Structural Mannequin of the ETR1 Ethylene Receptor Transmembrane Sensor Area


Hothorn, M. et al. Structural foundation of steroid hormone notion by the receptor kinase BRI1. Nature 474, 467–471, (2011).


She, J. et al. Structural perception into brassinosteroid notion by BRI1. Nature 474, 472–U496, (2011).


Miyazono, Okay. et al. Structural foundation of abscisic acid signalling. Nature 462, 609–614, (2009).


Nishimura, N. et al. Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science 326, 1373–1379, (2009).


Santiago, J., Henzler, C. & Hothorn, M. Molecular mechanism for plant steroid receptor activation by somatic embryogenesis co-receptor kinases. Science 341, 889–892, (2013).


Zhang, H. et al. SERK Household Receptor-like Kinases Operate as Co-receptors with PXY for Plant Vascular Improvement. Mol Plant 9, 1406–1414, (2016).


Cao, M. et al. An ABA-mimicking ligand that reduces water loss and promotes drought resistance in vegetation. Cell Res. 23, 1043–1054, (2013).


O’Malley, R. C. et al. Ethylene-binding exercise, gene expression ranges, and receptor system output for ethylene receptor relations from Arabidopsis and tomato. Plant J. 41, 651–659, (2005).


Chen, Y. F. et al. Ethylene receptors operate as elements of high-molecular-mass protein complexes in Arabidopsis. PLoS One 5, e8640, (2010).


Rodriguez, F. I. et al. A copper cofactor for the ethylene receptor ETR1 from Arabidopsis. Science (New York, N.Y.) 283, 996–998, (1999).


Suenaga, Y., Ping, W. L., Kuroda-sowa, T., Munakata, M. & Maekawa, M. Construction and 1H NMR examine of copper(I) advanced with ethylene and tetramethylethylenediamine. Polyhedron 16, 67–70, (1997).


Hirsch, J. et al. Raman and Prolonged X-ray Absorption High-quality Construction Characterization of a Sulfur-Ligated Cu (I) Ethylene Complicated: Modeling the Proposed Ethylene Binding Web site of Arabidopsis thaliana. 2439–2441 (2001).


Bleecker, A. B., Esch, J. J., Corridor, A. E., Rodriguez, F. I. & Binder, B. M. The ethylene-receptor household from Arabidopsis: construction and performance. Philos. Trans. R. Soc. Lond. B Biol. Sci. 353, 1405–1412, (1998).


Mayerhofer, H. et al. Structural Mannequin of the Cytosolic Area of the Plant Ethylene Receptor 1 (ETR1). Journal of Organic Chemistry 290, 2644–2658, (2015).


Müller-Dieckmann, H.-J., Grantz, A. A. & Kim, S.-H. The construction of the sign receiver area of the Arabidopsis thaliana ethylene receptor ETR1. Construction 7, 1547–1556, (1999).


Wang, W. et al. Identification of essential areas for ethylene binding and signaling within the transmembrane area of the ETR1 ethylene receptor of Arabidopsis. The Plant cell 18, 3429–3442, (2006).


Khelashvili, G. et al. Computational modeling of the N-terminus of the human dopamine transporter and its interplay with PIP2 -containing membranes. Proteins 83, 952–969, (2015).


Watschinger, Okay. et al. Catalytic residues and a predicted construction of tetrahydrobiopterin-dependent alkylglycerol mono-oxygenase. Biochem. J. 443, 279–286, (2012).


Antala, S., Ovchinnikov, S., Kamisetty, H., Baker, D. & Dempski, R. E. Computation and practical research present a mannequin for the construction of the zinc transporter hZIP4. J. Biol. Chem. 290, 17796–17805, (2015).


Zhang, T. et al. Crystal constructions of a ZIP zinc transporter reveal a binuclear metallic heart within the transport pathway. Science Advances Three, e1700344, (2017).


Ma, B. et al. Subcellular localization and membrane topology of the melon ethylene receptor CmERS1. Plant Physiol. 141, 587–597, (2006).


Li, S. C. & Ng, Y. Okay. Calibur: a device for clustering giant numbers of protein decoys. BMC Bioinform. 11, 25, (2010).


Jones, D. T., Singh, T., Kosciolek, T. & Tetchner, S. MetaPSICOV: Combining coevolution strategies for correct prediction of contacts and lengthy vary hydrogen bonding in proteins. Bioinformatics 31, 999–1006, (2015).


Kuzmanic, A. & Zagrovic, B. Dedication of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophys J 98, 861–871, (2010).


Dimura, M. et al. Quantitative FRET research and integrative modeling unravel the construction and dynamics of biomolecular methods. Curr Opin Struct Biol 40, 163–185, (2016).


Zhang, Y. & Skolnick, J. TM-align: a protein construction alignment algorithm based mostly on the TM-score. Nucleic Acids Res 33, 2302–2309, (2005).


Barth, P., Wallner, B. & Baker, D. Prediction of membrane protein constructions with advanced topologies utilizing restricted constraints. Proc. Natl. Acad. Sci. USA 106, 1409–1414, (2009).


Yatsunyk, L. A. & Rosenzweig, A. C. Cu(I) Binding and Switch by the N Terminus of the Wilson Illness Protein. The Journal of Organic Chemistry 282, 8622–8631, (2007).


Hill, A. V. The Mixtures of Haemoglobin with Oxygen and with Carbon Monoxide. I. Biochem. J. 7, 471–480 (1913).


Dutta, A. & Bahar, I. Metallic-binding websites are designed to attain optimum mechanical and signaling properties. Construction 18, 1140–1148, (2010).


De Feo, C. J., Mootien, S. & Unger, V. M. Tryptophan scanning evaluation of the membrane area of CTR-copper transporters. J. Membr. Biol. 234, 113–123, (2010).


Guzman, G. R. et al. Tryptophan scanning mutagenesis within the alphaM3 transmembrane area of the Torpedo californica acetylcholine receptor: practical and structural implications. Biochemistry 42, 12243–12250, (2003).


Schaller, G. E., Ladd, A. N., Lanahan, M. B., Spanbauer, J. M. & Bleecker, A. B. The ethylene response mediator ETR1 from Arabidopsis types a disulfide-linked dimer. J Biol Chem 270, 12526–12530, (1995).


Li, P., Music, L. F. & Merz, Okay. M. Jr. Systematic Parameterization of Monovalent Ions Using the Nonbonded Mannequin. J Chem Concept Comput 11, 1645–1657, (2015).


Ansbacher, T. & Shurki, A. Predicting the coordination quantity inside copper chaperones: Atox1 as case examine. J. Phys. Chem. B 116, 4425–4432, (2012).


Geri, J. B., Pernicone, N. C. & York, J. T. Evaluating the affect of various supporting ligands on copper(I)-ethylene interactions. Polyhedron 52, 207–215, (2013).


Gentle, Okay. M., Wisniewski, J. A., Vinyard, W. A. & Kieber-Emmons, M. T. Notion of the plant hormone ethylene: known-knowns and known-unknowns. J. Biol. Inorg. Chem. 21, 715–728, (2016).


Pinkas-Kramarski, R. et al. ErbB tyrosine kinases and the 2 neuregulin households represent a ligand-receptor community. Mol. Cell. Biol. 18, 6090–6101 (1998).


Junge, W., Hong, Y. Q., Qian, L. P. & Viale, A. Cooperative transient trapping of photosystem II protons by the integral membrane portion (CF0) of chloroplast ATP-synthase after delicate extraction of the four-subunit catalytic half (CF1). Proc. Natl. Acad. Sci. USA 81, 3078–3082 (1984).


Delrieu, M. J. Regulation of thermal dissipation of absorbed excitation vitality and violaxanthin deepoxidation within the thylakoids of lactuca sativa. Photoprotective mechanism of a inhabitants of photosystem II facilities. Biochim Biophys Acta 1363, 157–173, (1998).


McDaniel, B. Okay. & Binder, B. M. Ethylene receptor 1 (ETR1) is adequate and has the predominant function in mediating inhibition of ethylene responses by silver in Arabidopsis thaliana. J. Biol. Chem. 287, 26094–26103, (2012).


Hirayama, T. et al. Responsive-To-Antagonist1, a Menkes/Wilson Illness–Associated Copper Transporter, Is Required for Ethylene Signaling in Arabidopsis. Cell 97, 383–393, (1999).


Schaarschmidt, J., Monastyrskyy, B., Kryshtafovych, A. & Bonvin, A. Evaluation of contact predictions in CASP12: Co-evolution and deep studying coming of age. Proteins 86(Suppl 1), 51–66, (2018).


Rubino, J. T., Chenkin, M. P., Keller, M., Riggs-Gelasco, P. & Franz, Okay. J. A comparability of methionine, histidine and cysteine in copper(i)-binding peptides reveals variations related to copper uptake by organisms in numerous environments. Metallomics Three, 61–73, (2011).


Rubino, J. T. & Franz, Okay. J. Coordination chemistry of copper proteins: How nature handles a poisonous cargo for important operate. Journal of Inorganic Biochemistry 107, 129–143, (2012).


Hæffner, F., Brinck, T., Haeberlein, M. & Moberg, C. Power subject parameterization of copper(I)-olefin methods from density practical calculations. Journal of Molecular Construction: THEOCHEM 397, 39–50, (1997).


Bhate, M. P., Molnar, Okay. S., Goulian, M. & DeGrado, W. F. Sign transduction in histidine kinases: insights from new constructions. Construction 23, 981–994, (2015).


Dobson, L., Reményi, I. & Tusnády, G. E. CCTOP: A Consensus Constrained TOPology prediction net server. Nucleic Acids Res. 43, W408–W412, (2015).


Jones, D. T. Protein secondary construction prediction based mostly on position-specific scoring matrices. J Mol Biol 292, 195–202, (1999).


Adamian, L. & Liang, J. Prediction of transmembrane helix orientation in polytopic membrane proteins. BMC Struct. Biol. 6, 13, (2006).


Yarov-Yarovoy, V., Schonbrun, J. & Baker, D. Multipass membrane protein construction prediction utilizing Rosetta. Proteins 62, 1010–1025, (2006).


Yarov-Yarovoy, V., Schonbrun, J., Barth, P. & Wallner, B. Membrane Abinitio,


Kamisetty, H., Ovchinnikov, S. & Baker, D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich period. Proc. Natl. Acad. Sci. USA 110, 15674–15679, (2013).


Ovchinnikov, S., Kamisetty, H. & Baker, D., (2019).


Mitternacht, S. FreeSASA: An open supply C library for solvent accessible floor space calculations. F1000Res 5, 189, (2016).


Xu, J. & Zhang, Y. How important is a protein construction similarity with TM-score = Zero.5? Bioinformatics 26, 889–895, (2010).


Wallner, B. PQM-resample: Improved Mannequin High quality Evaluation for Membrane Proteins by Restricted Conformational Sampling. Bioinformatics (Oxford, England) 30, 2221–2223, (2014).


Studer, G., Biasini, M. & Schwede, T. Assessing the native structural high quality of transmembrane protein fashions utilizing statistical potentials (QMEANBrane). Bioinformatics 30, 505–511, (2014).


Kryshtafovych, A., Monastyrskyy, B., Fidelis, Okay., Schwede, T. & Tramontano, A. Evaluation of mannequin accuracy estimations in CASP12. Proteins 86(Suppl 1), 345–360, (2018).


Dominguez, C., Boelens, R. & Bonvin, A. M. J. J. HADDOCK: A protein-protein docking strategy based mostly on biochemical or biophysical info. Journal of the American Chemical Society 125, 1731–1737, (2003).


Wang, Y. & Barth, P. Evolutionary-guided de novo construction prediction of self-associated transmembrane helical proteins with near-atomic accuracy. Nature Communications 6, 7196, (2015).


Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234, 779–815, (1993).


Im, W., Lee, M. S. & Brooks, C. L. Generalized Born Mannequin with a Easy Smoothing Operate. J. Comput. Chem. 24, 1691–1702, (2003).


Feig, M. Computational protein construction refinement: nearly there, but nonetheless thus far to go. Wiley Interdisciplinary Evaluations: Computational Molecular Science, e1307, (2017).


Feig, M., Karanicolas, J. & Brooks, C. L. third MMTSB Software Set: enhanced sampling and multiscale modeling strategies for functions in structural biology. J Mol Graph Mannequin 22, 377–395, (2004).


Roe, D. R. & Cheatham, T. E. third PTRAJ and CPPTRAJ: Software program for Processing and Evaluation of Molecular Dynamics Trajectory Information. J. Chem. Concept Comput. 9, 3084–3095, (2013).


Coughlan, S. J., Hastings, C. & Winfrey, R. J. Molecular characterisation of plant endoplasmic reticulum – Identification of protein disulfide-isomerase as the main reticuloplasmin. European Journal of Biochemistry 235, 215–224, (1996).


Schott-Verdugo, S. & Gohlke, H. PACKMOL-Memgen: An easy-to-use generalized workflow for membrane-protein/lipid-bilayer system constructing. Journal of Chemical Data and Modeling (2019).


Le Grand, S., Götz, A. W. & Walker, R. C. SPFP: Pace with out compromise—A blended precision mannequin for GPU accelerated molecular dynamics simulations. Comput. Phys. Commun. 184, 374–380, (2013).


Maier, J. A. et al. ff14SB: Bettering the Accuracy of Protein Facet Chain and Spine Parameters from ff99SB. J. Chem. Concept Comput. 11, 3696–3713, (2015).


Dickson, C. J. et al. Lipid14: The Amber Lipid Power Subject. J. Chem. Concept Comput. 10, 865–879, (2014).


AMBER 2018 (College of California, San Francisco, 2018).


Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparability of Easy Potential Features for Simulating Liquid Water. J. Chem. Phys. 79, 926–935, (1983).


Ryckaert, J.-P., Ciccotti, G. & Berendsen, H. J. C. Numerical integration of the cartesian equations of movement of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327–341, (1977).


Quigley, D. & Probert, M. I. Langevin dynamics in fixed strain prolonged methods. J. Chem. Phys. 120, 11432–11441, (2004).


Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. Molecular-Dynamics with Coupling to an Exterior Bathtub. J. Chem. Phys. 81, 3684–3690, (1984).


Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Improvement and testing of a basic amber power subject. J Comput Chem 25, 1157–1174, (2004).


Bayly, C. I., Cieplak, P., Cornell, W. & Kollman, P. A. A well-behaved electrostatic potential based mostly technique utilizing cost restraints for deriving atomic costs: the RESP mannequin. J. Phys. Chem. 97, 10269–10280, (1993).


Gaussian 09 (Gaussian, Inc., Wallingford CT, 2009).


Wang, J., Wang, W., Kollman, P. A. & Case, D. A. Computerized atom kind and bond kind notion in molecular mechanical calculations. J Mol Graph Mannequin 25, 247–260, (2006).


Gohlke, H. et al. Binding Area of Alanopine Dehydrogenase Predicted by Unbiased Molecular Dynamics Simulations of Ligand Diffusion. J. Chem. Inf. Mannequin. 53, 2493–2498, (2013).


Bhatia, S. et al. Focusing on HSP90 dimerization through the C terminus is efficient in imatinib-resistant CML and lacks the warmth shock response. Blood 132, 307–320, (2018).


Bisson, M. M., Bleckmann, A., Allekotte, S. & Groth, G. EIN2, the central regulator of ethylene signalling, is localized on the ER membrane the place it interacts with the ethylene receptor ETR1. Biochem. J. 424, 1–6, (2009).


Follo, C. & Isidoro, C. A quick and easy technique for simultaneous blended site-specific mutagenesis of a large coding sequence. Biotechnol. Appl. Biochem. 49, 175–183, (2008).


Voet-van-Vormizeele, J. & Groth, G. Excessive-level expression of the Arabidopsis thaliana ethylene receptor protein ETR1 in Escherichia coli and purification of the recombinant protein. Protein Expr. Purif. 32, 89–94, (2003).


Drees, S. L. & Lübben, M. Analytical Gel Filtration for Probing Heavy Metallic Switch between Proteins. Bio-protocol 6(15), e1888, (2016).


Wernimont, A. Okay., Yatsunyk, L. A. & Rosenzweig, A. C. Binding of copper(I) by the Wilson illness protein and its copper chaperone. J Biol Chem 279, 12269–12276, (2004).


Shakeel, S. N., Wang, X., Binder, B. M. & Schaller, G. E. Mechanisms of sign transduction by ethylene: overlapping and non-overlapping signalling roles in a receptor household. AoB Vegetation 5, plt010–plt010, (2013).


Xiao, Z., Donnelly, P. S., Zimmermann, M. & Wedd, A. G. Switch of copper between bis(thiosemicarbazone) ligands and intracellular copper-binding proteins. insights into mechanisms of copper uptake and hypoxia selectivity. Inorg. Chem. 47, 4338–4347, (2008).

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