1
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Muok AR, Chua TK, Srivastava M, Yang W, Maschmann Z, Borbat PP, Chong J, Zhang S, Freed JH, Briegel A, Crane BR. Engineered chemotaxis core signaling units indicate a constrained kinase-off state. Sci Signal 2020; 13:13/657/eabc1328. [PMID: 33172954 DOI: 10.1126/scisignal.abc1328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacterial chemoreceptors, the histidine kinase CheA, and the coupling protein CheW form transmembrane molecular arrays with remarkable sensing properties. The receptors inhibit or stimulate CheA kinase activity depending on the presence of attractants or repellants, respectively. We engineered chemoreceptor cytoplasmic regions to assume a trimer of receptor dimers configuration that formed well-defined complexes with CheA and CheW and promoted a CheA kinase-off state. These mimics of core signaling units were assembled to homogeneity and investigated by site-directed spin-labeling with pulse-dipolar electron-spin resonance spectroscopy (PDS), small-angle x-ray scattering, targeted protein cross-linking, and cryo-electron microscopy. The kinase-off state was especially stable, had relatively low domain mobility, and associated the histidine substrate and docking domains with the kinase core, thus preventing catalytic activity. Together, these data provide an experimentally restrained model for the inhibited state of the core signaling unit and suggest that chemoreceptors indirectly sequester the kinase and substrate domains to limit histidine autophosphorylation.
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Affiliation(s)
- Alise R Muok
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Wen Yang
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Zach Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Petr P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Jenna Chong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sheng Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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2
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Meir A, Lepechkin-Zilbermintz V, Kahremany S, Schwerdtfeger F, Gevorkyan-Airapetov L, Munder A, Viskind O, Gruzman A, Ruthstein S. Inhibiting the copper efflux system in microbes as a novel approach for developing antibiotics. PLoS One 2019; 14:e0227070. [PMID: 31887125 PMCID: PMC6936879 DOI: 10.1371/journal.pone.0227070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022] Open
Abstract
Five out of six people receive at least one antibiotic prescription per year. However, the ever-expanding use of antibiotics in medicine, agriculture, and food production has accelerated the evolution of antibiotic-resistant bacteria, which, in turn, made the development of novel antibiotics based on new molecular targets a priority in medicinal chemistry. One way of possibly combatting resistant bacterial infections is by inhibiting the copper transporters in prokaryotic cells. Copper is a key element within all living cells, but it can be toxic in excess. Both eukaryotic and prokaryotic cells have developed distinct copper regulation systems to prevent its toxicity. Therefore, selectively targeting the prokaryotic copper regulation system might be an initial step in developing next-generation antibiotics. One such system is the Gram-negative bacterial CusCFBA efflux system. CusB is a key protein in this system and was previously reported to play an important role in opening the channel for efflux via significant structural changes upon copper binding while also controlling the assembly and disassembly process of the entire channel. In this study, we aimed to develop novel peptide copper channel blockers, designed by in silico calculations based on the structure of CusB. Using a combination of magnetic resonance spectroscopy and various biochemical methods, we found a lead peptide that promotes copper-induced cell toxicity. Targeting copper transport in bacteria has not yet been pursued as an antibiotic mechanism of action. Thus, our study lays the foundation for discovering novel antibiotics.
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Affiliation(s)
- Aviv Meir
- Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | | | - Shirin Kahremany
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California, United States of America
| | - Fabian Schwerdtfeger
- Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Centre for Biological Signaling Studies (BIOSS), Freiburg, Germany
| | | | - Anna Munder
- Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Olga Viskind
- Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Arie Gruzman
- Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
- * E-mail: (SR); (AG)
| | - Sharon Ruthstein
- Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
- * E-mail: (SR); (AG)
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3
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Exploring the role of the various methionine residues in the Escherichia coli CusB adapter protein. PLoS One 2019; 14:e0219337. [PMID: 31465444 PMCID: PMC6715271 DOI: 10.1371/journal.pone.0219337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/15/2019] [Indexed: 11/29/2022] Open
Abstract
The dissemination of resistant pathogenic microbes has become one of the most challenging problems that modern medicine has faced. Developing novel drugs based on new molecular targets that previously were not targeted, is therefore the highest priority in antibiotics research. One approach that has been recently suggested is to inhibit copper transporters in prokaryotic systems. Copper is required for many biological pathways, but sometimes it can harm the cell. Pathogenic systems have a highly sophisticated copper-regulation network; therefore, a better understanding of how this network operates at the molecular level should assist in developing the next generation of antibiotics. The CusB protein is part of the CusCBA periplasmic Cu(I) efflux system in Gram-negative bacteria, and was recently reported to play a key role in the functioning of the whole CusCBA system, in which conformational changes as well as the assembly/disassembly process control the opening of the transporter. More knowledge of the underlying mechanism is needed to attain a full understanding of CusB functioning, which is associated with targeting specific and crucial residues in CusB. Here, we combine in-vitro structural measurements, which use EPR spectroscopy and UV-Vis measurements, with cell experiments to explore the role of the various methionine residues in CusB. We targeted two methionine residues (M227 and M241) that are essential for the proper functioning of CusB.
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4
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Merz GE, Borbat PP, Muok AR, Srivastava M, Bunck DN, Freed JH, Crane BR. Site-Specific Incorporation of a Cu 2+ Spin Label into Proteins for Measuring Distances by Pulsed Dipolar Electron Spin Resonance Spectroscopy. J Phys Chem B 2018; 122:9443-9451. [PMID: 30222354 DOI: 10.1021/acs.jpcb.8b05619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pulsed dipolar electron spin resonance spectroscopy (PDS) is a powerful tool for measuring distances in solution-state macromolecules. Paramagnetic metal ions, such as Cu2+, are used as spin probes because they can report on metalloprotein features and can be spectroscopically distinguished from traditional nitroxide (NO)-based labels. Here, we demonstrate site-specific incorporation of Cu2+ into non-metalloproteins through the use of a genetically encodable non-natural amino acid, 3-pyrazolyltyrosine (PyTyr). We first incorporate PyTyr in cyan fluorescent protein to measure Cu2+-to-NO distances and examine the effects of solvent conditions on Cu2+ binding and protein aggregation. We then apply the method to characterize the complex formed by the histidine kinase CheA and its target response regulator CheY. The X-ray structure of CheY-PyTyr confirms Cu labeling at PyTyr but also reveals a secondary Cu site. Cu2+-to-NO and Cu2+-to-Cu2+ PDS measurements of CheY-PyTyr with nitroxide-labeled CheA provide new insights into the conformational landscape of the phosphotransfer complex and have implications for kinase regulation.
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Affiliation(s)
- Gregory E Merz
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Alise R Muok
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - David N Bunck
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
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5
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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6
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Sameach H, Narunsky A, Azoulay-Ginsburg S, Gevorkyan-Aiapetov L, Zehavi Y, Moskovitz Y, Juven-Gershon T, Ben-Tal N, Ruthstein S. Structural and Dynamics Characterization of the MerR Family Metalloregulator CueR in its Repression and Activation States. Structure 2017; 25:988-996.e3. [PMID: 28578875 DOI: 10.1016/j.str.2017.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/12/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
CueR (Cu export regulator) is a metalloregulator protein that "senses" Cu(I) ions with very high affinity, thereby stimulating DNA binding and the transcription activation of two other metalloregulator proteins. The crystal structures of CueR when unbound or bound to DNA and a metal ion are very similar to each other, and the role of CueR and Cu(I) in initiating the transcription has not been fully understood yet. Using double electron-electron resonance (DEER) measurements and structure modeling, we investigate the conformational changes that CueR undergoes upon binding Cu(I) and DNA in solution. We observe three distinct conformations, corresponding to apo-CueR, DNA-bound CueR in the absence of Cu(I) (the "repression" state), and CueR-Cu(I)-DNA (the "activation" state). We propose a detailed structural mechanism underlying CueR's regulation of the transcription process. The mechanism explicitly shows the dependence of CueR activity on copper, thereby revealing the important negative feedback mechanism essential for regulating the intracellular copper concentration.
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Affiliation(s)
- Hila Sameach
- The Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Aya Narunsky
- Department of Biochemistry and Molecular Biochemistry, George S. Wise Faculty of Life sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Salome Azoulay-Ginsburg
- The Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Lada Gevorkyan-Aiapetov
- The Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Yonathan Zehavi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Yoni Moskovitz
- The Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biochemistry, George S. Wise Faculty of Life sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Sharon Ruthstein
- The Chemistry Department, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel.
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7
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Levy AR, Turgeman M, Gevorkyan-Aiapetov L, Ruthstein S. The structural flexibility of the human copper chaperone Atox1: Insights from combined pulsed EPR studies and computations. Protein Sci 2017; 26:1609-1618. [PMID: 28543811 DOI: 10.1002/pro.3197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/15/2017] [Indexed: 01/20/2023]
Abstract
Metallochaperones are responsible for shuttling metal ions to target proteins. Thus, a metallochaperone's structure must be sufficiently flexible both to hold onto its ion while traversing the cytoplasm and to transfer the ion to or from a partner protein. Here, we sought to shed light on the structure of Atox1, a metallochaperone involved in the human copper regulation system. Atox1 shuttles copper ions from the main copper transporter, Ctr1, to the ATP7b transporter in the Golgi apparatus. Conventional biophysical tools such as X-ray or NMR cannot always target the various conformational states of metallochaperones, owing to a requirement for crystallography or low sensitivity and resolution. Electron paramagnetic resonance (EPR) spectroscopy has recently emerged as a powerful tool for resolving biological reactions and mechanisms in solution. When coupled with computational methods, EPR with site-directed spin labeling and nanoscale distance measurements can provide structural information on a protein or protein complex in solution. We use these methods to show that Atox1 can accommodate at least four different conformations in the apo state (unbound to copper), and two different conformations in the holo state (bound to copper). We also demonstrate that the structure of Atox1 in the holo form is more compact than in the apo form. Our data provide insight regarding the structural mechanisms through which Atox1 can fulfill its dual role of copper binding and transfer.
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Affiliation(s)
- Ariel R Levy
- The Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Meital Turgeman
- The Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Lada Gevorkyan-Aiapetov
- The Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Sharon Ruthstein
- The Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan, 5290002, Israel
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8
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Sukomon N, Widom J, Borbat PP, Freed JH, Crane BR. Stability and Conformation of a Chemoreceptor HAMP Domain Chimera Correlates with Signaling Properties. Biophys J 2017; 112:1383-1395. [PMID: 28402881 PMCID: PMC5390053 DOI: 10.1016/j.bpj.2017.02.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/15/2017] [Accepted: 02/21/2017] [Indexed: 12/15/2022] Open
Abstract
HAMP domains are dimeric, four-helix bundles that transduce conformational signals in bacterial receptors. Genetic studies of the Escherichia coli serine receptor (Tsr) provide an opportunity to understand HAMP conformational behavior in terms of functional output. To increase its stability, the Tsr HAMP domain was spliced into a poly-HAMP unit from the Pseudomonas aeruginosa Aer2 receptor. Within the chimera, the Tsr HAMP undergoes a thermal melting transition at a temperature much lower than that of the Aer2 HAMP domains. Pulse-dipolar electron spin resonance spectroscopy and site-specific spin-labeling confirm that the Tsr HAMP maintains a four-helix bundle. Pulse-dipolar electron spin resonance spectroscopy was also used to study three well-characterized HAMP mutational phenotypes: those that cause flagella rotation that is counterclockwise (CCW) A and kinase-off; CCW B and also kinase-off; and, clockwise (CW) and kinase-on. Conformational properties of the three HAMP variants support a biphasic model of dynamic bundle stability, but also indicate distinct conformational changes within the helix bundle. Functional kinase-on (CW) and kinase-off (CCW A) states differ by concerted changes in the positions of spin-label sites at the base of the bundle. Opposite shifts in the subunit separation distances of neighboring residues at the C-termini of the α1 and α2 helices are consistent with a helix scissors motion or a gearbox rotational model of HAMP activation. In the drastic kinase-off lesion of CCW B, the α1 helices unfold and the α2 helices form a tight two-helix coiled-coil. The substitution of a critical residue in the Tsr N-terminal linker or control cable reduces conformational heterogeneity at the N-terminus of α1 but does not affect structure at the C-terminus of α2. Overall, the data suggest that transitions from on- to off-states involve decreased motional amplitudes of the Tsr HAMP coupled with helix rotations and movements toward a two-helix packing mode.
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Affiliation(s)
- Nattakan Sukomon
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Joanne Widom
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca, New York
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca, New York
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York.
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9
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Burgess SG, Grazia Concilio M, Bayliss R, Fielding AJ. Detection of Ligand-induced Conformational Changes in the Activation Loop of Aurora-A Kinase by PELDOR Spectroscopy. ChemistryOpen 2016; 5:531-534. [PMID: 28032021 PMCID: PMC5167317 DOI: 10.1002/open.201600101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Indexed: 11/10/2022] Open
Abstract
The structure of protein kinases has been extensively studied by protein crystallography. Conformational movement of the kinase activation loop is thought to be crucial for regulation of activity; however, in many cases the position of the activation loop in solution is unknown. Protein kinases are an important class of therapeutic target and kinase inhibitors are classified by their effect on the activation loop. Here, we report the use of pulsed electron double resonance (PELDOR) and site-directed spin labeling to monitor conformational changes through the insertion of MTSL [S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1 H-pyrrol-3-yl)methyl methanesulfonothioate] on the dynamic activation loop and a stable site on the outer surface of the enzyme. The action of different ligands such as microtubule-associated protein (TPX2) and inhibitors could be discriminated as well as their ability to lock the activation loop in a fixed conformation. This study provides evidence for structural adaptations that could be used for drug design and a methodological approach that has potential to characterize inhibitors in development.
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Affiliation(s)
- Selena G. Burgess
- Astbury Centre for Structural and Molecular BiologyFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUnited Kingdom
| | - Maria Grazia Concilio
- The Photon Science Institute and School of ChemistryUniversity of ManchesterManchesterM13 9PLUnited Kingdom
| | - Richard Bayliss
- Astbury Centre for Structural and Molecular BiologyFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUnited Kingdom
| | - Alistair J. Fielding
- The Photon Science Institute and School of ChemistryUniversity of ManchesterManchesterM13 9PLUnited Kingdom
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10
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Samanta D, Widom J, Borbat PP, Freed JH, Crane BR. Bacterial Energy Sensor Aer Modulates the Activity of the Chemotaxis Kinase CheA Based on the Redox State of the Flavin Cofactor. J Biol Chem 2016; 291:25809-25814. [PMID: 27803157 DOI: 10.1074/jbc.c116.757492] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/13/2016] [Indexed: 11/06/2022] Open
Abstract
Flagellated bacteria modulate their swimming behavior in response to environmental cues through the CheA/CheY signaling pathway. In addition to responding to external chemicals, bacteria also monitor internal conditions that reflect the availability of oxygen, light, and reducing equivalents, in a process termed "energy taxis." In Escherichia coli, the transmembrane receptor Aer is the primary energy sensor for motility. Genetic and physiological data suggest that Aer monitors the electron transport chain through the redox state of its FAD cofactor. However, direct biochemical data correlating FAD redox chemistry with CheA kinase activity have been lacking. Here, we test this hypothesis via functional reconstitution of Aer into nanodiscs. As purified, Aer contains fully oxidized FAD, which can be chemically reduced to the anionic semiquinone (ASQ). Oxidized Aer activates CheA, whereas ASQ Aer reversibly inhibits CheA. Under these conditions, Aer cannot be further reduced to the hydroquinone, in contrast to the proposed Aer signaling model. Pulse ESR spectroscopy of the ASQ corroborates a potential mechanism for signaling in that the resulting distance between the two flavin-binding PAS (Per-Arnt-Sim) domains implies that they tightly sandwich the signal-transducing HAMP domain in the kinase-off state. Aer appears to follow oligomerization patterns observed for related chemoreceptors, as higher loading of Aer dimers into nanodiscs increases kinase activity. These results provide a new methodological platform to study Aer function along with new mechanistic details into its signal transduction process.
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Affiliation(s)
- Dipanjan Samanta
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and.,the National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca, New York 14853
| | - Joanne Widom
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and
| | - Peter P Borbat
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and.,the National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca, New York 14853
| | - Jack H Freed
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and.,the National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca, New York 14853
| | - Brian R Crane
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and
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11
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Georgieva ER, Borbat PP, Grushin K, Stoilova-McPhie S, Kulkarni NJ, Liang Z, Freed JH. Conformational Response of Influenza A M2 Transmembrane Domain to Amantadine Drug Binding at Low pH (pH 5.5). Front Physiol 2016; 7:317. [PMID: 27524969 PMCID: PMC4965473 DOI: 10.3389/fphys.2016.00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/13/2016] [Indexed: 12/27/2022] Open
Abstract
The M2 protein from influenza A plays important roles in its viral cycle. It contains a single transmembrane helix, which oligomerizes into a homotetrameric proton channel that conducts in the low-pH environment of the host-cell endosome and Golgi apparatus, leading to virion uncoating at an early stage of infection. We studied conformational rearrangements that occur in the M2 core transmembrane domain residing on the lipid bilayer, flanked by juxtamembrane residues (M2TMD21-49 fragment), upon its interaction with amantadine drug at pH 5.5 when M2 is conductive. We also tested the role of specific mutation and lipid chain length. Electron spin resonance (ESR) spectroscopy and electron microscopy were applied to M2TMD21-49, labeled at the residue L46C with either nitroxide spin-label or Nanogold® reagent, respectively. Electron microscopy confirmed that M2TMD21-49 reconstituted into DOPC/POPS at 1:10,000 peptide-to-lipid molar ratio (P/L) either with or without amantadine, is an admixture of monomers, dimers, and tetramers, confirming our model based on a dimer intermediate in the assembly of M2TMD21-49. As reported by double electron-electron resonance (DEER), in DOPC/POPS membranes amantadine shifts oligomer equilibrium to favor tetramers, as evidenced by an increase in DEER modulation depth for P/L's ranging from 1:18,000 to 1:160. Furthermore, amantadine binding shortens the inter-spin distances (for nitroxide labels) by 5-8 Å, indicating drug induced channel closure on the C-terminal side. No such effect was observed for the thinner membrane of DLPC/DLPS, emphasizing the role of bilayer thickness. The analysis of continuous wave (cw) ESR spectra of spin-labeled L46C residue provides additional support to a more compact helix bundle in amantadine-bound M2TMD 21-49 through increased motional ordering. In contrast to wild-type M2TMD21-49, the amantadine-bound form does not exhibit noticeable conformational changes in the case of G34A mutation found in certain drug-resistant influenza strains. Thus, the inhibited M2TMD21-49 channel is a stable tetramer with a closed C-terminal exit pore. This work is aimed at contributing to the development of structure-based anti-influenza pharmaceuticals.
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Affiliation(s)
- Elka R Georgieva
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY, USA; National Biomedical Center for Advanced ESR TechnologyIthaca, NY, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY, USA; National Biomedical Center for Advanced ESR TechnologyIthaca, NY, USA
| | - Kirill Grushin
- Department of Neuroscience and Cell Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston Galveston, TX, USA
| | - Svetla Stoilova-McPhie
- Department of Neuroscience and Cell Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston Galveston, TX, USA
| | | | - Zhichun Liang
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY, USA; National Biomedical Center for Advanced ESR TechnologyIthaca, NY, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY, USA; National Biomedical Center for Advanced ESR TechnologyIthaca, NY, USA
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Meyer V, Swanson MA, Clouston LJ, Boratyński PJ, Stein RA, Mchaourab HS, Rajca A, Eaton SS, Eaton GR. Room-temperature distance measurements of immobilized spin-labeled protein by DEER/PELDOR. Biophys J 2016; 108:1213-9. [PMID: 25762332 DOI: 10.1016/j.bpj.2015.01.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/17/2014] [Accepted: 01/14/2015] [Indexed: 11/18/2022] Open
Abstract
Nitroxide spin labels are used for double electron-electron resonance (DEER) measurements of distances between sites in biomolecules. Rotation of gem-dimethyls in commonly used nitroxides causes spin echo dephasing times (Tm) to be too short to perform DEER measurements at temperatures between ∼80 and 295 K, even in immobilized samples. A spirocyclohexyl spin label has been prepared that has longer Tm between 80 and 295 K in immobilized samples than conventional labels. Two of the spirocyclohexyl labels were attached to sites on T4 lysozyme introduced by site-directed spin labeling. Interspin distances up to ∼4 nm were measured by DEER at temperatures up to 160 K in water/glycerol glasses. In a glassy trehalose matrix the Tm for the doubly labeled T4 lysozyme was long enough to measure an interspin distance of 3.2 nm at 295 K, which could not be measured for the same protein labeled with the conventional 1-oxyl-2,2,5,5-tetramethyl-3-pyrroline-3-(methyl)methanethio-sulfonate label.
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Affiliation(s)
- Virginia Meyer
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Michael A Swanson
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Laura J Clouston
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska
| | | | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado.
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Mechanism of influenza A M2 transmembrane domain assembly in lipid membranes. Sci Rep 2015; 5:11757. [PMID: 26190831 PMCID: PMC4507135 DOI: 10.1038/srep11757] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/04/2015] [Indexed: 12/20/2022] Open
Abstract
M2 from influenza A virus functions as an oligomeric proton channel essential for the viral cycle, hence it is a high-priority pharmacological target whose structure and functions require better understanding. We studied the mechanism of M2 transmembrane domain (M2TMD) assembly in lipid membranes by the powerful biophysical technique of double electron-electron resonance (DEER) spectroscopy. By varying the M2TMD-to-lipid molar ratio over a wide range from 1:18,800 to 1:160, we found that M2TMD exists as monomers, dimers, and tetramers whose relative populations shift to tetramers with the increase of peptide-to-lipid (P/L) molar ratio. Our results strongly support the tandem mechanism of M2 assembly that is monomers-to-dimer then dimers-to-tetramer, since tight dimers are abundant at small P/L’s, and thereafter they assemble as dimers of dimers in weaker tetramers. The stepwise mechanism found for a single-pass membrane protein oligomeric assembly should contribute to the knowledge of the association steps in membrane protein folding.
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14
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Borbat PP, Freed JH. Pulse Dipolar Electron Spin Resonance: Distance Measurements. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2012_82] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Cafiso DS. Taking the pulse of protein interactions by EPR spectroscopy. Biophys J 2012; 103:2047-8. [PMID: 23200037 PMCID: PMC3512033 DOI: 10.1016/j.bpj.2012.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 10/09/2012] [Indexed: 11/20/2022] Open
Abstract
An article by Gaffney et al. in this issue establishes a method using pulse electron paramagnetic resonance spectroscopy to determine the location of protein substrates or binding partners with high precision.
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Affiliation(s)
- David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA.
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