Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition

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

CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates

Svergun, D. I., Barberato, C., & Koch, M. (1995) · Journal of Applied Crystallography · doi:10.1107/s0021889895007047 · Cited by 3,388 · see citing works

Dynamic personalities of proteins

Henzler-Wildman, K., & Kern, D. (2007) · Nature · doi:10.1038/nature06522 · Cited by 2,545 · see citing works

RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO

Hoege, C., Pfander, B., Moldovan, G., Pyrowolakis, G., & Jentsch, S. (2002) · Nature · doi:10.1038/nature00991 · Cited by 2,202 · see citing works

Structure of ubiquitin refined at 1.8 Å resolution

Vijay‐Kumar, S., Bugg, C. E., & Cook, W. J. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90679-6 · Cited by 1,753 · see citing works

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 · see citing works

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

Lange, O. F., Lakomek, N., Farès, C., Schroeder, G. F., Walter, K. F. A., Becker, S., Meiler, J., Grubmüller, H., Griesinger, C., & de Groot, B. L. (2008) · Science · doi:10.1126/science.1157092 · Cited by 1,044 · see citing works

Ubiquitin-binding domains — from structures to functions

Đikić, I., Wakatsuki, S., & Walters, K. J. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2767 · Cited by 859 · see citing works

Using Xplor–NIH for NMR molecular structure determination

Schwieters, C. D., Kuszewski, J. J., & Clore, G. M. (2005) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2005.10.001 · Cited by 795 · see citing works

Theory, Practice, and Applications of Paramagnetic Relaxation Enhancement for the Characterization of Transient Low-Population States of Biological Macromolecules and Their Complexes

Clore, G. M., & Iwahara, J. (2009) · Chemical Reviews · doi:10.1021/cr900033p · Cited by 778 · see citing works

Atypical ubiquitylation — the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages

Kulathu, Y., & Komander, D. (2012) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3394 · Cited by 642 · see citing works

Reconstitution of the RIG-I Pathway Reveals a Signaling Role of Unanchored Polyubiquitin Chains in Innate Immunity

Zeng, W., Sun, L., Jiang, X., Chen, X., Hou, F., Adhikari, A., Xu, M., & Chen, Z. J. (2010) · Cell · doi:10.1016/j.cell.2010.03.029 · Cited by 613 · see citing works

Molecular discrimination of structurally equivalent Lys 63‐linked and linear polyubiquitin chains

Komander, D., Reyes‐Turcu, F. E., Licchesi, J. D. F., Odenwälder, P., Wilkinson, K. D., & Barford, D. (2009) · EMBO Reports · doi:10.1038/embor.2009.55 · Cited by 575 · see citing works

Protein activity regulation by conformational entropy

Tzeng, S.-R., & Kalodimos, C. G. (2012) · Nature · doi:10.1038/nature11271 · Cited by 545 · see citing works

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

Tang, C., Schwieters, C. D., & Clore, G. M. (2007) · Nature · doi:10.1038/nature06232 · Cited by 416 · see citing works

K11-Linked Polyubiquitination in Cell Cycle Control Revealed by a K11 Linkage-Specific Antibody

Matsumoto, M. L., Wickliffe, K. E., Dong, K. C., Yu, C., Bosanac, I., Bustos, D. J., Phu, L., Kirkpatrick, D. S., Hymowitz, S. G., Rapé, M., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.07.001 · Cited by 401 · see citing works

Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains

Sato, Y., Yoshikawa, A., Yamagata, A., Mimura, H., Yamashita, M., Ookata, K., Nureki, O., Iwaï, K., Komada, M., & Fukai, S. (2008) · Nature · doi:10.1038/nature07254 · Cited by 341 · see citing works

Solution Conformation of Lys63-linked Di-ubiquitin Chain Provides Clues to Functional Diversity of Polyubiquitin Signaling

Varadan, R., Assfalg, M., Haririnia, A., Raasi, S., Pickart, C. M., & Fushman, D. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309184200 · Cited by 336 · see citing works

Ensemble Approach for NMR Structure Refinement against1H Paramagnetic Relaxation Enhancement Data Arising from a Flexible Paramagnetic Group Attached to a Macromolecule

Iwahara, J., Schwieters, C. D., & Clore, G. M. (2004) · Journal of the American Chemical Society · doi:10.1021/ja031580d · Cited by 328 · see citing works

Structural Properties of Polyubiquitin Chains in Solution

Varadan, R., Walker, O., Pickart, C. M., & Fushman, D. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01198-1 · Cited by 292 · see citing works

Controlled Synthesis of Polyubiquitin Chains

Pickart, C. M., & Raasi, S. (2005) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(05)99002-2 · Cited by 266 · see citing works

Practical aspects of 1H transverse paramagnetic relaxation enhancement measurements on macromolecules

Iwahara, J., Tang, C., & Clore, G. M. (2006) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2006.10.003 · Cited by 266 · see citing works

Regulation of NF-κB by ubiquitination

Chen, J., & Chen, Z. J. (2013) · Current Opinion in Immunology · doi:10.1016/j.coi.2012.12.005 · Cited by 258 · see citing works

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

Sekhar, A., & Kay, L. E. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305688110 · Cited by 251 · see citing works

Ubiquitin in the immune system

Zinngrebe, J., Montinaro, A., Peltzer, N., & Walczak, H. (2014) · The EMBO Reports · doi:10.1002/embr.201338025 · Cited by 227 · see citing works

Cellular functions of the DUBs

Clague, M. J., Coulson, J. M., & Urbé, S. (2012) · Journal of Cell Science · doi:10.1242/jcs.090985 · Cited by 221 · see citing works

Substrate degradation by the proteasome: A single-molecule kinetic analysis

Lu, Y., Lee, B., King, R. W., Finley, D. J., & Kirschner, M. W. (2015) · Science · doi:10.1126/science.1250834 · Cited by 218 · see citing works

Assembly and Specific Recognition of K29- and K33-Linked Polyubiquitin

Michel, M. A., Elliott, P. R., Swatek, K. N., Šimíček, M., Pruneda, J. N., Wagstaff, J. L., Freund, S. M. V., & Komander, D. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.01.042 · Cited by 215 · see citing works

Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF

Mackereth, C. D., Madl, T., Bonnal, S., Simon, B., Zanier, K., Gasch, A., Rybin, V., Valcárcel, J., & Sattler, M. (2011) · Nature · doi:10.1038/nature10171 · Cited by 210 · see citing works

Structural basis for specific recognition of Lys 63‐linked polyubiquitin chains by tandem UIMs of RAP80

Sato, Y., Yoshikawa, A., Mimura, H., Yamashita, M., Yamagata, A., & Fukai, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.160 · Cited by 202 · see citing works

Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain

Kulathu, Y., Akutsu, M., Bremm, A., Hofmann, K., & Komander, D. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1731 · Cited by 200 · see citing works

K63 polyubiquitination is a new modulator of the oxidative stress response

Silva, G. M., Finley, D. J., & Vogel, C. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2955 · Cited by 199 · see citing works

Proteasomes Activate Aggresome Disassembly and Clearance by Producing Unanchored Ubiquitin Chains

Hao, R., Nanduri, P., Rao, Y., Panichelli, R. S., Ito, A., Yoshida, M., & Yao, T. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.08.016 · Cited by 193 · see citing works

Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2).

Cook, W. J., Jeffrey, L. C., Carson, M., Chen, Z., & Pickart, C. M. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)42026-1 · Cited by 192 · see citing works

Ubiquitin chain conformation regulates recognition and activity of interacting proteins

Ye, Y., Blaser, G., Horrocks, M. H., Ruedas-Rama, M. J., Ibrahim, S., Zhukov, A. A., Orte, Á., Klenerman, D., Jackson, S., & Komander, D. (2012) · Nature · doi:10.1038/nature11722 · Cited by 191 · see citing works

Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-κB Signaling

Bosanac, I., Wertz, I. E., Pan, B., Yu, C., Kusam, S., Lam, C., Phu, L., Phung, Q. T., Maurer, B., Arnott, D. P., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.10.009 · Cited by 190 · see citing works

STRUCTURE OF A DIUBIQUITIN CONJUGATE AND A MODEL FOR INTERACTION WITH UBIQUITIN CONJUGATING ENZYME (E2)

Cook, W. J., Jeffrey, L. C., Carson, M. A., Chen, Z., & Pickart, C. M. (1992) · Worldwide Protein Data Bank · doi:10.2210/pdb1aar/pdb · Cited by 186 · see citing works

Structural basis for distinct roles of Lys63‐ and Lys48‐linked polyubiquitin chains

Tenno, T., Fujiwara, K., Tochio, H., Iwaï, K., Morita, E., Hayashi, H., Murata, S., Hiroaki, H., Sato, M., Tanaka, K., et al. (2004) · Genes to Cells · doi:10.1111/j.1365-2443.2004.00780.x · Cited by 182 · see citing works

Crystal Structure and Solution NMR Studies of Lys48-linked Tetraubiquitin at Neutral pH

Eddins, M. J., Varadan, R., Fushman, D., Pickart, C. M., & Wolberger, C. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.12.065 · Cited by 171 · see citing works

K29-Selective Ubiquitin Binding Domain Reveals Structural Basis of Specificity and Heterotypic Nature of K29 Polyubiquitin

Kristariyanto, Y. A., Rehman, S. A. A., Campbell, D. G., Morrice, N. A., Johnson, C., Toth, R. L., & Kulathu, Y. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.01.041 · Cited by 160 · see citing works

Structure of Tetraubiquitin Shows How Multiubiquitin Chains Can Be Formed

Cook, W. J., Jeffrey, L. C., Kasperek, E. M., & Pickart, C. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1169 · Cited by 156 · see citing works

Structural basis for specific recognition of Lys 63‐linked polyubiquitin chains by NZF domains of TAB2 and TAB3

Sato, Y., Yoshikawa, A., Yamashita, M., Yamagata, A., & Fukai, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.345 · Cited by 139 · see citing works

The Structure and Conformation of Lys63-Linked Tetraubiquitin

Datta, A. B., Hura, G. L., & Wolberger, C. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.090 · Cited by 129 · see citing works

Noncovalent Dimerization of Ubiquitin

Liu, Z., Zhang, W., Xing, Q., Ren, X., Liu, M., & Tang, C. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201106190 · Cited by 89 · see citing works

Cargo ubiquitination is essential for multivesicular body intralumenal vesicle formation

MacDonald, C., Buchkovich, N. J., Stringer, D. K., Emr, S. D., & Piper, R. C. (2012) · EMBO Reports · doi:10.1038/embor.2012.18 · Cited by 82 · see citing works

Structure of a new crystal form of tetraubiquitin

Phillips, C. L., Thrower, J. S., Pickart, C. M., & Hill, C. P. (2001) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744490001800x · Cited by 76 · see citing works

Transient Electrostatic Interactions Dominate the Conformational Equilibrium Sampled by Multidomain Splicing Factor U2AF65: A Combined NMR and SAXS Study

Huang, J., Warner, L., Sanchez, C., Gabel, F., Madl, T., Mackereth, C. D., Sattler, M., & Blackledge, M. J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja502030n · Cited by 76 · see citing works

Crystal structures of Lys‐63‐linked tri‐ and di‐ubiquitin reveal a highly extended chain architecture

Weeks, S. D., Grasty, K. C., Hernandez‐Cuebas, L., & Loll, P. J. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22568 · Cited by 73 · see citing works

Crystal structure of the NEMO ubiquitin‐binding domain in complex with Lys 63‐linked di‐ubiquitin

Yoshikawa, A., Sato, Y., Yamashita, M., Mimura, H., Yamagata, A., & Fukai, S. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.09.028 · Cited by 72 · see citing works

The Lysine48‐Based Polyubiquitin Chain Proteasomal Signal: Not a Single Child Anymore

Kravtsova‐Ivantsiv, Y., Sommer, T., & Ciechanover, A. J. (2012) · Angewandte Chemie International Edition · doi:10.1002/anie.201205656 · Cited by 68 · see citing works

Reweighted atomic densities to represent ensembles of NMR structures*

Schwieters, C. D., & Clore, G. M. (2002) · Journal of Biomolecular NMR · doi:10.1023/a:1019875223132 · Cited by 63 · see citing works

Unique Structural, Dynamical, and Functional Properties of K11-Linked Polyubiquitin Chains

Castañeda, C. A., Kashyap, T. R., Nakasone, M. A., Krueger, S., & Fushman, D. (2013) · Structure · doi:10.1016/j.str.2013.04.029 · Cited by 63 · see citing works

Exploring the Linkage Dependence of Polyubiquitin Conformations Using Molecular Modeling

Fushman, D., & Walker, O. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.10.039 · Cited by 63 · see citing works

Conformational Dynamics of Wild-type Lys-48-linked Diubiquitin in Solution

Hirano, T., Serve, O., Yagi‐Utsumi, M., Takemoto, E., Hiromoto, T., Satoh, T., Mizushima, T., & Kato, K. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.256354 · Cited by 56 · see citing works

TNFR1-activated NF-κB signal transduction: regulation by the ubiquitin/proteasome system

Wertz, I. E. (2014) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.10.011 · Cited by 53 · see citing works

Visualizing an Ultra‐Weak Protein–Protein Interaction in Phosphorylation Signaling

Xing, Q., Huang, P., Yang, J. H., Sun, J., Gong, Z., Xu, D., Guo, D., Chen, S., Yang, Y., Wang, Y., et al. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201405976 · Cited by 31 · see citing works

A20—A Bipartite Ubiquitin Editing Enzyme with Immunoregulatory Potential

Wertz, I. E., & Dixit, V. M. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-1-4939-0398-6_1 · Cited by 27 · see citing works

NMR analysis of Lys63-linked polyubiquitin recognition by the tandem ubiquitin-interacting motifs of Rap80

Sekiyama, N., Jee, J., Isogai, S., Akagi, K., Huang, T.-H., Ariyoshi, M., Tochio, H., & Shirakawa, M. (2012) · Journal of Biomolecular NMR · doi:10.1007/s10858-012-9614-9 · Cited by 16 · see citing works

The increasing complexity of the ubiquitin code

Yau, R., & Rape, M. (2016) · Nature Cell Biology · doi:10.1038/ncb3358 · Cited by 1,054 · 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

Requirement for p62 acetylation in the aggregation of ubiquitylated proteins under nutrient stress

You, Z., Jiang, W., Qin, L.-Y., Gong, Z., Wan, W., Li, J., Wang, Y., Zhang, H., Peng, C., Zhou, T., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13718-w · Cited by 159 · see citing works

Resolving the Complexity of Ubiquitin Networks

Kliza, K. W., & Husnjak, K. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00021 · Cited by 118 · see citing works

Recognition of Client Proteins by the Proteasome

Yu, H., & Matouschek, A. T. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070816-033719 · Cited by 109 · see citing works

Structure, Dynamics and Function of the 26S Proteasome

Mao, Y. (2020) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-030-58971-4_1 · Cited by 105 · see citing works

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

Mavor, D., Barlow, K., Thompson, S., Barad, B. A., Bonny, A. R., Cario, C. L., Gaskins, G., Liu, Z., Deming, L., Axen, S. D., et al. (2016) · eLife · doi:10.7554/elife.15802 · Cited by 89 · see citing works

Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13

Liu, Z., Xu, D., Yi, H.-W., Yang, J. H., Gong, Z., Wang, Y., Liu, K., Zhang, W., & Tang, C. (2019) · Cell Discovery · doi:10.1038/s41421-019-0089-7 · Cited by 64 · see citing works

A single MIU motif of MINDY‐1 recognizes K48‐linked polyubiquitin chains

Kristariyanto, Y. A., Rehman, S. A. A., Weidlich, S., Knebel, A., & Kulathu, Y. (2017) · EMBO Reports · doi:10.15252/embr.201643205 · Cited by 62 · see citing works

The dynamics of linear polyubiquitin

Jussupow, A., Messias, A. C., Stehle, R., Geerlof, A., Solbak, S. M. Ø., Paissoni, C., Bach, A., Sattler, M., & Camilloni, C. (2020) · Science Advances · doi:10.1126/sciadv.abc3786 · Cited by 53 · see citing works

Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch

Dong, X., Gong, Z., Lu, Y.-B., Liu, K., Qin, L., Ran, M.-L., Zhang, C.-L., Liu, Z., Zhang, W.-P., & Tang, C. (2017) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1705718114 · Cited by 47 · see citing works

Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics

Paissoni, C., Jussupow, A., & Camilloni, C. (2020) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b01181 · Cited by 44 · see citing works

The regulation of mitochondrial homeostasis by the ubiquitin proteasome system

Alsayyah, C., Ozturk, O., Cavellini, L., Belgareh‐Touzé, N., & Cohen, M. M. (2020) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2020.148302 · Cited by 28 · see citing works

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers

Berg, A., Kukharenko, O., Scheffner, M., & Peter, C. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006589 · Cited by 28 · see citing works

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance

Mavor, D., Barlow, K. A., Asarnow, D. E., Birman, Y., Britain, D., Chen, W., Green, E. M., Kenner, L. R., Mensa, B., Morinishi, L. S., et al. (2018) · Biology Open · doi:10.1242/bio.036103 · Cited by 25 · see citing works

The native state conformational heterogeneity in the energy landscape of protein folding

Mishra, P., & Jha, S. K. (2022) · Biophysical Chemistry · doi:10.1016/j.bpc.2022.106761 · Cited by 23 · see citing works

Integrating Non-NMR Distance Restraints to Augment NMR Depiction of Protein Structure and Dynamics

Tang, C., & Gong, Z. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.01.023 · Cited by 23 · see citing works

Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques

Liu, Z., Gong, Z., Cao, Y., Ding, Y., Dong, M., Lu, Y., Zhang, W., & Tang, C. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00817 · Cited by 22 · see citing works

Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities

Pham, G. H., Rana, A. S. J. B., Korkmaz, E. N., Trang, V. H., Cui, Q., & Strieter, E. R. (2016) · Protein Science · doi:10.1002/pro.2834 · Cited by 21 · see citing works

Specifying conformational heterogeneity of multi-domain proteins at atomic resolution

Schneider, T., Sawade, K., Berner, F., Peter, C., & Kovermann, M. (2023) · Structure · doi:10.1016/j.str.2023.07.008 · Cited by 19 · see citing works

ESI-IM-MS and Collision-Induced Unfolding That Provide Insight into the Linkage-Dependent Interfacial Interactions of Covalently Linked Diubiquitin

Wagner, N. D., Clemmer, D. E., & Russell, D. H. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b02932 · Cited by 19 · see citing works

Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations

Bowerman, S., Rana, A. S. J. B., Rice, A. M., Pham, G. H., Strieter, E. R., & Wereszczynski, J. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00059 · Cited by 18 · see citing works

How phosphorylation by PINK1 remodels the ubiquitin system, a perspective from structure and dynamics.

Tang, C., & Zhang, W.-P. (2020) · Biochemistry · doi:10.1021/acs.biochem.9b00715 · Cited by 9 · see citing works

Simulating and analysing configurational landscapes of protein–protein contact formation

Berg, A., & Peter, C. (2019) · Interface Focus · doi:10.1098/rsfs.2018.0062 · Cited by 16 · see citing works

Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL

Gong, Z., Liu, Z., Xu, D., Ding, Y., Dong, M., & Tang, C. (2017) · Biophysics Reports · doi:10.1007/s41048-017-0044-9 · Cited by 15 · see citing works

Defining Noncovalent Ubiquitin Homodimer Interfacial Interactions through Comparisons with Covalently Linked Diubiquitin

Wagner, N. D., & Russell, D. H. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b09829 · Cited by 14 · see citing works

The pros and cons of ubiquitination on the formation of protein condensates

Hou, X., & Tang, C. (2023) · Acta Biochimica et Biophysica Sinica · doi:10.3724/abbs.2023096 · Cited by 12 · see citing works

Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers

Schneider, T., Berg, A., Ulusoy, Z., Gamerdinger, M., Peter, C., & Kovermann, M. (2019) · Scientific Reports · doi:10.1038/s41598-019-56458-z · Cited by 12 · see citing works

Simultaneous detection of intra- and inter-molecular paramagnetic relaxation enhancements in protein complexes

Olivieri, C., Subrahmanian, M. V., Xia, Y., Kim, J., Porcelli, F., & Veglia, G. (2018) · Journal of Biomolecular NMR · doi:10.1007/s10858-018-0165-6 · Cited by 11 · see citing works

DUBing Primary Tumors of the Central Nervous System: Regulatory Roles of Deubiquitinases

Klonisch, T. C., Logue, S. E., Hombach‐Klonisch, S., & Vriend, J. P. (2023) · Biomolecules · doi:10.3390/biom13101503 · Cited by 9 · see citing works

Recent Developments in Data-Assisted Modeling of Flexible Proteins

Czaplewski, C. R., Gong, Z., Lubecka, E. A., Xue, K., Tang, C., & Liwo, A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.765562 · Cited by 10 · see citing works

Parkin-mediated ubiquitination inhibits BAK apoptotic activity by blocking its canonical hydrophobic groove

Cheng, P., Hou, Y., Bian, M., Fang, X., Liu, Y., Rao, Y., Cao, S., Liu, Y., Zhang, S., Chen, Y., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-05650-z · Cited by 9 · see citing works

GapR binds DNA through dynamic opening of its tetrameric interface

Huang, Q., Duan, B., Dong, X., Fan, S., & Xia, B. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa644 · Cited by 9 · see citing works

Conformational Space Sampled by Domain Reorientation of Linear Diubiquitin Reflected in Its Binding Mode for Target Proteins

Hou, X., Sekiyama, N., Ohtani, Y., Yang, F., Miyanoiri, Y., Akagi, K., Su, X., & Tochio, H. (2021) · ChemPhysChem · doi:10.1002/cphc.202100187 · Cited by 9 · see citing works

Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis

Yin, X., Liu, Q., Liu, F., Tian, X., Yan, T., Han, J., & Jiang, S. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.944460 · Cited by 8 · see citing works

Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR

Gong, Z., Yang, S., Yang, Q., Zhu, Y.-L., Jiang, J. S., & Tang, C. (2019) · Biophysics Reports · doi:10.1007/s41048-019-00099-2 · Cited by 7 · see citing works

Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1

Hameed, D. S., van Tilburg, G. B. A., Merkx, R., Flierman, D., Wienk, H., Oualid, F. E., Hofmann, K., Boelens, R., & Ovaa, H. (2020) · Frontiers in Chemistry · doi:10.3389/fchem.2019.00921 · Cited by 7 · see citing works

Ensemble structure description of Lys63-linked diubiquitin

Liu, Z., & Tang, C. (2016) · Data in Brief · doi:10.1016/j.dib.2016.02.003 · Cited by 6 · see citing works

Elevated ubiquitin phosphorylation by PINK1 contributes to proteasomal impairment and promotes neurodegenerationPreprint

Chen, C., Gao, T.-Y., Yi, H., Zhang, Y., Wang, T., Lou, Z., Wei, T.-F., Lu, Y.-B., Li, T., Tang, C., et al. (2025) · bioRxiv · doi:10.7554/elife.103945 · Cited by 7 · see citing works

Ubiquitin's Conformational Heterogeneity as Discerned by Nuclear Magnetic Resonance Spectroscopy

Beriashvili, D., Folkers, G. E., & Baldus, M. (2024) · ChemBioChem · doi:10.1002/cbic.202400508 · Cited by 4 · see citing works

The Ubiquitin Script: writing protein fates in chains

Gupta, D., & Maddika, S. (2025) · Essays in Biochemistry · doi:10.1042/ebc20253031 · Cited by 3 · see citing works

Ubiquitination in viral entry and replication: Mechanisms and implications

Brochero, M. I. V., Behera, P., Afreen, K. S., Odle, A. E., & Rajsbaum, R. (2024) · Advances in virus research · doi:10.1016/bs.aivir.2024.05.001 · Cited by 3 · see citing works

Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints

Hou, X., & Tochio, H. (2022) · Biophysical Reviews · doi:10.1007/s12551-021-00916-4 · Cited by 3 · see citing works

Interpreting the Language of Polyubiquitin with Linkage-Specific Antibodies and Mass Spectrometry

Matsumoto, M. L., Castellanos, E. R., Zeng, Y. J., & Kirkpatrick, D. S. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8706-1_24 · Cited by 3 · see citing works

NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains

Hiranyakorn, M., Yanaka, S., Satoh, T., Wilasri, T., Jityuti, B., Yagi‐Utsumi, M., & Kato, K. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21155351 · Cited by 3 · see citing works

Elevated ubiquitin phosphorylation by PINK1 contributes to proteasomal impairment and promotes neurodegeneration

Chen, C., Gao, T., Yi, H.-W., Zhang, Y., Wang, T., Lou, Z., Wei, T.-F., Lu, Y., Li, T., Tang, C., et al. (2025) · eLife · doi:10.7554/elife.103945.4 · Cited by 2 · see citing works

Unveiling the Structural and Dynamic Nature of the Ubiquitin Code

Lello, P. D., & Hymowitz, S. G. (2016) · Structure · doi:10.1016/j.str.2016.03.013 · Cited by 2 · see citing works

Branching and Mixing: New Signals of the Ubiquitin Signaling System

Pérez-Hernández, D., Mendes, M. L., & Dittmar, G. A. G. (2020) · IntechOpen eBooks · doi:10.5772/intechopen.91795 · Cited by 2 · see citing works

Dynamic aspects of pressure and temperature‐stabilized intermediates of outer surface protein A

Wakamoto, T., Kitazawa, S., Kameda, T., & Kitahara, R. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25962 · Cited by 1 · see citing works

Ubiquitin - Proteasome Pathway

Zhan, X. (2020) · IntechOpen eBooks · doi:10.5772/intechopen.87547 · Cited by 1 · see citing works

Elevated Ubiquitin Phosphorylation by PINK1 Contributes to Proteasomal Impairment and Promotes NeurodegenerationPreprint

Chen, C., Gao, T., Yi, H.-W., Zhang, Y., Wang, T., Lou, Z.-L., Wei, T.-F., Lu, Y., Li, T., Tang, C., et al. (2025) · eLife · doi:10.7554/elife.103945.1 · Cited by 1 · see citing works

Estimation of protein dynamic states with single molecule fluorescence data analysis at microsecond scale

Liu, K., Liu, Z., Peng, Y., Ding, Y., & Tang, C. (2016) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.2237125

Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experimentsPreprint

Jussupow, A., Messias, A. C., Stehle, R., Geerlof, A., Solbak, S. M. Ø., Bach, A., Sattler, M., & Camilloni, C. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.14.041327

Ubiquitin phosphorylation accelerates protein aggregation and promotes neurodegeneration in the aging brainPreprint

Chen, C., Yi, H.-W., Zhang, Y., Wang, T., Gao, T., Lou, Z.-L., Wei, T.-F., Lu, Y., Li, T., Zhang, W., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.10.552882

An integrative approach to understand structural dynamics of protein molecular machines across spatiotemporal scales

Zhu, Y., Gong, Z., & Tang, C. (2024) · Scientia Sinica Chimica · doi:10.1360/ssc-2023-0247

Studies on the regulation of E3 ubiquitin ligase APC3 and its interacting proteins on the tetraspore formation and release in Gracilariopsis lemaneiformis (Rhodophyta)

Wu, Q., Zhang, J., Jiang, M. H., Yin, J., Wang, L., Chen, R., & Sui, Z. (2025) · Plant Science · doi:10.1016/j.plantsci.2025.112488

Elevated Ubiquitin Phosphorylation by PINK1 Contributes to Proteasomal Impairment and Promotes NeurodegenerationPreprint

Chen, C., Gao, T., Yi, H.-W., Zhang, Y., Wang, T., Lou, Z.-L., Wei, T.-F., Lu, Y., Li, T., Tang, C., et al. (2025) · eLife · doi:10.7554/elife.103945.2

Elevated Ubiquitin Phosphorylation by PINK1 Contributes to Proteasomal Impairment and Promotes NeurodegenerationPreprint

Chen, C., Gao, T., Yi, H.-W., Zhang, Y., Wang, T., Lou, Z.-L., Wei, T.-F., Lu, Y., Li, T., Tang, C., et al. (2025) · eLife · doi:10.7554/elife.103945.3

Investigating Enzyme-Substrate Interactions in the Assembly of K48/K63 Heterotypic Ubiquitin Chains

Singh, G. P., Negi, H., Ravichandran, A., Yadav, S., & Das, R. (2026) · Biochemistry · doi:10.1021/acs.biochem.5c00709

Efficient and Controllable Assembly of Multitype Polyubiquitin Chains via Enzyme-Assisted Thiol Ligation for Structural Elucidation

Pan, B.-B., Zhou, C., Yang, Y., Zhang, X., Cui, C., Li, Y., & Su, X. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.6c04268

The Structure and Conformation of Lys63-Linked Tetraubiquitin

Datta, A. B., Hura, G. L., & Wolberger, C. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.090 · Cited by 129 · see citing works

Solution Conformation of Lys63-linked Di-ubiquitin Chain Provides Clues to Functional Diversity of Polyubiquitin Signaling

Varadan, R., Assfalg, M., Haririnia, A., Raasi, S., Pickart, C. M., & Fushman, D. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309184200 · Cited by 336 · see citing works

NMR studies of polyubiquitin chains: insights into structural basis of functional diversity

Varadan, R. (2004) · University Libraries (University of Maryland)

Ubiquitin chain conformation regulates recognition and activity of interacting proteins

Ye, Y., Blaser, G., Horrocks, M. H., Ruedas-Rama, M. J., Ibrahim, S., Zhukov, A. A., Orte, Á., Klenerman, D., Jackson, S., & Komander, D. (2012) · Nature · doi:10.1038/nature11722 · Cited by 191 · see citing works

Dynamic recognition and linkage specificity in K63 di-ubiquitin and TAB2 NZF domain complex

Moritsugu, K., Nishi, H., Inariyama, K., Kobayashi, M., & Kidera, A. (2018) · Scientific Reports · doi:10.1038/s41598-018-34605-2 · Cited by 3 · see citing works