Allosteric post-translational modification codes

The language of covalent histone modifications

Strahl, B. D., & Allis, C. D. (2000) · Nature · doi:10.1038/47412 · Cited by 8,679

The Universal Protein Resource (UniProt)

Bairoch, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki070 · Cited by 3,774

How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers

Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D., & Patel, D. J. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1338 · Cited by 1,476

The FoxO code

Calnan, D. R., & Brunet, A. (2008) · Oncogene · doi:10.1038/onc.2008.21 · Cited by 1,170

HDAC6 Regulates Hsp90 Acetylation and Chaperone-Dependent Activation of Glucocorticoid Receptor

Kovacs, J. J., Murphy, P. J. M., Gaillard, S., Zhao, X., Wu, J.-T., Nicchitta, C. V., Yoshida, M., Toft, D. O., Pratt, W. B., & Yao, T.-P. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.04.021 · Cited by 1,153

Quantitative Proteomics Reveals the Function of Unconventional Ubiquitin Chains in Proteasomal Degradation

Xu, P., Duong, D. M., Seyfried, N. T., Cheng, D., Xie, Y., Robert, J., Rush, A. J., Hochstrasser, M., Finley, D. J., & Peng, J. (2009) · Cell · doi:10.1016/j.cell.2009.01.041 · Cited by 1,125

Chromatin remodelling during development

Ho, L., & Crabtree, G. R. (2010) · Nature · doi:10.1038/nature08911 · Cited by 1,114

Nonproteolytic Functions of Ubiquitin in Cell Signaling

Chen, Z. J., & Sun, L. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.01.014 · Cited by 948

Is allostery an intrinsic property of all dynamic proteins?

Gunasekaran, K., Ma, B., & Nussinov, R. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20232 · Cited by 896

Post-translational modifications in signal integration

Deribe, Y. L., Pawson, T., & Dikic, I. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1842 · Cited by 876

The emerging complexity of protein ubiquitination

Komander, D. (2009) · Biochemical Society Transactions · doi:10.1042/bst0370937 · Cited by 821

Activation mechanism of the MAP kinase ERK2 by dual phosphorylation

Canagarajah, B. J., Khokhlatchev, A., Cobb, M. H., & Goldsmith, E. J. (1997) · Cell · doi:10.1016/s0092-8674(00)80351-7 · Cited by 729

Solution Structure of the KIX Domain of CBP Bound to the Transactivation Domain of CREB: A Model for Activator:Coactivator Interactions

Radhakrishnan, I., Pérez-Alvarado, G. C., Parker, D., Dyson, H. J., Montminy, M. R., & Wright, P. E. (1997) · Cell · doi:10.1016/s0092-8674(00)80463-8 · Cited by 728

Intrinsic Disorder and Functional Proteomics

Predrag Radivojac, A., Iakoucheva, L. M., Oldfield, C. J., Zoran Obradovic, A., Uversky, V. N., & Dunker, A. K. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.094045 · Cited by 714

Mechanisms, regulation and consequences of protein SUMOylation

Wilkinson, K. A., & Henley, J. M. (2010) · Biochemical Journal · doi:10.1042/bj20100158 · Cited by 711

Reading protein modifications with interaction domains

Seet, B. T., Đikić, I., Zhou, M., & Pawson, T. J. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1960 · Cited by 665

Structural Basis for Control by Phosphorylation

Johnson, L. N., & Lewis, R. J. (2001) · Chemical Reviews · doi:10.1021/cr000225s · Cited by 643

The Tubulin Code

Verhey, K. J., & Gaertig, J. (2007) · Cell Cycle · doi:10.4161/cc.6.17.4633 · Cited by 558

Principles of ubiquitin and SUMO modifications in DNA repair

Bergink, S., & Jentsch, S. (2009) · Nature · doi:10.1038/nature07963 · Cited by 554

The Universal Protein Resource (UniProt) 2009

The UniProt Consortium (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn664 · Cited by 546

Mechanism of Ubiquitin-Chain Formation by the Human Anaphase-Promoting Complex

Jin, L., Williamson, A. P., Banerjee, S., Philipp, I., & Rapé, M. (2008) · Cell · doi:10.1016/j.cell.2008.04.012 · Cited by 536

Nutrient starvation elicits an acute autophagic response mediated by Ulk1 dephosphorylation and its subsequent dissociation from AMPK

Shang, L., Chen, S., Du, F., Li, S., Zhao, L., & Wang, X. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100844108 · Cited by 517

Posttranslational Modification of p53: Cooperative Integrators of FunctionPreprint

Meek, D. W., & Anderson, C. W. (2009) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000950 · Cited by 510

Signals and Combinatorial Functions of Histone Modifications

Suganuma, T., & Workman, J. L. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061809-175347 · Cited by 508

Cooperative binding of two acetylation marks on a histone tail by a single bromodomain

Morinière, J., Rousseaux, S., Steuerwald, U., Soler-López, M., Curtet, S., Vitte, A.-L., Govin, J., Gaucher, J., Sadoul, K., Hart, D. J., et al. (2009) · Nature · doi:10.1038/nature08397 · Cited by 469

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

Structure, function and evolution of multidomain proteins

Vogel, C., Bashton, M., Kerrison, N. D., Chothia, C., & Teichmann, S. A. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.03.011 · Cited by 408

The spatial and temporal organization of ubiquitin networks

Grabbe, C., Husnjak, K., & Đikić, I. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3099 · Cited by 375

Lysine acetylation and the bromodomain: a new partnership for signaling

Yang, X. (2004) · BioEssays · doi:10.1002/bies.20104 · Cited by 371

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 367

Understanding the Words of Chromatin Regulation

Wu, J. I., Lessard, J. A., & Crabtree, G. R. (2009) · Cell · doi:10.1016/j.cell.2009.01.009 · Cited by 362

The CTD code

Buratowski, S. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb0903-679 · Cited by 350

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

Tsai, C., del Sol, A., & Nussinov, R. (2009) · Molecular BioSystems · doi:10.1039/b819720b · Cited by 324

Is there a code embedded in proteins that is based on post-translational modifications?

Sims, R. J., & Reinberg, D. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2502 · Cited by 289

Weak functional constraints on phosphoproteomes

Landry, C. R., Levy, E. D., & Michnick, S. W. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.03.003 · Cited by 272

The enhanceosome

Panne, D. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.12.002 · Cited by 257

Dynamic Allostery: Linkers Are Not Merely Flexible

Ma, B., Tsai, C.-J., Haliloğlu, T., & Nussinov, R. (2011) · Structure · doi:10.1016/j.str.2011.06.002 · Cited by 222

SUMO modification of the ubiquitin-conjugating enzyme E2-25K

Pichler, A., Knipscheer, P., Oberhofer, E., van Dijk, W. J., Körner, R., Olsen, J. V., Jentsch, S., Melchior, F., & Sixma, T. K. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb903 · Cited by 208

Crystal structure of the human FOXO3a-DBD/DNA complex suggests the effects of post-translational modification

Tsai, K., Sun, Y.-J., Huang, C., Yang, J.-Y., Hung, M., & Hsiao, C. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm703 · Cited by 199

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

Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR

Kato, H., van Ingen, H., Zhou, B., Feng, H., Bustin, M., Kay, L. E., & Bai, Y. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105848108 · Cited by 181

Dynamic protein–DNA recognition: beyond what can be seen

Fuxreiter, M., Simon, I., & Bondos, S. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.04.006 · Cited by 167

Mechanisms of transcription factor selectivity

Pan, Y., Tsai, C., Ma, B., & Nussinov, R. (2010) · Trends in Genetics · doi:10.1016/j.tig.2009.12.003 · Cited by 160

N-glycans are direct determinants of CFTR folding and stability in secretory and endocytic membrane traffic

Glozman, R., Okiyoneda, T., Mulvihill, C. M., Rini, J. M., Barrière, H., & Lukács, G. L. (2009) · The Journal of Cell Biology · doi:10.1083/jcb.200808124 · Cited by 149

Regulation of Sirtuin Function by Posttranslational Modifications

Flick, F., & Lüscher, B. (2012) · Frontiers in Pharmacology · doi:10.3389/fphar.2012.00029 · Cited by 144

Protein–protein interaction networks: how can a hub protein bind so many different partners?

Tsai, C.-J., Ma, B., & Nussinov, R. (2009) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2009.07.007 · Cited by 138

Quantitative Mass Spectrometry of Histones H3.2 and H3.3 in Suz12-deficient Mouse Embryonic Stem Cells Reveals Distinct, Dynamic Post-translational Modifications at Lys-27 and Lys-36

Jung, H. R., Pasini, D., Helin, K., & Jensen, O. N. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900489-mcp200 · Cited by 136

A post-translational modification code for transcription factors: sorting through a sea of signals

Benayoun, B. A., & Veitia, R. A. (2009) · Trends in Cell Biology · doi:10.1016/j.tcb.2009.02.003 · Cited by 121

Circadian Conformational Change of the Neurospora Clock Protein FREQUENCY Triggered by Clustered Hyperphosphorylation of a Basic Domain

Querfurth, C., Diernfellner, A. C. R., Gin, E., Malzahn, E., Höfer, T., & Brunner, M. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.06.033 · Cited by 116

An overlapping kinase and phosphatase docking site regulates activity of the retinoblastoma protein

Hirschi, A., Cecchini, M. J., Steinhardt, R. C., Schamber, M. R., Dick, F. A., & Rubin, S. M. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1868 · Cited by 103

Ubiquitination-induced conformational change within the deiodinase dimer is a switch regulating enzyme activity

Sagar, G. D. V., Gereben, B., Callebaut, I., Mornon, J.-P., Zeöld, A., da Silva, W. S., Luongo, C., Dentice, M., Tente, S. M., Freitas, B. C. G., et al. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00283-07 · Cited by 103

Flexibility of the C-terminal, or CII, ring of KaiC governs the rhythm of the circadian clock of cyanobacteria

Chang, Y.-G., Kuo, N.-W., Tseng, R., & LiWang, A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104221108 · Cited by 91

Emerging roles of the SUMO pathway in development

Lomelı́, H., & Vâzquez, M. (2011) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-011-0792-5 · Cited by 74

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive ReviewPreprint

Csermely, P., Sandhu, K. S., Hazai, E., Hoksza, Z., Kiss, H., Miozzo, F., Veres, D. V., Piazza, F., & Nussinov, R. (2011) · Nature Precedings · doi:10.2174/138920312799277992 · Cited by 63

Systems-wide proteomic characterization of combinatorial post-translational modification patterns

Young, N. L., Plazas-Mayorca, M. D., & Garcia, B. A. (2010) · Expert Review of Proteomics · doi:10.1586/epr.09.100 · Cited by 62

Regulation of SRC family coactivators by post-translational modifications

Li, S., & Shang, Y. (2007) · Cellular Signalling · doi:10.1016/j.cellsig.2007.02.002 · Cited by 62

SnapShot: The SUMO System

Creton, S., & Jentsch, S. (2010) · Cell · doi:10.1016/j.cell.2010.11.026 · Cited by 47

Probing structural differences between PrP C and PrP Sc by surface nitration and acetylation: evidence of conformational change in the C-terminus

Gong, B., Ramos, A., Vázquez-Fernández, E., Silva, C. J., Alonso, J., Liu, Z., & Requena, J. R. (2011) · Biochemistry · doi:10.1021/bi102073j · Cited by 43

Phosphorylation-induced Conformational Changes in Rap1b

Edreira, M. M., Li, S., Hochbaum, D. R., Wong, S., Gorfe, A. A., Ribeiro-Neto, F., Woods, V. L., & Altschuler, D. L. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.011312 · Cited by 43

Chemical Synthesis, Folding, and Structural Insights into O-Fucosylated Epidermal Growth Factor-like Repeat 12 of Mouse Notch-1 Receptor

Hiruma‐Shimizu, K., Hosoguchi, K., Liu, Y., Fujitani, N., Ohta, T., Hinou, H., Matsushita, T., Shimizu, H., Feizi, T., & Nishimura, S. (2010) · Journal of the American Chemical Society · doi:10.1021/ja105216u · Cited by 40

High Resolution Electron Transfer Dissociation Studies of Unfractionated Intact Histones from Murine Embryonic Stem Cells Using On-line Capillary LC Separation

Eliuk, S. M., Maltby, D. A., Panning, B., & Burlingame, A. L. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900569-mcp200 · Cited by 37

Conformational changes accompany phosphorylation of the epidermal growth factor receptor C‐terminal domain

Lee, N. Y., & Koland, J. G. (2005) · Protein Science · doi:10.1110/ps.051630305 · Cited by 35

How do dynamic cellular signals travel long distances?

Nussinov, R. (2011) · Molecular BioSystems · doi:10.1039/c1mb05205e · Cited by 34

Intracellular Ubiquitylation of the Epithelial Na+ Channel Controls Extracellular Proteolytic Channel Activation via Conformational Change

Ruffieux-Daidié, D., & Staub, O. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.176156 · Cited by 34

A combinatorial mechanism for determining the specificity of E2F activation and repression

Freedman, J. A., Chang, J. T., Jakoi, L., & Nevins, J. R. (2009) · Oncogene · doi:10.1038/onc.2009.153 · Cited by 32

Carboxyl-Group Footprinting Maps the Dimerization Interface and Phosphorylation-induced Conformational Changes of a Membrane-associated Tyrosine Kinase

Zhang, H., Shen, W., Rempel, D. L., Monsey, J. D., Vidavsky, I., Gross, M. L., & Bose, R. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.005678 · Cited by 32

Phosphorylation of Prion Protein at Serine 43 Induces Prion Protein Conformational Change

Giannopoulos, P. N., Robertson, C., Jodoin, J., Paudel, H. K., Booth, S. A., & LeBlanc, A. C. (2009) · Journal of Neuroscience · doi:10.1523/jneurosci.2294-09.2009 · Cited by 28

Mitotic Phosphorylation of Cdc25B Ser321 Disrupts 14-3-3 Binding to the High Affinity Ser323 Site

Astuti, P., Boutros, R., Ducommun, B., & Gabrielli, B. G. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.138412 · Cited by 25

A Biosensor Study Indicating That Entropy, Electrostatics, and Receptor Glycosylation Drive the Binding Interaction between Interleukin-7 and Its Receptor

Walsh, S. T. R. (2010) · Biochemistry · doi:10.1021/bi101050h · Cited by 22

The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example

Pan, Y., & Nussinov, R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002077 · Cited by 21

Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a

Young, N. L., Plazas-Mayorca, M. D., DiMaggio, P. A., Flaniken, I. Z., Beltran, A., Mishra, N., LeRoy, G., Floudas, C. A., & Garcia, B. A. (2010) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2010.01.020 · Cited by 19

A New Twist on Clock Protein Phosphorylation: A Conformational Change Leads to Protein Degradation

Menet, J. S., & Rosbash, M. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.015 · Cited by 14

p38γ Activation Triggers Dynamical Changes in Allosteric Docking Sites

Limardo, R. G. R., Ferreiro, D. N., Roitberg, A. E., Marti, M. A., & Turjanski, A. G. (2011) · Biochemistry · doi:10.1021/bi1007518 · Cited by 13

Simplifying a complex code

Turner, B. M. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb0608-542 · Cited by 6

Allostery in Disease and in Drug Discovery

Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 769

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

Papaleo, E., Saladino, G., Lambrughi, M., Lindorff‐Larsen, K., Gervasio, F. L., & Nussinov, R. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00623 · Cited by 434

Protein Language: Post-Translational Modifications Talking to Each Other.

Vu, L. D., Gevaert, K., & Smet, I. D. (2018) · Trends in Plant Science · doi:10.1016/j.tplants.2018.09.004 · Cited by 340

The structural and functional signatures of proteins that undergo multiple events of post‐translational modification

Pejaver, V., Hsu, W., Xin, F., Dunker, A. K., Uversky, V. N., & Radivojac, P. (2014) · Protein Science · doi:10.1002/pro.2494 · Cited by 349

Deciphering post‐translational modification codes

Lothrop, A. P., Torres, M. P., & Fuchs, S. M. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.01.047 · Cited by 192

From The Editors

(2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1970 · Cited by 1

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Mínguez, P., Letunić, I., Parca, L., & Bork, P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1230 · Cited by 138

Towards the computational design of protein post-translational regulation

Strumillo, M., & Beltrão, P. (2015) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2015.04.056 · Cited by 28

Unveiling the post translational modification code in Alzheimer’s pathogenesis: crosstalk between phosphorylation and acetylation

Romero-Murillo, S., Cartas‐Cejudo, P., Miguel, M. D., Extramiana, L., Fernández‐Irigoyen, J., & Santamaría, E. (2026) · Expert Review of Proteomics · doi:10.1080/14789450.2026.2698463