Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs

Veggiani, Gianluca; Yates, Bradley P.; Martyn, Gregory D.; Manczyk, Noah; Singer, Alex U.; Kurinov, Igor; Sicheri, Frank; Sidhu, Sachdev S.

doi:10.1021/acschembio.2c00089

Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs

Journal Article · 01 April 2022 · ACS Chem. Biol.

DOI:https://doi.org/10.1021/acschembio.2c00089· OSTI ID:1863977

Veggiani, Gianluca; Yates, Bradley P.; Martyn, Gregory D.; Manczyk, Noah; Singer, Alex U.; Kurinov, Igor; Sicheri, Frank; Sidhu, Sachdev S.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; FOREIGN

OSTI ID:: 1863977

Journal Information:: ACS Chem. Biol., Journal Name: ACS Chem. Biol. Journal Issue: (4) Vol. 17

Country of Publication:: United States

Language:: ENGLISH

References (78)

Peptides meet ubiquitin: Simple interactions regulating complex cell signaling Veggiani, Gianluca; Sidhu, Sachdev S. Peptide Science, Vol. 111, Issue 1 https://doi.org/10.1002/pep2.24091	journal	September 2018
Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif: Ubiquitin Variants Engineered for Binding to UIMs Manczyk, Noah; Yates, Bradley P.; Veggiani, Gianluca Protein Science, Vol. 26, Issue 5 https://doi.org/10.1002/pro.3155	journal	March 2017
Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif Manczyk, Noah; Veggiani, Gianluca; Gish, Gerald D. Protein Science, Vol. 28, Issue 5 https://doi.org/10.1002/pro.3593	journal	March 2019
Detection of Protein Assemblies in Crystals Krissinel, Evgeny; Henrick, Kim Lecture Notes in Computer Science https://doi.org/10.1007/11560500_15	book	January 2005
A Role for the Deubiquitinating Enzyme USP28 in Control of the DNA-Damage Response Zhang, Dong; Zaugg, Kathrin; Mak, Tak W. Cell, Vol. 126, Issue 3 https://doi.org/10.1016/j.cell.2006.06.039	journal	August 2006
ATG8-Binding UIM Proteins Define a New Class of Autophagy Adaptors and Receptors Marshall, Richard S.; Hua, Zhihua; Mali, Sujina Cell, Vol. 177, Issue 3 https://doi.org/10.1016/j.cell.2019.02.009	journal	April 2019
Roles of ubiquitin signaling in transcription regulation Hammond-Martel, Ian; Yu, Helen; Affar, El Bachir Cellular Signalling, Vol. 24, Issue 2 https://doi.org/10.1016/j.cellsig.2011.10.009	journal	February 2012
USP7-Specific Inhibitors Target and Modify the Enzyme's Active Site via Distinct Chemical Mechanisms Pozhidaeva, Alexandra; Valles, Gabrielle; Wang, Feng Cell Chemical Biology, Vol. 24, Issue 12 https://doi.org/10.1016/j.chembiol.2017.09.004	journal	December 2017
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
High-throughput Generation of Synthetic Antibodies from Highly Functional Minimalist Phage-displayed Libraries Fellouse, Frederic A.; Esaki, Kaori; Birtalan, Sara Journal of Molecular Biology, Vol. 373, Issue 4 https://doi.org/10.1016/j.jmb.2007.08.005	journal	November 2007
Generation and Validation of Intracellular Ubiquitin Variant Inhibitors for USP7 and USP10 Zhang, Wei; Sartori, Maria A.; Makhnevych, Taras Journal of Molecular Biology, Vol. 429, Issue 22 https://doi.org/10.1016/j.jmb.2017.05.025	journal	November 2017
Structure of USP7 catalytic domain and three Ubl-domains reveals a connector α-helix with regulatory role Kim, Robbert Q.; van Dijk, Willem J.; Sixma, Titia K. Journal of Structural Biology, Vol. 195, Issue 1 https://doi.org/10.1016/j.jsb.2016.05.005	journal	July 2016
Monoubiquitination of RPN10 Regulates Substrate Recruitment to the Proteasome Isasa, Marta; Katz, Elijah J.; Kim, Woong Molecular Cell, Vol. 38, Issue 5 https://doi.org/10.1016/j.molcel.2010.05.001	journal	June 2010
The Diversity of Ubiquitin Recognition: Hot Spots and Varied Specificity Winget, Jason M.; Mayor, Thibault Molecular Cell, Vol. 38, Issue 5 https://doi.org/10.1016/j.molcel.2010.05.003	journal	June 2010
System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes Zhang, Wei; Wu, Kuen-Phon; Sartori, Maria A. Molecular Cell, Vol. 62, Issue 1 https://doi.org/10.1016/j.molcel.2016.02.005	journal	April 2016
An Interaction Landscape of Ubiquitin Signaling Zhang, Xiaofei; Smits, Arne H.; van Tilburg, Gabrielle B. A. Molecular Cell, Vol. 65, Issue 5 https://doi.org/10.1016/j.molcel.2017.01.004	journal	March 2017
A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants Gabrielsen, Mads; Buetow, Lori; Nakasone, Mark A. Molecular Cell, Vol. 68, Issue 2 https://doi.org/10.1016/j.molcel.2017.09.027	journal	October 2017
Improved quantitative and qualitative production of single-domain intrabodies mediated by the co-expression of Erv1p sulfhydryl oxidase Veggiani, Gianluca; de Marco, Ario Protein Expression and Purification, Vol. 79, Issue 1 https://doi.org/10.1016/j.pep.2011.03.005	journal	September 2011
Structural Characterization of a Noncovalent Complex between Ubiquitin and the Transactivation Domain of the Erythroid-Specific Factor EKLF Raiola, Luca; Lussier-Price, Mathieu; Gagnon, David Structure, Vol. 21, Issue 11 https://doi.org/10.1016/j.str.2013.08.027	journal	November 2013
Selective Binding of AIRAPL Tandem UIMs to Lys48-Linked Tri-Ubiquitin Chains Rahighi, Simin; Braunstein, Ilana; Ternette, Nicola Structure, Vol. 24, Issue 3 https://doi.org/10.1016/j.str.2015.12.017	journal	March 2016
Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15 Teyra, Joan; Singer, Alex U.; Schmitges, Frank W. Structure, Vol. 27, Issue 4 https://doi.org/10.1016/j.str.2019.01.002	journal	April 2019
K11-linked ubiquitin chains as novel regulators of cell division Wickliffe, Katherine E.; Williamson, Adam; Meyer, Hermann-Josef Trends in Cell Biology, Vol. 21, Issue 11 https://doi.org/10.1016/j.tcb.2011.08.008	journal	November 2011
[21] Phage display for selection of novel binding peptides Sidhu, Sachdev S.; Lowman, Henry B.; Cunningham, Brian C. Methods in Enzymology, Vol. 328, p. 333-IN5 https://doi.org/10.1016/s0076-6879(00)28406-1	book	January 2000
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/s0076-6879(97)76066-x	book	January 1997
A ubiquitin-interacting motif conserved in components of the proteasomal and lysosomal protein degradation systems Hofmann, Kay; Falquet, Laurent Trends in Biochemical Sciences, Vol. 26, Issue 6 https://doi.org/10.1016/s0968-0004(01)01835-7	journal	June 2001
The “Recognition Helix” of the Type II Acyl Carrier Protein (ACP) Utilizes a “Ubiquitin Interacting Motif (UIM)”-like Surface To Bind Its Partners Yadav, Usha; Arya, Richa; Kundu, Suman Biochemistry, Vol. 57, Issue 26 https://doi.org/10.1021/acs.biochem.8b00220	journal	June 2018
Ubiquitin modifications Swatek, Kirby N.; Komander, David Cell Research, Vol. 26, Issue 4 https://doi.org/10.1038/cr.2016.39	journal	March 2016
Ubiquitin signaling in immune responses Hu, Hongbo; Sun, Shao-Cong Cell Research, Vol. 26, Issue 4 https://doi.org/10.1038/cr.2016.40	journal	March 2016
Ubiquitination directly enhances activity of the deubiquitinating enzyme ataxin-3 Todi, Sokol V.; Winborn, Brett J.; Scaglione, K. Matthew The EMBO Journal, Vol. 28, Issue 4 https://doi.org/10.1038/emboj.2008.289	journal	January 2009
Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by tandem UIMs of RAP80 Sato, Yusuke; Yoshikawa, Azusa; Mimura, Hisatoshi The EMBO Journal, Vol. 28, Issue 16 https://doi.org/10.1038/emboj.2009.160	journal	June 2009
The ubiquitin-specific protease USP28 is required for MYC stability Popov, Nikita; Wanzel, Michael; Madiredjo, Mandy Nature Cell Biology, Vol. 9, Issue 7 https://doi.org/10.1038/ncb1601	journal	June 2007
Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling Sims, Joshua J.; Scavone, Francesco; Cooper, Eric M. Nature Methods, Vol. 9, Issue 3 https://doi.org/10.1038/nmeth.1888	journal	February 2012
Ubiquitylation at the crossroads of development and disease Rape, Michael Nature Reviews Molecular Cell Biology, Vol. 19, Issue 1 https://doi.org/10.1038/nrm.2017.83	journal	September 2017
Breaking the chains: structure and function of the deubiquitinases Komander, David; Clague, Michael J.; Urbé, Sylvie Nature Reviews Molecular Cell Biology, Vol. 10, Issue 8 https://doi.org/10.1038/nrm2731	journal	August 2009
Familial breast cancer screening reveals an alteration in the RAP80 UIM domain that impairs DNA damage response function Nikkilä, J.; Coleman, K. A.; Morrissey, D. Oncogene, Vol. 28, Issue 16 https://doi.org/10.1038/onc.2009.33	journal	March 2009
Targeting deubiquitinase USP28 for cancer therapy Wang, Xiaofang; Liu, Zhiyi; Zhang, Li Cell Death & Disease, Vol. 9, Issue 2 https://doi.org/10.1038/s41419-017-0208-z	journal	February 2018
The ubiquitin interacting motifs of USP37 act on the proximal Ub of a di-Ub chain to enhance catalytic efficiency Manczyk, Noah; Veggiani, Gianluca; Teyra, Joan Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-40815-z	journal	March 2019
Tandem UIMs confer Lys48 ubiquitin chain substrate preference to deubiquitinase USP25 Kawaguchi, Kohei; Uo, Kazune; Tanaka, Toshiaki Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep45037	journal	March 2017
Ubiquitin-binding domains Hurley, James H.; Lee, Sangho; Prag, Gali Biochemical Journal, Vol. 399, Issue 3 https://doi.org/10.1042/BJ20061138	journal	October 2006
Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1–F-box interface Gorelik, Maryna; Orlicky, Stephen; Sartori, Maria A. Proceedings of the National Academy of Sciences, Vol. 113, Issue 13 https://doi.org/10.1073/pnas.1519389113	journal	March 2016
Rapid mapping of protein functional epitopes by combinatorial alanine scanning Weiss, G. A.; Watanabe, C. K.; Zhong, A. Proceedings of the National Academy of Sciences, Vol. 97, Issue 16 https://doi.org/10.1073/pnas.160252097	journal	July 2000
Gα _s protein binds ubiquitin to regulate epidermal growth factor receptor endosomal sorting Li, Xuezhi; Létourneau, Danny; Holleran, Brian Proceedings of the National Academy of Sciences, Vol. 114, Issue 51 https://doi.org/10.1073/pnas.1708215114	journal	November 2017
Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site Watson, Edmond R.; Grace, Christy R. R.; Zhang, Wei Proceedings of the National Academy of Sciences, Vol. 116, Issue 35 https://doi.org/10.1073/pnas.1902889116	journal	July 2019
Evidence for Cooperative and Domain-specific Binding of the Signal Transducing Adaptor Molecule 2 (STAM2) to Lys63-linked Diubiquitin Lange, Anja; Castañeda, Carlos; Hoeller, Daniela Journal of Biological Chemistry, Vol. 287, Issue 22 https://doi.org/10.1074/jbc.m111.324954	journal	May 2012
A Ubiquitin-interacting Motif (UIM) Is Essential for Eps15 and Eps15R Ubiquitination Klapisz, Elsa; Sorokina, Irina; Lemeer, Simone Journal of Biological Chemistry, Vol. 277, Issue 34 https://doi.org/10.1074/jbc.m203004200	journal	August 2002
Structure and Ubiquitin Binding of the Ubiquitin-interacting Motif Fisher, Robert D.; Wang, Bin; Alam, Steven L. Journal of Biological Chemistry, Vol. 278, Issue 31 https://doi.org/10.1074/jbc.m302596200	journal	August 2003
Analysis of the Role of Ubiquitin-interacting Motifs in Ubiquitin Binding and Ubiquitylation Miller, Stephanie L. H.; Malotky, Erica; O'Bryan, John P. Journal of Biological Chemistry, Vol. 279, Issue 32 https://doi.org/10.1074/jbc.m313097200	journal	August 2004
Structure of the Ubiquitin Hydrolase UCH-L3 Complexed with a Suicide Substrate Misaghi, Shahram; Galardy, Paul J.; Meester, Wim J. N. Journal of Biological Chemistry, Vol. 280, Issue 2 https://doi.org/10.1074/jbc.m410770200	journal	January 2005
Defining the Role of Ubiquitin-interacting Motifs in the Polyglutamine Disease Protein, Ataxin-3 Berke, Sarah J. Shoesmith; Chai, Yaohui; Marrs, Ginger L. Journal of Biological Chemistry, Vol. 280, Issue 36 https://doi.org/10.1074/jbc.m506084200	journal	September 2005
The Deubiquitinating Enzyme Ataxin-3, a Polyglutamine Disease Protein, Edits Lys63 Linkages in Mixed Linkage Ubiquitin Chains Winborn, Brett J.; Travis, Sue M.; Todi, Sokol V. Journal of Biological Chemistry, Vol. 283, Issue 39 https://doi.org/10.1074/jbc.m803692200	journal	September 2008
Ubiquitin signaling and autophagy Grumati, Paolo; Dikic, Ivan Journal of Biological Chemistry, Vol. 293, Issue 15 https://doi.org/10.1074/jbc.tm117.000117	journal	November 2017
TLS from fundamentals to practice Urzhumtsev, Alexandre; Afonine, Pavel V.; Adams, Paul D. Crystallography Reviews, Vol. 19, Issue 4 https://doi.org/10.1080/0889311x.2013.835806	journal	October 2013
Sensitive protein comparisons with profiles and hidden Markov models Hofmann, K. Briefings in Bioinformatics, Vol. 1, Issue 2 https://doi.org/10.1093/bib/1.2.167	journal	January 2000
Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation Swanson, K. A. The EMBO Journal, Vol. 22, Issue 18 https://doi.org/10.1093/emboj/cdg471	journal	September 2003
SMART: a web-based tool for the study of genetically mobile domains Schultz, J. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.231	journal	January 2000
UniProt: the universal protein knowledgebase UniProt Consortium, The Nucleic Acids Research, Vol. 46, Issue 5 https://doi.org/10.1093/nar/gky092	journal	February 2018
The Pfam protein families database in 2019 El-Gebali, Sara; Mistry, Jaina; Bateman, Alex Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky995	journal	October 2018
Interactive Tree Of Life (iTOL) v4: recent updates and new developments Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz239	journal	April 2019
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/s0021889807021206	journal	July 2007
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/s0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/s0907444910007493	journal	March 2010
Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution Lange, O. F.; Lakomek, N. -A.; Fares, C. Science, Vol. 320, Issue 5882 https://doi.org/10.1126/science.1157092	journal	June 2008
A Strategy for Modulation of Enzymes in the Ubiquitin System Ernst, Andreas; Avvakumov, George; Tong, Jiefei Science, Vol. 339, Issue 6119 https://doi.org/10.1126/science.1230161	journal	January 2013
High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis Cunningham, B.; Wells, J. Science, Vol. 244, Issue 4908 https://doi.org/10.1126/science.2471267	journal	June 1989
The Ubiquitin-Interacting Motif–Containing Protein RAP80 Interacts with BRCA1 and Functions in DNA Damage Repair Response Yan, Jun; Kim, Yong-Sik; Yang, Xiao-Ping Cancer Research, Vol. 67, Issue 14 https://doi.org/10.1158/0008-5472.can-07-0924	journal	July 2007
USP28 Deficiency Promotes Breast and Liver Carcinogenesis as well as Tumor Angiogenesis in a HIF-independent Manner Richter, Kati; Paakkola, Teija; Mennerich, Daniela Molecular Cancer Research, Vol. 16, Issue 6 https://doi.org/10.1158/1541-7786.mcr-17-0452	journal	March 2018
The deubiquitinase USP28 controls intestinal homeostasis and promotes colorectal cancer Diefenbacher, Markus E.; Popov, Nikita; Blake, Sophia M. Journal of Clinical Investigation, Vol. 124, Issue 8 https://doi.org/10.1172/jci73733	journal	June 2014
Motif mimetic of epsin perturbs tumor growth and metastasis Dong, Yunzhou; Wu, Hao; Rahman, H. N. Ashiqur Journal of Clinical Investigation, Vol. 125, Issue 12 https://doi.org/10.1172/jci80349	journal	October 2015
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models Wheeler, Travis J.; Clements, Jody; Finn, Robert D. BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2105-15-7	journal	January 2014
Machado-Joseph Disease: from first descriptions to new perspectives Bettencourt, Conceição; Lima, Manuela Orphanet Journal of Rare Diseases, Vol. 6, Issue 1 https://doi.org/10.1186/1750-1172-6-35	journal	January 2011
ImageJ2: ImageJ for the next generation of scientific image data Rueden, Curtis T.; Schindelin, Johannes; Hiner, Mark C. BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1934-z	journal	November 2017
Ubiquitin chain diversity at a glance Akutsu, Masato; Dikic, Ivan; Bremm, Anja Journal of Cell Science https://doi.org/10.1242/jcs.183954	journal	January 2016
The UBA-UIM Domains of the USP25 Regulate the Enzyme Ubiquitination State and Modulate Substrate Recognition Denuc, Amanda; Bosch-Comas, Anna; Gonzàlez-Duarte, Roser PLoS ONE, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pone.0005571	journal	May 2009
Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants Zhang, Wei; Bailey-Elkin, Ben A.; Knaap, Robert C. M. PLOS Pathogens, Vol. 13, Issue 5 https://doi.org/10.1371/journal.ppat.1006372	journal	May 2017
Protein Identification and Analysis Tools in the ExPASy Server Wilkins, Marc R.; Gasteiger, Elisabeth; Bairoch, Amos 2-D Proteome Analysis Protocols https://doi.org/10.1385/1-59259-584-7:531	book	January 2003
Ubiquitin and its binding domains Randles, Leah Frontiers in Bioscience, Vol. 17, Issue 7 https://doi.org/10.2741/4042	journal	January 2012

Similar Records

Structure and ubiquitin binding of the ubiquitin-interacting motif

Journal Article · 2002 · Journal of Biological Chemistry · OSTI ID:930071

Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1–F-box interface

Journal Article · 2016 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1247362

Structural Basis for WDR5 Interaction (Win) Motif Recognition in Human SET1 Family Histone Methyltransferases

Journal Article · 2012 · Journal of Biological Chemistry · OSTI ID:1069672

Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs

Citation Formats

References (78)

Similar Records

Related Subjects