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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128
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Matei E, Gronenborn AM. (19)F Paramagnetic Relaxation Enhancement: A Valuable Tool for Distance Measurements in Proteins. Angew Chem Int Ed Engl 2015; 55:150-4. [PMID: 26510989 DOI: 10.1002/anie.201508464] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 11/11/2022]
Abstract
Fluorine NMR paramagnetic relaxation enhancement was evaluated as a versatile approach for extracting distance information in selectively F-labeled proteins. Proof of concept and initial applications are presented for the HIV-inactivating lectin cyanovirin-N. Single F atoms were introduced at the 4-, 5-, 6- or 7 positions of Trp49 and the 4-position of Phe4, Phe54, and Phe80. The paramagnetic nitroxide spin label was attached to Cys residues that were placed into the protein at positions 50 or 52. (19)F-T2 NMR spectra with different relaxation delays were recorded and the transverse (19)F-PRE rate, (19)F-Γ2 , was used to determine the average distance between the F nucleus and the paramagnetic center. Our data show that experimental (19)F PRE-based distances correspond to 0.93 of the (1)HN-PRE distances, in perfect agreement with the gyromagnetic γ(19)F/γ(1)H ratio, thereby demonstrating that (19)F PREs are excellent alternative parameters for quantitative distance measurements in selectively F-labeled proteins.
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Affiliation(s)
- Elena Matei
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15260 (USA)
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15260 (USA).
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129
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Fehr N, Dietz C, Polyhach Y, von Hagens T, Jeschke G, Paulsen H. Modeling of the N-terminal Section and the Lumenal Loop of Trimeric Light Harvesting Complex II (LHCII) by Using EPR. J Biol Chem 2015; 290:26007-20. [PMID: 26316535 PMCID: PMC4646254 DOI: 10.1074/jbc.m115.669804] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/26/2015] [Indexed: 12/31/2022] Open
Abstract
The major light harvesting complex II (LHCII) of green plants plays a key role in the absorption of sunlight, the regulation of photosynthesis, and in preventing photodamage by excess light. The latter two functions are thought to involve the lumenal loop and the N-terminal domain. Their structure and mobility in an aqueous environment are only partially known. Electron paramagnetic resonance (EPR) has been used to measure the structure of these hydrophilic protein domains in detergent-solubilized LHCII. A new technique is introduced to prepare LHCII trimers in which only one monomer is spin-labeled. These heterogeneous trimers allow to measure intra-molecular distances within one LHCII monomer in the context of a trimer by using double electron-electron resonance (DEER). These data together with data from electron spin echo envelope modulation (ESEEM) allowed to model the N-terminal protein section, which has not been resolved in current crystal structures, and the lumenal loop domain. The N-terminal domain covers only a restricted area above the superhelix in LHCII, which is consistent with the "Velcro" hypothesis to explain thylakoid grana stacking (Standfuss, J., van Terwisscha Scheltinga, A. C., Lamborghini, M., and Kühlbrandt, W. (2005) EMBO J. 24, 919-928). The conformation of the lumenal loop domain is surprisingly different between LHCII monomers and trimers but not between complexes with and without neoxanthin bound.
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Affiliation(s)
- Niklas Fehr
- From the Department of General Botany, Johannes Gutenberg-University, 55128 Mainz, Germany and
| | - Carsten Dietz
- From the Department of General Botany, Johannes Gutenberg-University, 55128 Mainz, Germany and
| | - Yevhen Polyhach
- the Department of Physical Chemistry, ETH Zürich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Tona von Hagens
- the Department of Physical Chemistry, ETH Zürich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Gunnar Jeschke
- the Department of Physical Chemistry, ETH Zürich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Harald Paulsen
- From the Department of General Botany, Johannes Gutenberg-University, 55128 Mainz, Germany and
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130
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Osterberg JR, Chon NL, Boo A, Maynard FA, Lin H, Knight JD. Membrane Docking of the Synaptotagmin 7 C2A Domain: Electron Paramagnetic Resonance Measurements Show Contributions from Two Membrane Binding Loops. Biochemistry 2015; 54:5684-95. [PMID: 26322740 DOI: 10.1021/acs.biochem.5b00421] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The synaptotagmin (Syt) family of proteins plays an important role in vesicle docking and fusion during Ca(2+)-induced exocytosis in a wide variety of cell types. Its role as a Ca(2+) sensor derives primarily from its two C2 domains, C2A and C2B, which insert into anionic lipid membranes upon binding Ca(2+). Syt isoforms 1 and 7 differ significantly in their Ca(2+) sensitivity; the C2A domain from Syt7 binds Ca(2+) and membranes much more tightly than the C2A domain from Syt1, at least in part because of greater contributions from the hydrophobic effect. While the structure and membrane activity of Syt1 have been extensively studied, the structural origins of differences between Syt1 and Syt7 are unknown. This study used site-directed spin labeling and electron paramagnetic resonance spectroscopy to determine depth parameters for the Syt7 C2A domain, for comparison to analogous previous measurements with the Syt1 C2A domain. In a novel approach, the membrane docking geometry of both Syt1 and Syt7 C2A was modeled by mapping depth parameters onto multiple molecular dynamics-simulated structures of the Ca(2+)-bound protein. The models reveal membrane penetration of Ca(2+) binding loops 1 (CBL1) and 3 (CBL3), and membrane binding is more sensitive to mutations in CBL3. On average, Syt7 C2A inserts more deeply into the membrane than Syt1 C2A, although depths vary among the different structural models. This observation provides a partial structural explanation for the hydrophobically driven membrane docking of Syt7 C2A.
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Affiliation(s)
- J Ryan Osterberg
- Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217, United States
| | - Nara Lee Chon
- Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217, United States
| | - Arthur Boo
- Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217, United States
| | - Favinn A Maynard
- Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217, United States
| | - Jefferson D Knight
- Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217, United States
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131
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Beasley KN, Sutch BT, Hatmal MM, Langen R, Qin PZ, Haworth IS. Computer Modeling of Spin Labels: NASNOX, PRONOX, and ALLNOX. Methods Enzymol 2015; 563:569-93. [PMID: 26478499 DOI: 10.1016/bs.mie.2015.07.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Measurement of distances between spin labels using electron paramagnetic resonance with the double electron-electron resonance (DEER) technique is an important method for evaluation of biomolecular structures. Computation of interlabel distances is of value for experimental planning, validation of known structures using DEER-measured distances, and determination of theoretical data for comparison with experiment. This requires steps of building labels at two defined sites on proteins, DNA or RNA; calculation of allowable label conformers based on rotation around torsional angles; computation of pairwise interlabel distances on a per conformer basis; and calculation of an average distance between the two label ensembles. We have described and validated two programs for this purpose: NASNOX, which permits computation of distances between R5 labels on DNA or RNA; and PRONOX, which similarly computes distances between R1 labels on proteins. However, these programs are limited to a specific single label and single target types. Therefore, we have developed a program, which we refer to as ALLNOX (Addition of Labels and Linkers), which permits addition of any label to any site on any target. The main principle in the program is to break the molecular system into a "label," a "linker," and a "target." The user can upload a "label" with any chemistry, define a "linker" based on a SMILES-like string, and then define the "target" site. The flexibility of ALLNOX facilitates theoretical evaluation of labels prior to synthesis and accommodates evaluation of experimental data in biochemical complexes containing multiple molecular types.
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Affiliation(s)
- Kathleen N Beasley
- Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Brian T Sutch
- Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Ma'mon M Hatmal
- Department of Laboratory Medical Sciences, Faculty of Allied Health Sciences, Hashemite University, Zarqa, Jordan
| | - Ralf Langen
- Department of Biochemistry, University of Southern California, Los Angeles, California, USA
| | - Peter Z Qin
- Department of Chemistry and Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Ian S Haworth
- Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA; Department of Biochemistry, University of Southern California, Los Angeles, California, USA.
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132
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Bordignon E, Nalepa AI, Savitsky A, Braun L, Jeschke G. Changes in the Microenvironment of Nitroxide Radicals around the Glass Transition Temperature. J Phys Chem B 2015; 119:13797-806. [DOI: 10.1021/acs.jpcb.5b04104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Enrica Bordignon
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
- Berlin
Joint EPR Laboratories, Department of Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Anna I. Nalepa
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Lukas Braun
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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133
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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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134
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Hahn A, Engelhard C, Reschke S, Teutloff C, Bittl R, Leimkühler S, Risse T. Strukturelle Einblicke in den Mo-Cofaktor-Einbau in Sulfitoxidase durch ortsspezifische Spinmarkierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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135
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Hahn A, Engelhard C, Reschke S, Teutloff C, Bittl R, Leimkühler S, Risse T. Structural Insights into the Incorporation of the Mo Cofactor into Sulfite Oxidase from Site‐Directed Spin Labeling. Angew Chem Int Ed Engl 2015; 54:11865-9. [DOI: 10.1002/anie.201504772] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 06/29/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Aaron Hahn
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin (Germany)
| | | | - Stefan Reschke
- Institut für Biochemie und Biologie, Universität Potsdam, Karl‐Liebknecht‐Str. 24‐25, 14476 Golm (Germany)
| | - Christian Teutloff
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin (Germany)
- Berlin Joint EPR Laboratory Freie Universität Berlin (Germany)
| | - Robert Bittl
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin (Germany)
- Berlin Joint EPR Laboratory Freie Universität Berlin (Germany)
| | - Silke Leimkühler
- Institut für Biochemie und Biologie, Universität Potsdam, Karl‐Liebknecht‐Str. 24‐25, 14476 Golm (Germany)
| | - Thomas Risse
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin (Germany)
- Berlin Joint EPR Laboratory Freie Universität Berlin (Germany)
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136
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Evans EGB, Millhauser GL. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling. Methods Enzymol 2015; 563:503-27. [PMID: 26478497 PMCID: PMC4841275 DOI: 10.1016/bs.mie.2015.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain "K1," and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron-electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite reagents, should make K1 labeling an increasingly viable alternative to cysteine-based methods for SDSL in proteins.
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Affiliation(s)
- Eric G B Evans
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA.
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137
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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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138
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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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139
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Manglik A, Kim TH, Masureel M, Altenbach C, Yang Z, Hilger D, Lerch MT, Kobilka TS, Thian FS, Hubbell WL, Prosser RS, Kobilka BK. Structural Insights into the Dynamic Process of β2-Adrenergic Receptor Signaling. Cell 2015; 161:1101-1111. [PMID: 25981665 DOI: 10.1016/j.cell.2015.04.043] [Citation(s) in RCA: 492] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 03/04/2015] [Accepted: 03/26/2015] [Indexed: 01/01/2023]
Abstract
G-protein-coupled receptors (GPCRs) transduce signals from the extracellular environment to intracellular proteins. To gain structural insight into the regulation of receptor cytoplasmic conformations by extracellular ligands during signaling, we examine the structural dynamics of the cytoplasmic domain of the β2-adrenergic receptor (β2AR) using (19)F-fluorine NMR and double electron-electron resonance spectroscopy. These studies show that unliganded and inverse-agonist-bound β2AR exists predominantly in two inactive conformations that exchange within hundreds of microseconds. Although agonists shift the equilibrium toward a conformation capable of engaging cytoplasmic G proteins, they do so incompletely, resulting in increased conformational heterogeneity and the coexistence of inactive, intermediate, and active states. Complete transition to the active conformation requires subsequent interaction with a G protein or an intracellular G protein mimetic. These studies demonstrate a loose allosteric coupling of the agonist-binding site and G-protein-coupling interface that may generally be responsible for the complex signaling behavior observed for many GPCRs.
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Affiliation(s)
- Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Tae Hun Kim
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
| | - Matthieu Masureel
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Christian Altenbach
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7008, USA
| | - Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7008, USA
| | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Michael T Lerch
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7008, USA
| | - Tong Sun Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Foon Sun Thian
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7008, USA
| | - R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.
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140
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Cunningham TF, Putterman MR, Desai A, Horne WS, Saxena S. The double-histidine Cu²⁺-binding motif: a highly rigid, site-specific spin probe for electron spin resonance distance measurements. Angew Chem Int Ed Engl 2015; 54:6330-4. [PMID: 25821033 DOI: 10.1002/anie.201501968] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/07/2022]
Abstract
The development of ESR methods that measure long-range distance distributions has advanced biophysical research. However, the spin labels commonly employed are highly flexible, which leads to ambiguity in relating ESR measurements to protein-backbone structure. Herein we present the double-histidine (dHis) Cu(2+)-binding motif as a rigid spin probe for double electron-electron resonance (DEER) distance measurements. The spin label is assembled in situ from natural amino acid residues and a metal salt, requires no postexpression synthetic modification, and provides distance distributions that are dramatically narrower than those found with the commonly used protein spin label. Simple molecular modeling based on an X-ray crystal structure of an unlabeled protein led to a predicted most probable distance within 0.5 Å of the experimental value. Cu(2+) DEER with the dHis motif shows great promise for the resolution of precise, unambiguous distance constraints that relate directly to protein-backbone structure and flexibility.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - Miriam R Putterman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - Astha Desai
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - W Seth Horne
- 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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141
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Cunningham TF, Putterman MR, Desai A, Horne WS, Saxena S. The Double-Histidine Cu2+-Binding Motif: A Highly Rigid, Site-Specific Spin Probe for Electron Spin Resonance Distance Measurements. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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142
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Islam SM, Roux B. Simulating the distance distribution between spin-labels attached to proteins. J Phys Chem B 2015; 119:3901-11. [PMID: 25645890 PMCID: PMC4509421 DOI: 10.1021/jp510745d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
EPR/DEER spectroscopy is playing
an increasingly important role
in the characterization of the conformational states of proteins.
In this study, force field parameters for the bifunctional spin-label
(RX) used in EPR/DEER are parametrized and tested with molecular dynamics
(MD) simulations. The dihedral angles connecting the Cα atom of the backbone to the nitroxide ring moiety of the RX spin-label
attached to i and i + 4 positions
in a polyalanine α-helix agree very well with those observed
in the X-ray crystallography. Both RXi,i+4 and RXi,i+3 are more rigid than the monofunctional spin-label (R1) commonly
used in EPR/DEER, while RXi,i+4 is more rigid and causes less distortion in a protein backbone
than RXi,i+3. Simplified
dummy spin-label models with a single effective particle representing
the RXi,i+3 and RXi,i+4 are also developed
and parametrized from the all-atom simulations. MD simulations with
dummy spin-labels (MDDS) provide distance distributions that can be
directly compared to distance distributions obtained from EPR/DEER
to rapidly assess if a hypothetical three-dimensional (3D) structural
model is consistent with experiment. The dummy spin-labels can also
be used in the restrained-ensemble MD (re-MD) simulations to carry
out structural refinement of 3D models. Applications of this methodology
to T4 lysozyme, KCNE1, and LeuT are shown to provide important insights
about their conformational dynamics.
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Affiliation(s)
- Shahidul M Islam
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, University of Chicago , Chicago, Illinois 60637, United States
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143
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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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144
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Tangprasertchai NS, Zhang X, Ding Y, Tham K, Rohs R, Haworth IS, Qin PZ. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids. Methods Enzymol 2015; 564:427-53. [PMID: 26477260 PMCID: PMC4641853 DOI: 10.1016/bs.mie.2015.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements.
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Affiliation(s)
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yuan Ding
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Kenneth Tham
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Remo Rohs
- Department of Chemistry, University of Southern California, Los Angeles, California, USA,Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Ian S. Haworth
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA,Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA,Corresponding author:
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145
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H. DeLuca S, L. DeLuca S, Leaver-Fay A, Meiler J. RosettaTMH: a method for membrane protein structure elucidation combining EPR distance restraints with assembly of transmembrane helices. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2016.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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146
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147
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Klare JP, Steinhoff HJ. Spin Labeling Studies of Transmembrane Signaling and Transport. Methods Enzymol 2015; 564:315-47. [DOI: 10.1016/bs.mie.2015.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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148
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Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution. Methods Enzymol 2015; 558:279-331. [DOI: 10.1016/bs.mie.2015.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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149
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Kaminker I, Bye M, Mendelman N, Gislason K, Sigurdsson ST, Goldfarb D. Distance measurements between manganese(ii) and nitroxide spin-labels by DEER determine a binding site of Mn2+ in the HP92 loop of ribosomal RNA. Phys Chem Chem Phys 2015; 17:15098-102. [DOI: 10.1039/c5cp01624j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
W-band (95 GHz) double electron–electron resonance (DEER) distance measurements between Mn2+ and nitroxide spin labels were used to determine the location of a Mn2+ binding site within an RNA molecule.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Morgan Bye
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Natanel Mendelman
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Kristmann Gislason
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Snorri Th. Sigurdsson
- University of Iceland
- Department of Chemistry
- Science Institute Dunhaga 3
- 107 Reykjavik
- Iceland
| | - Daniella Goldfarb
- University of Iceland
- Department of Chemistry
- Science Institute Dunhaga 3
- 107 Reykjavik
- Iceland
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150
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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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