The Caenorhabditis elegans DAF-12 nuclear receptor: Structure, dynamics, and interaction with ligands
A structure for the ligand binding domain (LBD) of the DAF-12 receptor from Caenorhabditis elegans was obtained from the X-ray crystal structure of the receptor LBD from Strongyloides stercoralis bound to (25R)-Δ7-dafachronic acid (DA) (pdb:3GYU). The model was constructed in the presence of the lig...
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2012
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| Acceso en línea: | Registro en Scopus DOI Handle Registro en la Biblioteca Digital |
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| LEADER | 09351caa a22010697a 4500 | ||
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| 001 | PAPER-9540 | ||
| 003 | AR-BaUEN | ||
| 005 | 20230518203928.0 | ||
| 008 | 190411s2012 xx ||||fo|||| 00| 0 eng|d | ||
| 024 | 7 | |2 scopus |a 2-s2.0-84862193963 | |
| 024 | 7 | |2 cas |a arginine, 1119-34-2, 15595-35-4, 7004-12-8, 74-79-3; Arginine, 74-79-3; Caenorhabditis elegans Proteins; Cholestenes; DAF-12 protein, C elegans; Ligands; Receptors, Cytoplasmic and Nuclear; dafachronic acid | |
| 040 | |a Scopus |b spa |c AR-BaUEN |d AR-BaUEN | ||
| 100 | 1 | |a Alvarez, L.D. | |
| 245 | 1 | 4 | |a The Caenorhabditis elegans DAF-12 nuclear receptor: Structure, dynamics, and interaction with ligands |
| 260 | |c 2012 | ||
| 270 | 1 | 0 | |m Burton, G.; Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Pabellón 2, C1428EGA Ciudad de Buenos Aires, Argentina; email: burton@qo.fcen.uba.ar |
| 506 | |2 openaire |e Política editorial | ||
| 504 | |a Kaletta, T., Hengartner, M.O., Finding function in novel targets: C. elegans as a model organism (2006) Nat Rev Drug Discov, 5, pp. 387-398 | ||
| 504 | |a Motola, D.L., Cummins, C.L., Rottiers, V., Sharma, K.K., Li, T., Li, Y., Suino-Powell, K., Mangelsdorf, D.J., Identification of ligands for DAF-12 that govern dauer formation and reproduction in C. elegans (2006) Cell, 124, pp. 1209-1223 | ||
| 504 | |a Beckstead, R.B., Thummel, C.S., Indicted: worms caught using steroids (2006) Cell, 124, pp. 1137-1140 | ||
| 504 | |a Hochbaum, D., Zhang, Y., Stuckenholz, C., Labhart, P., Alexiadis, V., Martin, R., Knölker, H.J., Fisher, A.L., DAF-12 regulates a connected network of genes to ensure robust developmental decisions (2011) PLoS Genet, 7, pp. e1002179 | ||
| 504 | |a Antebi, A., Yeh, W.H., Tait, D., Hedgecock, E.M., Riddle, D.L., daf-12 encodes a nuclear receptor that regulates the dauer diapause and developmental age in C. elegans (2000) Genes Dev, 14, pp. 1512-1527 | ||
| 504 | |a Gerisch, B., Weitzel, C., Kober-Eisermann, C., Rottiers, V., Antebi, A., A hormonal signaling pathway influencing C. elegans metabolism, reproductive development, and life span (2001) Dev Cell, 1, pp. 841-851 | ||
| 504 | |a Wang, Z., Zhou, X.E., Motola, D.L., Gao, X., Suino-Powell, K., Conneely, A., Ogata, C., Mangelsdorf, D.J., Identification of the nuclear receptor DAF-12 as a therapeutic target in parasitic nematodes (2009) Proc Natl Acad Sci USA, 106, pp. 9138-9143 | ||
| 504 | |a Martin, R., Entchev, E.V., Däbritz, F., Kurzchalia, T.V., Knölker, H.J., Synthesis and hormonal activity of the (25S)-cholesten-26-oic acids-potent ligands for the DAF-12 receptor in Caenorhabditis elegans (2009) Eur J Org Chem, pp. 3703-3714 | ||
| 504 | |a Sharma, K.K., Wang, Z., Motola, D.L., Cummins, C.L., Mangelsdorf, D.J., Auchus, R.J., Synthesis and activity of dafachronic acid ligands for the C. elegans DAF-12 nuclear hormone receptor (2009) Mol Endocrinol, 23, pp. 640-648 | ||
| 504 | |a Martin, R., Entchev, E.V., Kurzchalia, T.V., Knölker, H.J., Steroid hormones controlling the life cycle of the nematode Caenorhabditis elegans: stereoselective synthesis and biology (2010) Org Biomol Chem, 8, pp. 739-750 | ||
| 504 | |a Sali, A., Blundell, T.L., Comparative protein modelling by satisfaction of spatial restraints (1993) J Mol Biol, 234, pp. 779-815 | ||
| 504 | |a Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., Olson, A.J., Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function (1998) J Comp Chem, 19, pp. 1639-1662 | ||
| 504 | |a Case, D.A., Darden, T.A., Cheatham III, T.E., Simmerling, C.L., Wang, J., Duke, R.E., Luo, R., Kollman, P.A., (2010) Amber, Version 11, , San Francisco: University of California | ||
| 504 | |a Weichenberger, C.X., Sippl, M.J., NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures (2007) Nucleic Acids Res, 35, pp. W403-W406. , Web Server Issue | ||
| 504 | |a Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Montgomery Jr., J.A., Pople, J.A., (2004) Gaussian, Version 03, Revision C, , Wallingford: Gaussian Inc | ||
| 504 | |a Cheatham, T.E., Cieplak, P., Kollman, P.A., A modified version of the Cornell force field with improved sugar pucker phases and helical repeat (1999) Biomol Struct Dyn, 16, pp. 845-862 | ||
| 504 | |a Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., DiNola, A., Haak, J.R., Molecular dynamics with coupling to an external bath (1984) J Chem Phys, 81, pp. 3684-3690 | ||
| 504 | |a Kabsch, W., Sander, C., Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features (1983) Biopolymers, 22, pp. 2577-2637 | ||
| 504 | |a Luthy, R., Bowie, J.U., Eisenberg, D., Assessment of protein models with three-dimensional profiles (1992) Nature, 356, pp. 83-85 | ||
| 504 | |a Michel, J., Foloppe, N., Essex, J.W., Rigorous free energy calculations in structure-based drug design (2010) Mol Inform, 29, pp. 570-578 | ||
| 520 | 3 | |a A structure for the ligand binding domain (LBD) of the DAF-12 receptor from Caenorhabditis elegans was obtained from the X-ray crystal structure of the receptor LBD from Strongyloides stercoralis bound to (25R)-Δ7-dafachronic acid (DA) (pdb:3GYU). The model was constructed in the presence of the ligand using a combination of Modeller, Autodock, and molecular dynamics (MD) programs, and then its dynamical behavior was studied by MD. A strong ligand binding mode (LBM) was found, with the three arginines in the ligand binding pocket (LBP) contacting the C-26 carboxylate group of the DA. The quality of the ceDAF-12 model was then evaluated by constructing several ligand systems for which the experimental activity is known. Thus, the dynamical behavior of the ceDAF-12 complex with the more active (25S)-Δ7-DA showed two distinct binding modes, one of them being energetically more favorable compared with the 25R isomer. Then the effect of the Arg564Cys and Arg598Met mutations on the (25R)-Δ7-DA binding was analyzed. The MD simulations showed that in the first case the complex was unstable, consistent with the lack of transactivation activity of (25R)-Δ7-DA in this mutant. Instead, in the case of the Arg598Met mutant, known to produce a partial loss of activity, our model predicted smaller effects on the LBM with a more stable MD trajectory. The model also showed that removal of the C-25 methyl does not impede the simultaneous strong interaction of the carboxylate with the three arginines, predicting that 27-nor-DAs are putative ceDAF-12 ligands. © 2012 Wiley Periodicals, Inc. |l eng | |
| 593 | |a Departamento de Química Orgánica and UMYMFOR (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina | ||
| 593 | |a IFIBYNE (CONICET-UBA), Argentina | ||
| 593 | |a Departamento de Química Inorgánica, Analitica y Quimica Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina | ||
| 690 | 1 | 0 | |a C. ELEGANS |
| 690 | 1 | 0 | |a DAFACHRONIC ACID |
| 690 | 1 | 0 | |a MOLECULAR DYNAMICS |
| 690 | 1 | 0 | |a NUCLEAR RECEPTOR, DAF-12 |
| 690 | 1 | 0 | |a ARGININE |
| 690 | 1 | 0 | |a CAENORHABDITIS ELEGANS PROTEIN |
| 690 | 1 | 0 | |a CARBOXYLIC ACID |
| 690 | 1 | 0 | |a CELL NUCLEUS RECEPTOR |
| 690 | 1 | 0 | |a DAF 12 NUCLEAR RECEPTOR |
| 690 | 1 | 0 | |a UNCLASSIFIED DRUG |
| 690 | 1 | 0 | |a ARTICLE |
| 690 | 1 | 0 | |a BINDING SITE |
| 690 | 1 | 0 | |a CAENORHABDITIS ELEGANS |
| 690 | 1 | 0 | |a CRYSTAL STRUCTURE |
| 690 | 1 | 0 | |a GENE MUTATION |
| 690 | 1 | 0 | |a MOLECULAR DOCKING |
| 690 | 1 | 0 | |a MOLECULAR DYNAMICS |
| 690 | 1 | 0 | |a MOLECULAR MODEL |
| 690 | 1 | 0 | |a NONHUMAN |
| 690 | 1 | 0 | |a PRIORITY JOURNAL |
| 690 | 1 | 0 | |a PROTEIN ANALYSIS |
| 690 | 1 | 0 | |a PROTEIN INTERACTION |
| 690 | 1 | 0 | |a PROTEIN STRUCTURE |
| 690 | 1 | 0 | |a STRONGYLOIDES STERCORALIS |
| 690 | 1 | 0 | |a TRANSACTIVATION |
| 690 | 1 | 0 | |a X RAY CRYSTALLOGRAPHY |
| 690 | 1 | 0 | |a AMINO ACID SEQUENCE |
| 690 | 1 | 0 | |a ANIMALS |
| 690 | 1 | 0 | |a ARGININE |
| 690 | 1 | 0 | |a BINDING SITES |
| 690 | 1 | 0 | |a CAENORHABDITIS ELEGANS PROTEINS |
| 690 | 1 | 0 | |a CHOLESTENES |
| 690 | 1 | 0 | |a LIGANDS |
| 690 | 1 | 0 | |a MOLECULAR DYNAMICS SIMULATION |
| 690 | 1 | 0 | |a MOLECULAR SEQUENCE DATA |
| 690 | 1 | 0 | |a PROTEIN BINDING |
| 690 | 1 | 0 | |a RECEPTORS, CYTOPLASMIC AND NUCLEAR |
| 690 | 1 | 0 | |a SEQUENCE ALIGNMENT |
| 690 | 1 | 0 | |a CAENORHABDITIS ELEGANS |
| 690 | 1 | 0 | |a STRONGYLOIDES STERCORALIS |
| 700 | 1 | |a Mañez, P.A. | |
| 700 | 1 | |a Estrin, D.A. | |
| 700 | 1 | |a Burton, G. | |
| 773 | 0 | |d 2012 |g v. 80 |h pp. 1798-1809 |k n. 7 |p Proteins Struct. Funct. Bioinformatics |x 08873585 |t Proteins: Structure, Function and Bioinformatics | |
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| 856 | 4 | 0 | |u https://doi.org/10.1002/prot.24076 |y DOI |
| 856 | 4 | 0 | |u https://hdl.handle.net/20.500.12110/paper_08873585_v80_n7_p1798_Alvarez |y Handle |
| 856 | 4 | 0 | |u https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_08873585_v80_n7_p1798_Alvarez |y Registro en la Biblioteca Digital |
| 961 | |a paper_08873585_v80_n7_p1798_Alvarez |b paper |c PE | ||
| 962 | |a info:eu-repo/semantics/article |a info:ar-repo/semantics/artículo |b info:eu-repo/semantics/publishedVersion | ||
| 999 | |c 70493 | ||