Allosteric post-translational modification codes

The language of covalent histone modifications

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The Universal Protein Resource (UniProt)

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

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The FoxO code

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

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

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Chromatin remodelling during development

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

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 921 · see citing works

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 882 · see citing works

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 · see citing works

The emerging complexity of protein ubiquitination

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

Activation mechanism of the MAP kinase ERK2 by dual phosphorylation

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

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Intrinsic Disorder and Functional Proteomics

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Mechanisms, regulation and consequences of protein SUMOylation

Wilkinson, K. A., & Henley, J. M. (2010) · Biochemical Journal · doi:10.1042/bj20100158 · Cited by 686 · see citing works

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 662 · see citing works

Structural Basis for Control by Phosphorylation

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

The Tubulin Code

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

The Universal Protein Resource (UniProt) 2009

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

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

Shang, L., Chen, S., Du, F., Shen, L., Zhao, L., & Wang, X. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100844108 · Cited by 540 · see citing works

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 · see citing works

Principles of ubiquitin and SUMO modifications in DNA repair

Bergink, S., & Jentsch, S. (2009) · Nature · doi:10.1038/nature07963 · Cited by 525 · see citing works

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 498 · see citing works

Posttranslational Modification of p53: Cooperative Integrators of FunctionPreprint

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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 · 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

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 · see citing works

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 368 · 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

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 364 · see citing works

Lysine acetylation and the bromodomain: a new partnership for signaling

Yang, X. (2004) · BioEssays · doi:10.1002/bies.20104 · Cited by 359 · see citing works

The CTD code

Buratowski, S. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb0903-679 · Cited by 334 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

The enhanceosome

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

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 · see citing works

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 · see citing works

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 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

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 186 · see citing works

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 · see citing works

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 158 · see citing works

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 · see citing works

Regulation of Sirtuin Function by Posttranslational Modifications

Flick, F., & Lüscher, B. (2012) · Frontiers in Pharmacology · doi:10.3389/fphar.2012.00029 · Cited by 140 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 119 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 61 · see citing works

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

Csermely, P., Sandhu, K. S., Hazai, E., Hoksza, Z., Kiss, H., Miozzo, F., Veres, D. V., Piazza, F., & Nussinov, R. (2012) · Florence Research (University of Florence) · doi:10.2174/138920312799277992 · Cited by 53 · see citing works

SnapShot: The SUMO System

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

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

How do dynamic cellular signals travel long distances?

Nussinov, R. (2011) · Molecular BioSystems · doi:10.1039/c1mb05205e · Cited by 33 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 20 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Simplifying a complex code

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

Allostery in Disease and in Drug Discovery

Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 764 · see citing works

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 · see citing works

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 426 · see citing works

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 · see citing works

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 · see citing works

The next level of complexity: Crosstalk of posttranslational modifications

Venne, A. S., Kollipara, L., & Zahedi, R. P. (2013) · PROTEOMICS · doi:10.1002/pmic.201300344 · Cited by 325 · see citing works

Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study

Lee, H. S., Qi, Y., & Im, W. (2015) · Scientific Reports · doi:10.1038/srep08926 · Cited by 290 · see citing works

The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces

Roey, K. V., Dinkel, H., Weatheritt, R. J., Gibson, T. J., & Davey, N. E. (2013) · Science Signaling · doi:10.1126/scisignal.2003345 · Cited by 247 · see citing works

Physicochemical mechanisms of protein regulation by phosphorylation

Nishi, H., Shaytan, A. К., & Panchenko, A. R. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00270 · Cited by 223 · see citing works

Allostery without a conformational change? Revisiting the paradigm

Nussinov, R., & Tsai, C.-J. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.11.005 · Cited by 202 · see citing works

Post-translational regulation of inflammasomes

Yang, J., Liu, Z., & Xiao, T. S. (2016) · Cellular and Molecular Immunology · doi:10.1038/cmi.2016.29 · Cited by 201 · see citing works

Hot spots in protein–protein interfaces: Towards drug discovery

Cukuroglu, E., Engin, H. B., Gürsoy, A., & Keskin, Ö. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.06.003 · Cited by 177 · see citing works

Update: Post-translational protein modifications in plant metabolism

Friso, G., & van Wijk, K. J. (2015) · PLANT PHYSIOLOGY · doi:10.1104/pp.15.01378 · Cited by 178 · see citing works

Allosteric Modulator Discovery: From Serendipity to Structure-Based Design

Lu, S., He, X., Ni, D., & Zhang, J. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01749 · Cited by 176 · see citing works

SERCA2a: a key protein in the Ca2+ cycle of the heart failure

Liu, Z., Ni, J., Lan, L., Michael, S., Rui, G., Bian, X., Liu, X., & Guanwei, F. (2019) · Heart Failure Reviews · doi:10.1007/s10741-019-09873-3 · Cited by 173 · see citing works

The Underappreciated Role of Allostery in the Cellular Network

Nussinov, R., Tsai, C., & Ma, B. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130257 · Cited by 174 · see citing works

Principles of Allosteric Interactions in Cell Signaling

Nussinov, R., Tsai, C.-J., & Liu, J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510028c · Cited by 154 · see citing works

Harnessing Allostery: A Novel Approach to Drug Discovery

Lu, S., Li, S., & Zhang, J. (2014) · Medicinal Research Reviews · doi:10.1002/med.21317 · Cited by 146 · see citing works

Lysine Malonylation Is Elevated in Type 2 Diabetic Mouse Models and Enriched in Metabolic Associated Proteins

Du, Y., Cai, T., Li, T., Xue, P., Zhou, B., He, X., Peng, W., Liu, P., Yang, F., & Wei, T. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.041947 · Cited by 134 · see citing works

TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets

Devabhaktuni, A., Lin, S., Zhang, L., Swaminathan, K., Gonzalez, C. G., Olsson, N., Pearlman, S. M., Rawson, K., & Elias, J. E. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0067-5 · Cited by 134 · see citing works

Disordered Proteinaceous Machines

Fuxreiter, M., Tóth-Petróczy, Á., Kraut, D. A., Matouschek, A. T., Lim, R. Y. H., Xue, B., Kurgan, L., & Uversky, V. N. (2014) · Chemical Reviews · doi:10.1021/cr4007329 · Cited by 133 · see citing works

Multiple conformational selection and induced fit events take place in allosteric propagation

Nussinov, R., Ma, B., & Tsai, C. (2013) · Biophysical Chemistry · doi:10.1016/j.bpc.2013.10.002 · Cited by 130 · see citing works

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Nussinov, R., Jang, H., Tsai, C., & Cheng, F. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006658 · Cited by 129 · see citing works

Serine-129 phosphorylation of α-synuclein is an activity-dependent trigger for physiologic protein-protein interactions and synaptic function

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Complex regulatory mechanisms mediated by the interplay of multiple post-translational modifications

Csizmók, V., & Forman-Kay, J. D. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.10.013 · Cited by 123 · see citing works

The Design of Covalent Allosteric Drugs

Nussinov, R., & Tsai, C.-J. (2015) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124401 · Cited by 112 · see citing works

Protein conformational ensembles in function: roles and mechanisms

Nussinov, R., Liu, Y., Zhang, W., & Jang, H. (2023) · RSC Chemical Biology · doi:10.1039/d3cb00114h · Cited by 111 · see citing works

Protein flexibility in the light of structural alphabets

Craveur, P., Joseph, A. P., Esque, J., Narwani, T., Noël, F., Shinada, N. K., Goguet, M., Léonard, S., Poulain, P., Bertrand, O., et al. (2015) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2015.00020 · Cited by 109 · see citing works

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

Mínguez, P., Letunić, I., Parca, L., García‐Alonso, L., Dopazo, J., Huerta‐Cepas, J., & Peer Bork, B. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1081 · Cited by 106 · see citing works

Forcefield_PTM:Ab InitioCharge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications

Khoury, G. A., Thompson, J. P., Smadbeck, J. B., Kieslich, C. A., & Floudas, C. A. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400556v · Cited by 104 · see citing works

ASD v2.0: updated content and novel features focusing on allosteric regulation

Huang, Z., Mou, L., Shen, Q., Lu, S., Li, C., Liu, X., Wang, G., Li, S., Geng, L., Liu, Y., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1247 · Cited by 102 · see citing works

Protein ensembles link genotype to phenotype

Nussinov, R., Tsai, C., & Jang, H. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006648 · Cited by 102 · see citing works

Hepatic glucose sensing and integrative pathways in the liver

Oosterveer, M. H., & Schoonjans, K. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1505-z · Cited by 96 · see citing works

‘Latent drivers’ expand the cancer mutational landscape

Nussinov, R., & Tsai, C. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.01.004 · Cited by 86 · see citing works

The Structural Basis of ATP as an Allosteric Modulator

Lu, S., Huang, W., Wang, Q., Shen, Q., Li, S., Nussinov, R., & Zhang, J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003831 · Cited by 86 · see citing works

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

Srivastava, A., Nagai, T., Srivastava, A., Miyashita, O., & Tama, F. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19113401 · Cited by 85 · see citing works

Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis

Volkova, S., Matos, M. R. A., Mattanovich, M., & de Mas, I. M. (2020) · Metabolites · doi:10.3390/metabo10080303 · Cited by 75 · see citing works

An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles

Sudha, G., Nussinov, R., & Srinivasan, N. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.07.004 · Cited by 69 · see citing works

The Mechanism of ATP-Dependent Allosteric Protection of Akt Kinase Phosphorylation

Lu, S., Deng, R., Jiang, H., Song, H., Li, S., Shen, Q., Huang, W., Nussinov, R., Yu, J., & Zhang, J. (2015) · Structure · doi:10.1016/j.str.2015.06.027 · Cited by 69 · see citing works

Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs

Nussinov, R., Zhang, M., Maloney, R., Liu, Y., Tsai, C.-J., & Jang, H. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167569 · Cited by 66 · see citing works

Post-translational modifications as key regulators of bacterial metabolic fluxes

Pisithkul, T., Patel, N. M., & Amador‐Noguez, D. (2015) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.12.006 · Cited by 66 · see citing works

PRMT5-mediated arginine methylation stabilizes GPX4 to suppress ferroptosis in cancer

Fan, Y., Wang, Y., Dan, W., Zhang, Y., Nie, L., Ma, Z., Zhuang, Y., Liu, B., Li, M., Liu, T., et al. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01610-3 · Cited by 62 · see citing works

Co-occurring protein phosphorylation are functionally associated

Li, Y., Zhou, X., Zhai, Z., & Li, T. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005502 · Cited by 60 · see citing works

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

Vishwanath, S., de Brevern, A. G., & Srinivasan, N. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006008 · Cited by 59 · see citing works

Drug design targeting active posttranslational modification protein isoforms

Meng, F., Liang, Z. T., Zhao, K., & Luo, C. (2020) · Medicinal Research Reviews · doi:10.1002/med.21774 · Cited by 56 · see citing works

Allosteric Conformational Barcodes Direct Signaling in the Cell

Nussinov, R., Ma, B., Tsai, C.-J., & Csermely, P. (2013) · Structure · doi:10.1016/j.str.2013.06.002 · Cited by 55 · see citing works

Precision medicine review: rare driver mutations and their biophysical classification

Nussinov, R., Jang, H., Tsai, C., & Cheng, F. (2019) · Biophysical Reviews · doi:10.1007/s12551-018-0496-2 · Cited by 56 · see citing works

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins

Craveur, P., Rebehmed, J., & de Brevern, A. G. (2014) · Database · doi:10.1093/database/bau041 · Cited by 54 · see citing works

Turnover of protein phosphorylation evolving under stabilizing selection

Landry, C. R., Freschi, L., Zarin, T., & Moses, A. M. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00245 · Cited by 51 · see citing works

Lessons from computer simulations of Ras proteins in solution and in membrane

Prakash, P., & Gorfe, A. A. (2013) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2013.07.024 · Cited by 49 · see citing works

Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones

Stetz, G., Tse, A., & Verkhivker, G. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-25329-4 · Cited by 50 · see citing works

Regulation of Lignin Biosynthesis by Post-translational Protein Modifications

Sulis, D. B., & Wang, J. P. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.00914 · Cited by 50 · see citing works

Protein function machinery: from basic structural units to modulation of activity

Berezovsky, I. N., Guarnera, E., Zheng, Z., Eisenhaber, B., & Eisenhaber, F. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.10.021 · Cited by 49 · see citing works

Posttranslational modifications and proteinopathies: how guardians of the proteome are defeated

Olzscha, H. (2019) · Biological Chemistry · doi:10.1515/hsz-2018-0458 · Cited by 48 · see citing works

The spatial structure of cell signaling systems

Nussinov, R. (2013) · Physical Biology · doi:10.1088/1478-3975/10/4/045004 · Cited by 49 · see citing works

Relaxation dispersion NMR spectroscopy for the study of protein allostery

Farber, P. J., & Mittermaier, A. (2015) · Biophysical Reviews · doi:10.1007/s12551-015-0166-6 · Cited by 48 · see citing works

Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma

Kulkarni, P., Leite, V. B. P., Roy, S., Bhattacharyya, S., Mohanty, A. R., Achuthan, S., Singh, D., Appadurai, R., Govindan Rangarajan, C., Weninger, K., et al. (2022) · Biophysics Reviews · doi:10.1063/5.0080512 · Cited by 50 · see citing works

Multisite Phosphorylation of S6K1 Directs a Kinase Phospho-code that Determines Substrate Selection

Arif, A., Jia, J., Willard, B. B., Li, X., & Fox, P. L. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.11.017 · Cited by 48 · see citing works

Why Are Some Driver Mutations Rare?

Nussinov, R., Tsai, C., & Jang, H. (2019) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2019.10.003 · Cited by 47 · see citing works

Functional Divergence and Evolutionary Turnover in Mammalian Phosphoproteomes

Freschi, L., Osseni, M. A., & Landry, C. R. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004062 · Cited by 46 · see citing works

Autoinhibition in Ras effectors Raf, PI3Kα, and RASSF5: a comprehensive review underscoring the challenges in pharmacological intervention

Nussinov, R., Zhang, M., Tsai, C., Liao, T.-J., Fushman, D., & Jang, H. (2018) · Biophysical Reviews · doi:10.1007/s12551-018-0461-0 · Cited by 46 · see citing works

Exogenous H2S reduces the acetylation levels of mitochondrial respiratory enzymes via regulating the NAD+-SIRT3 pathway in cardiac tissues of db/db mice

Sun, Y., Teng, Z., Sun, X., Zhang, L., Chen, J., Wang, B., Lu, F., Liu, N., Yu, M., Peng, S., et al. (2019) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00326.2018 · Cited by 46 · see citing works

Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms

Vu, L. D., Zhu, T., Verstraeten, I., van de Cotte, B., IWGSC, Gevaert, K., & Smet, I. D. (2018) · Journal of Experimental Botany · doi:10.1093/jxb/ery204 · Cited by 45 · see citing works

The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation?

Tsai, C., & Nussinov, R. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c3cp54253j · Cited by 45 · see citing works

Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development

Duran‐Frigola, M., Mosca, R., & Aloy, P. (2013) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.03.004 · Cited by 44 · see citing works

A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery

Nussinov, R., Ma, B., & Tsai, C. (2013) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2012.12.014 · Cited by 45 · see citing works

Engineered control of enzyme structural dynamics and function

Boehr, D. D., D’Amico, R. N., & O’Rourke, K. F. (2018) · Protein Science · doi:10.1002/pro.3379 · Cited by 45 · see citing works

Oligomerization and nanocluster organization render specificity

Nussinov, R., Jang, H., & Tsai, C. (2014) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12124 · Cited by 44 · see citing works

From glycophenotyping by (plant) lectin histochemistry to defining functionality of glycans by pairing with endogenous lectins

Kaltner, H., Caballero, G. G., Ludwig, A., Manning, J. C., & Gabius, H. (2018) · Histochemistry and Cell Biology · doi:10.1007/s00418-018-1676-7 · Cited by 44 · see citing works

Identification of Enriched PTM Crosstalk Motifs from Large-Scale Experimental Data Sets

Peng, M., Scholten, A., Heck, A. J. R., & van Breukelen, B. (2013) · Journal of Proteome Research · doi:10.1021/pr4005579 · Cited by 42 · see citing works

A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments

Noell, S. E., Hellweger, F. L., Temperton, B., & Giovannoni, S. J. (2023) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00124-22 · Cited by 40 · see citing works

Systematic Characterization and Prediction of Post-Translational Modification Cross-Talk *

Huang, Y., Xu, B., Zhou, X., Li, Y., Lü, M., Jiang, R., & Li, T. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.037994 · Cited by 40 · see citing works

How to gather useful and valuable information from protein binding measurements using Langmuir lipid monolayers

Boisselier, É., Demers, É., Cantin, L., & Salesse, C. (2017) · Advances in Colloid and Interface Science · doi:10.1016/j.cis.2017.03.004 · Cited by 40 · see citing works

Characterization of intact sialylated glycopeptides and phosphorylated glycopeptides from IMAC enriched samples by EThcD fragmentation: Toward combining phosphoproteomics and glycoproteomics

Glover, M. S., Yu, Q., Chen, Z., Shi, X., Kent, K. C., & Li, L. (2017) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2017.09.002 · Cited by 40 · see citing works

Small Molecules Govern Thiol Redox Switches

Knuesting, J., & Scheibe, R. (2018) · Trends in Plant Science · doi:10.1016/j.tplants.2018.06.007 · Cited by 40 · see citing works

Allosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein

Tan, Z. W., Tee, W.-V., Samsudin, F., Guarnera, E., Bond, P. J., & Berezovsky, I. N. (2022) · Structure · doi:10.1016/j.str.2021.12.011 · Cited by 37 · see citing works

A methylated lysine is a switch point for conformational communication in the chaperone Hsp90

Rehn, A., Lawatscheck, J., Jokisch, M.-L., Mader, S. L., Luo, Q., Tippel, F., Blank, B., Richter, K., Lang, K., Kaila, V. R. I., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15048-8 · Cited by 38 · see citing works

Allosteric Control of a Plant Receptor Kinase through S-Glutathionylation

Moffett, A. S., Bender, K. W., Huber, S. C., & Shukla, D. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.08.059 · Cited by 37 · see citing works

Dynamic multiprotein assemblies shape the spatial structure of cell signaling

Nussinov, R., & Jang, H. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.07.002 · Cited by 38 · see citing works

PRMT5-Mediated Methylation of NF-κB p65 at Arg174 Is Required for Endothelial CXCL11 Gene Induction in Response to TNF-α and IFN-γ Costimulation

Harris, D. P., Chandrasekharan, U. M., Bandyopadhyay, S., Willard, B. B., & DiCorleto, P. E. (2016) · PLoS ONE · doi:10.1371/journal.pone.0148905 · Cited by 37 · see citing works

PINE: An Automation Tool to Extract and Visualize Protein-Centric Functional Networks

Sundararaman, N., Go, J. L., Robinson, A., Mato, J. M., Lu, S. C.-L., Eyk, J. E. V., & Venkatraman, V. (2020) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00032 · Cited by 33 · see citing works

The role of allostery in the ubiquitin–proteasome system

Liu, J., & Nussinov, R. (2012) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2012.742856 · Cited by 35 · see citing works

Engineering an Allosteric Control of Protein Function

Vishweshwaraiah, Y. L., Chen, J., & Dokholyan, N. V. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c11640 · Cited by 33 · see citing works

Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1

Ruegenberg, S., Mayr, F. A. M. C., Atanassov, I., Baumann, U., & Denzel, M. S. (2021) · Nature Communications · doi:10.1038/s41467-021-22320-y · Cited by 35 · see citing works

ISG15 promotes esophageal squamous cell carcinoma tumorigenesis via c-MET/Fyn/β-catenin signaling pathway

Yuan, H., Zhou, W., Yang, Y., Xue, L., Liu, L., & Song, Y. (2018) · Experimental Cell Research · doi:10.1016/j.yexcr.2018.03.017 · Cited by 34 · see citing works

Selective Modulation of Dynamic Protein Complexes

Garlick, J. M., & Mapp, A. K. (2020) · Cell chemical biology · doi:10.1016/j.chembiol.2020.07.019 · Cited by 34 · see citing works

PRMT5 K240lac confers ferroptosis resistance via ALKBH5/SLC7A11 axis in colorectal cancer

Qu, S., Feng, B., Xing, M., Qiu, Y.-Y., Ma, L., Yang, Z., Ji, Y., Huang, F., Wang, Y., Zhou, J., et al. (2025) · Oncogene · doi:10.1038/s41388-025-03457-2 · Cited by 35 · see citing works

Allosteric inhibitors of the STAT3 signaling pathway

Qin, J., Shen, X., Zhang, J., & Jia, D. (2020) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2020.112122 · Cited by 33 · see citing works

Regulation of the EphA2 receptor intracellular region by phosphomimetic negative charges in the kinase-SAM linker

Lechtenberg, B. C., Gehring, M. P., Light, T. P., Horne, C. R., Matsumoto, M. W., Hristova, K. A., & Pasquale, E. B. (2021) · Nature Communications · doi:10.1038/s41467-021-27343-z · Cited by 33 · see citing works

Global Profiling of 2-Hydroxyisobutyrylome in Common Wheat

Zhang, N., Zhang, L., Li, L., Geng, J., Zhao, L., Ren, Y. N., Dong, Z., & Chen, F. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.06.008 · Cited by 31 · see citing works

Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A

Maree, J. P., Tvardovskiy, A., Ravnsborg, T., Jensen, O. N., Rudenko, G., & Patterton, H. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac759 · Cited by 30 · see citing works

Cell phenotypes can be predicted from propensities of protein conformations

Nussinov, R., Liu, Y., Zhang, W., & Jang, H. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102722 · Cited by 30 · see citing works

TRIM-NHL as RNA Binding Ubiquitin E3 Ligase (RBUL): Implication in development and disease pathogenesis

Goyani, S., Roy, M., & Singh, R. K. (2021) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2020.166066 · Cited by 30 · see citing works

Mechanism of activation and the rewired network: New drug design concepts

Nussinov, R., Zhang, M., Maloney, R., Tsai, C., Yavuz, B. R., Tunçbağ, N., & Jang, H. (2021) · Medicinal Research Reviews · doi:10.1002/med.21863 · Cited by 30 · see citing works

The value of protein allostery in rational anticancer drug design: an update

Nussinov, R., & Jang, H. (2024) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2024.2384467 · Cited by 29 · see citing works

Investigation of the impact of PTMs on the protein backbone conformation

Craveur, P., Narwani, T., Rebehmed, J., & de Brevern, A. G. (2019) · Amino Acids · doi:10.1007/s00726-019-02747-w · Cited by 26 · see citing works

Dynamic View of Allosteric Regulation in the Hsp70 Chaperones by J-Domain Cochaperone and Post-Translational Modifications: Computational Analysis of Hsp70 Mechanisms by Exploring Conformational Landscapes and Residue Interaction Networks

Astl, L., & Verkhivker, G. M. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b01045 · Cited by 26 · see citing works

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

Weigle, A. T., Feng, J.-Y., & Shukla, D. (2022) · Physical Chemistry, Chemical Physics - PCCP · doi:10.1039/d2cp02883b · Cited by 20 · see citing works

Linking Post-Translational Modifications and Variation of Phenotypic Traits

Albertin, W., Marullo, P., Bely, M., Aigle, M., Bourgais, A., Langella, O., Balliau, T., Chevret, D., Valot, B., da Silva, T., et al. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.024349 · Cited by 26 · see citing works

Regulation of nicotinic acetylcholine receptors by post-translational modifications

Chrestia, J. F., Turani, O., Araujo, N. R., Hernando, G., Esandi, M. D. C., & Bouzat, C. (2023) · Pharmacological Research · doi:10.1016/j.phrs.2023.106712 · Cited by 24 · see citing works

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 182 · see citing works

From The Editors

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

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 · see citing works

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 · see citing works

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