Intrinsic protein disorder and protein modifications in the processing of biological signals

Translating the Histone Code

Jenuwein, T., & Allis, C. D. (2001) · Science · doi:10.1126/science.1063127 · Cited by 9,756 · see citing works

Regulation of chromatin by histone modifications

Bannister, A. J., & Kouzarides, T. (2011) · Cell Research · doi:10.1038/cr.2011.22 · Cited by 6,012 · see citing works

The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction

Glickman, M. H., & Ciechanover, A. J. (2002) · Physiological Reviews · doi:10.1152/physrev.00027.2001 · Cited by 4,216 · see citing works

The ubiquitin code

Komander, D., & Rape, M. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060310-170328 · Cited by 3,679 · see citing works

Glycosylation in Cellular Mechanisms of Health and Disease

Ohtsubo, K., & Marth, J. D. (2006) · Cell · doi:10.1016/j.cell.2006.08.019 · Cited by 2,765 · see citing works

Caspase Functions in Cell Death and DiseasePreprint

McIlwain, D. R., Berger, T., & Mak, T. W. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a008656 · Cited by 2,607 · see citing works

Intrinsically disordered proteins in cellular signalling and regulation

Wright, P. E., & Dyson, H. J. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3920 · Cited by 2,371 · see citing works

Regulation of cellular metabolism by protein lysine acetylation

Zhao, S., Xu, W., Jiang, W., Yu, W., Lin, Y., Zhang, T., Yao, J., Zhou, L., Zeng, Y., Li, H., et al. (2010) · Science · doi:10.1126/science.1179689 · Cited by 1,910 · see citing works

A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins

Wang, J., Choi, J.-M., Holehouse, A., Lee, H. O., Zhang, X., Jahnel, M., Maharana, S., Lemaitre, R., Pozniakovsky, A., Drechsel, D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.006 · Cited by 1,876 · see citing works

Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux

Wang, Q., Zhang, Y., Yang, C., Xiong, H., Lin, Y., Yao, J., Li, H., Xie, L., Zhao, W., Yao, Y., et al. (2010) · Science · doi:10.1126/science.1179687 · Cited by 1,008 · see citing works

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

Khoury, G. A., Baliban, R. C., & Floudas, C. A. (2011) · Scientific Reports · doi:10.1038/srep00090 · Cited by 936 · see citing works

FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions

Qamar, S., Wang, G., Randle, S. J., Ruggeri, F. S., Varela, J. A., Lin, J. Q., Phillips, E. C., Miyashita, A., Williams, D., Ströhl, F., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.056 · Cited by 907 · see citing works

Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication

Nash, P., Tang, X., Orlicky, S. M., Chen, Q., Gertler, F. B., Mendenhall, M. D., Sicheri, F., Pawson, T. J., & Tyers, M. (2001) · Nature · doi:10.1038/35107009 · Cited by 761 · see citing works

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

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

Guo, Y. E., Manteiga, J. C., Henninger, J. E., Sabari, B. R., Dall’Agnese, A., Hannett, N. M., Spille, J.-H., Afeyan, L. K., Zamudio, A. V., Shrinivas, K., et al. (2019) · Nature · doi:10.1038/s41586-019-1464-0 · Cited by 676 · see citing works

Phase Separation of FUS Is Suppressed by Its Nuclear Import Receptor and Arginine Methylation

Hofweber, M., Hutten, S., Bourgeois, B. M. R., Spreitzer, E., Niedner, A., Schifferer, M., Ruepp, M., Simons, M., Niessing, D., Madl, T., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.004 · Cited by 654 · see citing works

Attributes of short linear motifs

Davey, N. E., Roey, K. V., Weatheritt, R. J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H., & Gibson, T. J. (2011) · Molecular BioSystems · doi:10.1039/c1mb05231d · Cited by 626 · see citing works

Protein neddylation: beyond cullin–RING ligases

Enchev, R. I., Schulman, B. A., & Peter, M. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3919 · Cited by 622 · see citing works

The Language of Histone Crosstalk

Lee, J., Smith, E. R., & Shilatifard, A. (2010) · Cell · doi:10.1016/j.cell.2010.08.011 · Cited by 598 · see citing works

Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

Romero, P. R., Zaidi, S., Fang, Y. Y., Uversky, V. N., Radivojac, P., Oldfield, C. J., Cortese, M. S., Sickmeier, M., LeGall, T., Obradovic, Z., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507916103 · Cited by 480 · see citing works

SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer

Mazur, P., Reynoird, N., Khatri, P., Jansen, P., Wilkinson, A. W., Liu, S.-C., Barbash, O., Aller, G. V. V., Huddleston, M. J., Dhanak, D., et al. (2014) · Nature · doi:10.1038/nature13320 · Cited by 370 · see citing works

Crosstalk among Histone Modifications

Suganuma, T., & Workman, J. L. (2008) · Cell · doi:10.1016/j.cell.2008.10.036 · Cited by 369 · see citing works

GSK3-TIP60-ULK1 Signaling Pathway Links Growth Factor Deprivation to Autophagy

Lin, S.-Y., Li, T. Y., Liu, Q., Zhang, C., Li, X., Chen, Y., Zhang, S.-M., Lian, G., Liu, Q., Ruan, K., et al. (2012) · Science · doi:10.1126/science.1217032 · Cited by 365 · see citing works

Cdk-Inhibitory Activity and Stability of p27 Are Directly Regulated by Oncogenic Tyrosine Kinases

Grimmler, M., Wang, Y., Mund, T., Cilenšek, Z., Keidel, E.-M., Waddell, M. B., Jäkel, H., Kullmann, M., Kriwacki, R. W., & Hengst, L. (2007) · Cell · doi:10.1016/j.cell.2006.11.047 · Cited by 337 · see citing works

Programmable protein circuits in living cells

Gao, X. J., Chong, L. S., Kim, M. S., & Elowitz, M. B. (2018) · Science · doi:10.1126/science.aat5062 · Cited by 310 · see citing works

Protease signalling: the cutting edge

Turk, B., Turk, D., & Türk, V. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.42 · Cited by 288 · see citing works

The alphabet of intrinsic disorder

Theillet, F., Kalmár, L., Tompa, P., Han, K., Selenko, P., Dunker, A. K., Daughdrill, G. W., & Uversky, V. N. (2013) · Intrinsically Disordered Proteins · doi:10.4161/idp.24360 · Cited by 283 · see citing works

Protein Lipidation in Cell Signaling and Diseases: Function, Regulation, and Therapeutic Opportunities

Chen, B., Sun, Y., Niu, J., Jarugumilli, G. K., & Wu, X. (2018) · Cell chemical biology · doi:10.1016/j.chembiol.2018.05.003 · Cited by 274 · see citing works

Function and Molecular Mechanism of Acetylation in Autophagy Regulation

Yi, C., Ma, M., Ran, L., Zheng, J., Tong, J., Zhu, J., Ma, C., Sun, Y., Zhang, S., Feng, W., et al. (2012) · Science · doi:10.1126/science.1216990 · Cited by 258 · see citing works

Proline Isomer-Specific Antibodies Reveal the Early Pathogenic Tau Conformation in Alzheimer's Disease

Nakamura, K., Greenwood, A., Binder, L. I., Bigio, E. H., Denial, S., Nicholson, L. K., Zhou, X. Z., & Lu, K. P. (2012) · Cell · doi:10.1016/j.cell.2012.02.016 · Cited by 255 · see citing works

Cascades of multisite phosphorylation control Sic1 destruction at the onset of S phase

Kõivomägi, M., Valk, E., Venta, R., Iofik, A., Lepiku, M., Balog, E. R. M., Rubin, S. M., Morgan, D. O., & Loog, M. (2011) · Nature · doi:10.1038/nature10560 · Cited by 201 · see citing works

Species-Specific Deamidation of cGAS by Herpes Simplex Virus UL37 Protein Facilitates Viral Replication

Zhang, J., Zhao, J., Xu, S., Li, J., He, S., Zeng, Y. A., Xie, L., Xie, N., Liu, T., Lee, K., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.07.004 · Cited by 196 · see citing works

SETDB1-mediated methylation of Akt promotes its K63-linked ubiquitination and activation leading to tumorigenesis

Wang, G., Long, J., Gao, Y., Zhang, W., Han, F., Xu, C. S., Sun, L., Yang, S.-C., Lan, J., Hou, Z., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-018-0266-1 · Cited by 185 · see citing works

Functional advantages of dynamic protein disorder

Berlow, R. B., Dyson, H. J., & Wright, P. E. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.06.003 · Cited by 181 · see citing works

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

Buljan, M., Chalancon, G., Dunker, A. K., Bateman, A. G., Balaji, S., Fuxreiter, M., & Babu, M. M. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.03.006 · Cited by 179 · see citing works

Design of fast proteolysis-based signaling and logic circuits in mammalian cells

Fink, T., Lonzarić, J., Praznik, A., Plaper, T., Merljak, E., Leben, K., Jerala, N., Lebar, T., Strmšek, Ž., Lapenta, F., et al. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0181-6 · Cited by 175 · see citing works

AKT methylation by SETDB1 promotes AKT kinase activity and oncogenic functions

Guo, J., Dai, X., Laurent, B., Zheng, N., Gan, W., Zhang, J., Guo, A., Yuan, M., Liu, P., Asara, J. M., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-018-0261-6 · Cited by 153 · see citing works

Pin1-Induced Proline Isomerization in Cytosolic p53 Mediates BAX Activation and Apoptosis

Follis, A. V., Llambi, F., Merritt, P., Chipuk, J. E., Green, D. R., & Kriwacki, R. W. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.06.029 · Cited by 96 · see citing works

Proteases in blood clotting

Walsh, P. N., & Ahmad, S. S. (2002) · Essays in Biochemistry · doi:10.1042/bse0380095 · Cited by 94 · see citing works

Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain

Gibbs, E. B., Lu, F., Portz, B., et al. (2017) · Nature Communications · doi:10.1038/ncomms15233 · Cited by 92 · see citing works

Intrinsically Disordered Proteins Link Alternative Splicing and Post-translational Modifications to Complex Cell Signaling and Regulation

Zhou, J., Zhao, S., & Dunker, A. K. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.03.028 · Cited by 90 · see citing works

Cross-talk between the H3K36me3 and H4K16ac histone epigenetic marks in DNA double-strand break repair

Li, L., & Wang, Y. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.788224 · Cited by 87 · see citing works

Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation

Tsytlonok, M., Sanabria, H., Wang, Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09446-w · Cited by 86 · see citing works

Multisite phosphorylation code of CDK

Örd, M., Möll, K., Agerova, A., Kivi, R., Faustova, I., Venta, R., Valk, E., & Loog, M. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0256-4 · Cited by 86 · see citing works

Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity

Kulkarni, P., Jolly, M. K., Jia, D., Mooney, S. M., Bhargava, A., Kagohara, L. T., Chen, Y., Hao, P., He, Y., Veltri, R. W., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1700082114 · Cited by 85 · see citing works

A proline switch explains kinetic heterogeneity in a coupled folding and binding reaction

Zosel, F., Mercadante, D., Nettels, D., & Schuler, B. (2018) · Nature Communications · doi:10.1038/s41467-018-05725-0 · Cited by 85 · see citing works

PTEN arginine methylation by PRMT6 suppresses PI3K–AKT signaling and modulates pre-mRNA splicing

Feng, J., Dang, Y., Zhang, W., Zhao, X., Zhang, C., Hou, Z., Jin, Y., McNutt, M. A., Marks, A. R., & Yin, Y. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1811028116 · Cited by 82 · see citing works

Chronic starvation induces non-canonical pro-death stress granules

Reineke, L. C., Cheema, S. A., Dubrulle, J., & Neilson, J. R. (2018) · Journal of Cell Science · doi:10.1242/jcs.220244 · Cited by 77 · see citing works

A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms

Gustafson, C. L., Parsley, N. C., Asimgil, H., Lee, H., Ahlbach, C., Michael, A. K., Xu, H., Williams, O. L., Davis, T. L., Liu, A. C., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.011 · Cited by 75 · see citing works

Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation

Tsytlonok, M., Sanabria, H., Wang, Y., et al. (2019) · Repository of the Academy's Library (Library of the Hungarian Academy of Sciences) · Cited by 70 · see citing works

Sequential primed kinases create a damage-responsive phosphodegron on Eco1

Lyons, N. A., Fonslow, B. R., Diedrich, J. K., Yates, J. R., & Morgan, D. O. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2478 · Cited by 65 · see citing works

Engineering dynamical control of cell fate switching using synthetic phospho-regulons

Gordley, R. M., Williams, R. E., Bashor, C. J., Toettcher, J. E., Yan, S., & Lim, W. A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1610973113 · Cited by 60 · see citing works

Dual regulation of Arabidopsis AGO2 by arginine methylation

Hu, P., Zhao, H., Zhu, P., Xiao, Y., Miao, W., Wang, Y., & Jin, H. (2019) · Nature Communications · doi:10.1038/s41467-019-08787-w · Cited by 53 · see citing works

Regulation of apoptosis by an intrinsically disordered region of Bcl-xL

Follis, A. V., Llambi, F., Kalkavan, H., Yao, Y., Phillips, A. H., Park, C.-G., Marassi, F. M., Green, D. R., & Kriwacki, R. W. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0011-x · Cited by 47 · see citing works

Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology

Janssen, K. A., Sidoli, S., & Garcia, B. A. (2017) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.10.021 · Cited by 45 · see citing works

Emerging Roles of Protein Deamidation in Innate Immune Signaling

Zhao, J., Li, J., Xu, S., & Feng, P. (2016) · Journal of Virology · doi:10.1128/jvi.01980-15 · Cited by 43 · see citing works

Salmonella Typhimurium effector SseI inhibits chemotaxis and increases host cell survival by deamidation of heterotrimeric Gi proteins

Brink, T., Leiss, V., Siegert, P., et al. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1007248 · Cited by 40 · see citing works

Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase

Won, A. P., Garbarino, J. E., & Lim, W. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016337108 · Cited by 35 · see citing works

A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process

Schumacher, P., Demarsy, E., Waridel, P., Petrolati, L. A., Trévisan, M., & Fankhauser, C. (2018) · Nature Communications · doi:10.1038/s41467-018-04752-1 · Cited by 27 · see citing works

Protease-Activatable Scaffold Proteins as Versatile Molecular Hubs in Synthetic Signaling Networks

Aper, S. J. A., den Hamer, A., Wouters, S. F. A., Lemmens, L. J. M., Ottmann, C., Brunsveld, L., & Merkx, M. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00217 · Cited by 16 · see citing works

AlphaFold, Artificial Intelligence (AI), and Allostery

Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04346 · Cited by 190 · see citing works

Binding without folding – the biomolecular function of disordered polyelectrolyte complexes

Schuler, B., Borgia, A., Borgia, M. B., Heidarsson, P. O., Holmstrom, E. D., Nettels, D., & Sottini, A. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.12.006 · Cited by 91 · see citing works

Activity of Amino Acid-activating Enzymes in Tissues from Protein-depleted Rats

Gaetani, S., Paolucci, A. M., Spadoni, M. A., et al. (1964) · Journal of Nutrition · doi:10.1093/jn/84.2.173 · Cited by 43 · see citing works

Structural Annotation of the Mycobacterium tuberculosis Proteome

Chandra, N. R., Sandhya, S., & Anand, P. (2014) · Microbiology Spectrum · doi:10.1128/microbiolspec.mgm2-0027-2013 · Cited by 3 · see citing works

Establishing comprehensive quaternary structural proteomes from genome sequencePreprint

Mih, N., Lu, M., Palsson, B. Ø., & Catoiu, E. (2023) · Research Square · doi:10.21203/rs.3.rs-2923626/v1 · Cited by 3 · see citing works

PPI discovery using proteome coevolution

Singh, A. (2019) · Nature Methods · doi:10.1038/s41592-019-0566-9 · Cited by 3 · see citing works

Deciphering the complexity of the cancer proteome for diagnostic applications

Hanash, S., Taguchi, A., Wang, H., et al. (2015) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2016.1135738 · Cited by 5 · see citing works