Phosphorylation of the retinoic acid receptor alpha induces a mechanical allosteric regulation and changes in internal dynamics
Open accessAbstract
Nuclear receptor proteins constitute a superfamily of proteins that function as ligand dependent transcription factors. They are implicated in the transcriptional cascades underlying many physiological phenomena, such as embryogenesis, cell growth and differentiation, and apoptosis, making them one of the major signal transduction paradigms in metazoans. Regulation of these receptors occurs through the binding of hormones, and in the case of the retinoic acid receptor (RAR), through the binding of retinoic acid (RA). In addition to this canonical scenario of RAR activity, recent discoveries have shown that RAR regulation also occurs as a result of phosphorylation. In fact, RA induces non-genomic effects, such as the activation of kinase signaling pathways, resulting in the phosphorylation of several targets including RARs themselves. In the case of RARα, phosphorylation of Ser369 located in loop L9-10 of the ligand-binding domain leads to an increase in the affinity for the protein cyclin H, which is part of the Cdk-activating kinase complex of the general transcription factor TFIIH. The cyclin H binding site in RARα is situated more than 40 Å from the phosphorylated serine. Using molecular dynamics simulations of the unphosphorylated and phosphorylated forms of the receptor RARα, we analyzed the structural implications of receptor phosphorylation, which led to the identification of a structural mechanism for the allosteric coupling between the two remote sites of interest. The results show that phosphorylation leads to a reorganization of a local salt bridge network, which induces changes in helix extension and orientation that affects the cyclin H binding site. This results in changes in conformation and flexibility of the latter. The high conservation of the residues implicated in this signal transduction suggests a mechanism that could be applied to other nuclear receptor proteins.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Phosphorylation of the RARγ (and RARα) receptors leads to subtle changes in the dynamic properties of the protein without producing significant conformational rearrangements.
“Crystallographic studies of phospho-mimetic mutations of RARγ (S371E) and MD simulations showed that phosphorylation of the RARγ (and RARα) receptors of this family leads to subtle changes in the dynamic properties of the protein without producing significant conformational rearrangements (Chebaro et al., 2013, 2017).”
From Allostery in Its Many Disguises: From Theory to Applications (2019) · cites this paper as Chebaro et al., 2013
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952 · see citing works
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
Darden, T., York, D., & Pedersen, L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464397 · Cited by 29,588 · see citing works
Ryckaert, J., Ciccotti, G., & Berendsen, H. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 19,525 · see citing works
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914 · see citing works
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320 · see citing works
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,270 · see citing works
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736 · see citing works
WebLogo: A Sequence Logo Generator: Figure 1Preprint
Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,433 · see citing works
CHARMM: The biomolecular simulation program
Brooks, B. R., Brooks, C. L., MacKerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., et al. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21287 · Cited by 8,994 · see citing works
MacKerell, A. D., Feig, M., & Brooks, C. L. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20065 · Cited by 3,336 · see citing works
Fpocket: An open source platform for ligand pocket detection
Guilloux, V. L., Schmidtke, P., & Tufféry, P. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-168 · Cited by 1,666 · see citing works
H++: a server for estimating pKas and adding missing hydrogens to macromolecules
Gordon, J. C., Myers, J., Folta, T., Shoja, V., Heath, L. S., & Onufriev, A. (2005) · Nucleic Acids Res. · doi:10.1093/nar/gki464 · Cited by 1,657 · see citing works
Crystal structure of the RAR-γ ligand-binding domain bound to all-trans retinoic acid
Renaud, J., Rochel, N., Ruff, M., Vivat, V., Chambon, P., Gronemeyer, H., & Moras, D. (1995) · Nature · doi:10.1038/378681a0 · Cited by 1,098 · see citing works
Very fast prediction and rationalization of pKa values for protein–ligand complexes
Bas, D., Rogers, D. M., & Jensen, J. H. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22102 · Cited by 1,096 · see citing works
Rosenfeld, M. G., Lunyak, V. V., & Glass, C. K. (2006) · Genes & Development · doi:10.1101/gad.1424806 · Cited by 952 · see citing works
Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA
Chandra, V., Huang, P., Hamuro, Y., Raghuram, S., Wang, Y., Burris, T. P., & Rastinejad, F. (2008) · Nature · doi:10.1038/nature07413 · Cited by 808 · see citing works
Allostery without conformational change
Cooper, A., & Dryden, D. T. F. (1984) · European Biophysics Journal · doi:10.1007/bf00276625 · Cited by 740 · see citing works
Allostery and cooperativity revisited
Cui, Q., & Karplus, M. (2008) · Protein Science · doi:10.1110/ps.03259908 · Cited by 680 · see citing works
The role of dynamics in allosteric regulation
Kern, D., & Zuiderweg, E. R. P. (2003) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2003.10.008 · Cited by 653 · see citing works
Mark, M. P., Ghyselinck, N. B., & Chambon, P. (2005) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.46.120604.141156 · Cited by 596 · see citing works
Homodimer formation of retinoid X receptor induced by 9-cis retinoic acid
Zhang, X.-K., Lehmann, J., Hoffmann, B., Dawson, M. I., Cameron, J., Graupner, G., Hermann, T. W., Tran, P., & Pfahl, M. (1992) · Nature · doi:10.1038/358587a0 · Cited by 565 · see citing works
Helix to helix packing in proteins.
Chothia, C., Levitt, M., & Richardson, D. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90341-7 · Cited by 537 · see citing works
Deconstructing repression: evolving models of co-repressor action
Perissi, V., Jepsen, K., Glass, C. K., & Rosenfeld, M. G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2736 · Cited by 532 · see citing works
Controlling nuclear receptors: the circular logic of cofactor cycles
Perissi, V., & Rosenfeld, M. G. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1680 · Cited by 507 · see citing works
Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
Brünger, A. T., & Karplus, M. (1988) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340040208 · Cited by 504 · see citing works
The retinoid signaling pathway: molecular and genetic analyses
Chambon, P. (1994) · Seminars in Cell Biology · doi:10.1006/scel.1994.1015 · Cited by 502 · see citing works
Allostery: Absence of a change in shape does not imply that allostery is not at play
Tsai, C.-J., del Sol, A., & Nussinov, R. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.02.034 · Cited by 453 · see citing works
Hünenberger, P. H., Mark, A. E., & van Gunsteren, W. F. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0514 · Cited by 441 · see citing works
The Structural Basis for Control of Eukaryotic Protein Kinases
Endicott, J., Noble, M. E. M., & Johnson, L. N. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-052410-090317 · Cited by 431 · see citing works
Crystal Structure of a Heterodimeric Complex of RAR and RXR Ligand-Binding Domains
Bourguet, W., Vivat, V., Wurtz, J., Chambon, P., Gronemeyer, H., & Moras, D. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)80424-4 · Cited by 405 · see citing works
The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways
del Sol, A., Tsai, C., Ma, B., & Nussinov, R. (2009) · Structure · doi:10.1016/j.str.2009.06.008 · Cited by 365 · see citing works
Altucci, L., Rossin, A., Raffelsberger, W., Reitmair, A., Chomienne, C., & Gronemeyer, H. (2001) · Nature Medicine · doi:10.1038/89050 · Cited by 340 · see citing works
Tsai, C., del Sol, A., & Nussinov, R. (2009) · Molecular BioSystems · doi:10.1039/b819720b · Cited by 324 · see citing works
Rochette-Egly, C., Adam, S., Rossignol, M., Egly, J.-M., & Chambon, P. (1997) · Cell · doi:10.1016/s0092-8674(00)80317-7 · Cited by 308 · cited 1× · see citing works
“CAK complex so that the cdk7 kinase can phosphorylate a second serine of RARa (S77) located in the NTD [24,25].”
BackgroundDynamic and combinatorial control of gene expression by nuclear retinoic acid receptors (RARs)
Rochette‐Egly, C., & Germain, P. (2009) · Nuclear Receptor Signaling · doi:10.1621/nrs.07005 · Cited by 244 · see citing works
Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA
Orlov, I. M., Rochel, N., Moras, D., & Klaholz, B. P. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.445 · Cited by 219 · see citing works
Structure of the RXR–RAR DNA‐binding complex on the retinoic acid response element DR1
Rastinejad, F., Wagner, T., Zhao, Q., & Khorasanizadeh, S. (2000) · The EMBO Journal · doi:10.1093/emboj/19.5.1045 · Cited by 217 · see citing works
Rochel, N., Ciesielski, F., Godet, J., Momán, E., Roessle, M. W., Peluso‐Iltis, C., Moulin, M., Haertlein, M., Callow, P., Mély, Y., et al. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2054 · Cited by 193 · see citing works
Allostery and population shift in drug discovery
Kar, G., Keskin, Ö., Gürsoy, A., & Nussinov, R. (2010) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2010.09.002 · Cited by 190 · see citing works
Masiá, S., Alvarez, S., de Lera, A. R., & Barettino, D. (2007) · Molecular Endocrinology · doi:10.1210/me.2007-0062 · Cited by 184 · see citing works
A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor
le Maire, A., Teyssier, C., Erb, C., Grimaldi, M., Álvarez, S., de Lera, Á. R., Balaguer, P., Gronemeyer, H., Royer, C. A., Germain, P., et al. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1855 · Cited by 163 · see citing works
Alsayed, Y., Uddin, S., Mahmud, N., Lekmine, F., Kalvakolanu, D. V., Minucci, S., Bokoch, G., & Platanias, L. C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m007431200 · Cited by 161 · see citing works
Jones, S. W. (1999) · The Journal of General Physiology · doi:10.1085/jgp.114.2.271 · Cited by 140 · see citing works
Ensemble-Based Convergence Analysis of Biomolecular Trajectories
Lyman, E. R., & Zuckerman, D. M. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.082941 · Cited by 124 · see citing works
Nuclear retinoic acid receptors: Conductors of the retinoic acid symphony during development
Samarut, É., & Rochette‐Egly, C. (2011) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2011.03.025 · Cited by 113 · see citing works
A coordinated phosphorylation cascade initiated by p38MAPK/MSK1 directs RARα to target promoters
Bruck, N., Vitoux, D., Ferry, C., Duong, V., Bauer, A., de Thé, H., & Rochette‐Egly, C. (2009) · The EMBO Journal · doi:10.1038/emboj.2008.256 · Cited by 108 · see citing works
Bastien, J., Adam-Stitah, S., Riedl, T., Egly, J.-M., Chambon, P., & Rochette-Egly, C. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m001985200 · Cited by 107 · see citing works
Simulaid: A simulation facilitator and analysis program
Mezei, M. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21551 · Cited by 97 · see citing works
Piskunov, A., & Rochette-Egly, C. (2012) · Oncogene · doi:10.1038/onc.2011.499 · Cited by 95 · see citing works
Rational design of RAR‐selective ligands revealed by RARβ crystal stucture
Germain, P., Kammerer, S., Pérez‐Santín, E., Peluso‐Iltis, C., Tortolani, D. R., Zusi, F. C., Starrett, J. E. J., Lapointe, P., Daris, J., Marinier, A., et al. (2004) · EMBO Reports · doi:10.1038/sj.embor.7400235 · Cited by 91 · see citing works
Signature of the oligomeric behaviour of nuclear receptors at the sequence and structural level
Brélivet, Y., Kammerer, S., Rochel, N., Poch, O., & Moras, D. (2004) · EMBO Reports · doi:10.1038/sj.embor.7400119 · Cited by 87 · see citing works
Synthesis and Crystal Structure of a Phosphorylated Estrogen Receptor Ligand Binding Domain
Möcklinghoff, S., Rose, R., Carraz, M., Visser, A., Ottmann, C., & Brunsveld, L. (2010) · ChemBioChem · doi:10.1002/cbic.201000532 · Cited by 87 · see citing works
Osz, J., Brélivet, Y., Peluso-Iltis, C., Cura, V., Eiler, S., Ruff, M., Bourguet, W., Rochel, N., & Moras, D. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118192109 · Cited by 84 · see citing works
Laine, É., de Beauchêne, I. C., Pérahia, D., Auclair, C., & Tchertanov, L. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002068 · Cited by 80 · see citing works
Gaillard, E., Bruck, N., Brelivet, Y., Bour, G., Lalevée, S., Bauer, A., Poch, O., Moras, D., & Rochette-Egly, C. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509717103 · Cited by 76 · see citing works
The “Phantom Effect” of the Rexinoid LG100754: Structural and Functional Insights
Sato, Y., Ramalanjaona, N., Huet, T., Potier, N., Ősz, J., Antony, P., Peluso‐Iltis, C., Poussin‐Courmontagne, P., Ennifar, E., Mély, Y., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015119 · Cited by 75 · see citing works
Gupta, P., Ho, P.-C., Huq, M. M., Ha, S. G., Park, S. W., Khan, A. A., Tsai, N.-P., & Wei, L.-N. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0710561105 · Cited by 74 · see citing works
Bour, G., Lalevée, S., & Rochette‐Egly, C. (2007) · Trends in Cell Biology · doi:10.1016/j.tcb.2007.04.003 · Cited by 69 · see citing works
McNamara, S., Wang, H., Hanna, N., & Miller, W. H. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01576-07 · Cited by 61 · see citing works
Gekko, K., Obu, N., Li, J., & Lee, J. C. (2004) · Biochemistry · doi:10.1021/bi036271e · Cited by 58 · see citing works
NMR reveals novel mechanisms of protein activity regulation
Kalodimos, C. G. (2011) · Protein Science · doi:10.1002/pro.614 · Cited by 47 · see citing works
Simulations of allosteric transitions.
Elber, R. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.01.012 · Cited by 41 · see citing works
Protein function and allostery: a dynamic relationship
Kalodimos, C. G. (2012) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2011.06319.x · Cited by 37 · see citing works
Mezei, M., & Filizola, M. (2006) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-006-9039-1 · Cited by 36 · see citing works
Samarut, E., Amal, I., Markov, G. V., Stote, R., Dejaegere, A., Laudet, V., & Rochette-Egly, C. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr035 · Cited by 26 · see citing works
The statistical theory of allostery
Vendruscolo, M. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.603 · Cited by 24 · see citing works
Computational studies of LXR molecular interactions reveal an allosteric communication pathway
Burendahl, S., & Nilsson, L. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23209 · Cited by 22 · see citing works
Fidelak, J., Ferrer, S., Oberlin, M., Moras, D., Dejaegere, A. P., & Stote, R. H. (2010) · European Biophysics Journal · doi:10.1007/s00249-010-0608-9 · Cited by 18 · see citing works
Morange, M. (2012) · Journal of Biosciences · doi:10.1007/s12038-012-9186-6 · Cited by 12 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [35]Rochel N, Ciesielski F, Godet J, Moman E, Roessle M, Peluso-Iltis C, Moulin M, Haertlein M, Callow P, Mély Y, Svergun DI, Moras D (2011) Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings. Nat Struct Mol Biol 18: 564– 570. 21478865
Cited by
Sorted by citations
Allostery in Its Many Disguises: From Theory to Applications
Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., et al. (2019) · Structure · doi:10.1016/j.str.2019.01.003 · Cited by 404 · see citing works
Retinoic acid receptors: From molecular mechanisms to cancer therapy
di Masi, A., Leboffe, L., De Marinis, E., Pagano, F., Cicconi, L., Rochette-Egly, C., Lo-Coco, F., Ascenzi, P., & Nervi, C. (2015) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2014.12.003 · Cited by 403 · see citing works
Rochette‐Egly, C. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2014.04.003 · Cited by 97 · see citing works
Belorusova, A. Y., Eberhardt, J., Potier, N., Stote, R. H., Dejaegere, A. P., & Rochel, N. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm5002524 · Cited by 53 · see citing works
Nuclear and extranuclear effects of vitamin A
Iskakova, M., Karbyshev, M. S., Piskunov, A., & Rochette‐Egly, C. (2015) · Canadian Journal of Physiology and Pharmacology · doi:10.1139/cjpp-2014-0522 · Cited by 44 · see citing works
Cell adhesion signals regulate the nuclear receptor activity
Sugimoto, K., Ichikawa‐Tomikawa, N., Kashiwagi, K., Endo, C., Tanaka, S., Sawada, N., Watabe, T., Higashi, T., & Chiba, H. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1913346116 · Cited by 44 · see citing works
History of Retinoic Acid Receptors
Benbrook, D. M., Chambon, P., Rochette‐Egly, C., & Asson–Batres, M. A. (2014) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-94-017-9050-5_1 · Cited by 41 · see citing works
Chen, G. (2021) · Cells · doi:10.3390/cells10082160 · Cited by 40 · see citing works
Nuclear and Extra-Nuclear Effects of Retinoid Acid Receptors: How They Are Interconnected
Piskunov, A., Tanoury, Z. A., & Rochette‐Egly, C. (2014) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-94-017-9050-5_6 · Cited by 34 · see citing works
Tanoury, Z. A., Piskunov, A., Andriamoratsiresy, D., Gaouar, S., Lutzing, R., Ye, T., Jost, B., Keime, C., & Rochette‐Egly, C. (2013) · Journal of Cell Science · doi:10.1242/jcs.131946 · Cited by 33 · see citing works
Thouënnon, E., Delfosse, V., Bailly, R., Blanc, P., Boulahtouf, A., Grimaldi, M., Barducci, A., Bourguet, W., & Balaguer, P. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-019-03129-x · Cited by 32 · see citing works
Larangé, A., Takazawa, I., Kakugawa, K., Thiault, N., Ngoi, S., Olive, M. E., Iwaya, H., Seguin, L., Vicente-Suarez, I., Bécart, S., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.07.017 · Cited by 26 · see citing works
Allosteric mechanisms of nuclear receptors: insights from computational simulations
Mackinnon, J. A. G., Gallastegui, N., Osguthorpe, D. J., Hagler, A. T., & Estébanez‐Perpiñá, E. (2014) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2014.05.017 · Cited by 26 · see citing works
Yang, B., Zhang, H., & Wang, H. (2015) · Journal of Molecular Modeling · doi:10.1007/s00894-015-2580-x · Cited by 18 · see citing works
Subtype-Specific Modulation of Estrogen Receptor–Coactivator Interaction by Phosphorylation
Tharun, I. M., Nieto, L., Haase, C., Scheepstra, M., Balk, M., Möcklinghoff, S., Adriaens, W., Dames, S. A., & Brunsveld, L. (2014) · ACS Chemical Biology · doi:10.1021/cb5007097 · Cited by 16 · see citing works
Zhu, Y., Wu, Y., Luo, Y., Zou, Y. F., Ma, B., & Zhang, Q. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp507936a · Cited by 15 · see citing works
Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex
Lemkul, J. A., Lewis, S. N., Bassaganya-Riera, J., & Bevan, D. R. (2015) · PLoS ONE · doi:10.1371/journal.pone.0123984 · Cited by 15 · see citing works
Crystal structure of human ERRg LBD in complex with bisphenol-B
Delfosse, V., Blanc, P., & Bourguet, W. (2018) · Worldwide Protein Data Bank · doi:10.2210/pdb6i61/pdb · Cited by 14 · see citing works
A structural signature motif enlightens the origin and diversification of nuclear receptors
Beinsteiner, B., Markov, G. V., Erb, S., Chebaro, Y., McEwen, A. G., Cianférani, S., Laudet, V., Moras, D., & Billas, I. M. L. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009492 · Cited by 12 · see citing works
Langenfeld, F., Guarracino, Y., Arock, M., Trouvé, A., & Tchertanov, L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0145142 · Cited by 9 · see citing works
Allosteric Regulation in the Ligand Binding Domain of Retinoic Acid Receptorγ
Chebaro, Y., Sirigu, S., Amal, I., Lutzing, R., Stote, R. H., Rochette-Egly, C., Rochel, N., & Dejaegere, A. (2017) · PLOS ONE · doi:10.1371/journal.pone.0171043 · Cited by 8 · see citing works
Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle
Yu, M., Ma, X., Cao, H., Chong, B., Lai, L., & Liu, Z. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25586 · Cited by 5 · see citing works
Designing complex behaviors using transition-based allosteric self-assembly
Metson, J. (2025) · Physical Review Research · doi:10.1103/hx18-tm3p · Cited by 4 · see citing works
Zhu, H., Yang, S., Zhao, J., Wang, L., Gao, C., Sheng, Y., Lin, X., Su, Z., Sato, K., Hu, Z., et al. (2025) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.5c00470 · Cited by 1 · see citing works
Control of Gene Expression by Nuclear Retinoic Acid Receptors
Carrier, M., & Rochette‐Egly, C. (2015) · doi:10.1002/9781118628003.ch5 · Cited by 1 · see citing works
Impact of force field polarization on the collective motions of proteinsPreprint
Milinski, A., Dejaegere, A. P., & Stote, R. H. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.01.626224
- Authors
- Chebaro, Y., Amal, I., Rochel, N., Rochette-Egly, C., Stote, R. H., & Dejaegere, A.
- Affiliations
- Institut de génétique et de biologie moléculaire et cellulaire (FR)
- Corresponding author
- Stote, Roland H.
- Dejaegere, Annick
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-04-18
- Volume
- 9
- Issue
- 4
- Pages
- e1003012
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC3630199
- OpenAlex
- W1982211946
- Cited by
- 25
- References
- 70
- Citations by year
- 2025: 2 · 2024: 1 · 2023: 1 · 2021: 2 · 2019: 3 · 2018: 1 · 2017: 1 · 2015: 5 · 2014: 8 · 2013: 1
- FWCI
- 2.24
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Agence Nationale de la Recherche (ANR-10-BINF-0003, ANR-09-BLAN-0127, ANR-05-BLAN-0390, ANR-05)
- Institut National de la Santé et de la Recherche Médicale
- Centre National de la Recherche Scientifique
- Institut National Du Cancer (INCa-PL09-194, PL09-194)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Retinoids in leukemia and cellular processes
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- retinoic acid receptor alpha, phosphorylation, allosteric regulation, TFIIH, ligand-binding domain, salt bridge network, protein conformational dynamics, nuclear receptors, kinase signaling
- MeSH terms
- Retinoic Acid Receptor alpha, Allosteric Regulation, Allosteric Site, Animals, Binding Sites, Cell Nucleus, Computer Simulation, Gene Expression Regulation, Ligands, Phosphorylation, Protein Binding, Salts, Serine, Solvents, Tretinoin, Signal Transduction, Transcriptional Activation, Protein Structure, Secondary, Receptors, Retinoic Acid, Crystallography, X-Ray, Mice, Cyclin H
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
