1
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Husain S, Mohamed R, Abd Halim KB, Mohd Mutalip SS. Homology modeling of human BAP1 and analysis of its binding properties through molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:7158-7173. [PMID: 36039769 DOI: 10.1080/07391102.2022.2117244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/19/2022] [Indexed: 10/14/2022]
Abstract
BRCA1-associated protein 1 (BAP1) is a nuclear-localized Ubiquitin C-terminal hydrolase (UCH) that functions as a tumour suppressor, and although BAP1 has been linked to cancer, the molecular mechanism by which BAP1 regulates cancer and its crystal structure have not been elucidated. In this study, computational approaches were used to identify the protein model of BAP1 and its potential inhibitors. The structure of the BAP1 model was constructed through homology modeling and the generated BAP1 model was observed to exhibit good quality protein model as the distribution of its amino acids in the Ramachandran's plot corresponded to 87.7% in the most favoured regions. Docking and simulating of the ubiquitin on the BAP1 model structure revealed the rearrangement of F228, F50, and H169 residues of the BAP1 and switching of BAP1's conformation into a productive state. Our screening results of potential BAP1 inhibitors against the FDA approved drugs shortlisted two potential inhibitors, which are FDA1065 and FDA755. We then performed molecular dynamics simulations and Molecular mechanics Poisson-Boltzmann surface area (MMPBSA) analysis on both inhibitors and found that only the BAP1-FDA755 formed a stable complex and the FDA755 ligand remained its position inside the active site of the BAP1 with a total binding energy of (-51.77 ± 3.49 kcal/mol). We speculate that the presence of methyl group in FDA755 play an important role in stabilizing the BAP1-FDA755 complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syarifuddin Husain
- Bioinformatics Unit, Faculty of Pharmacy, UiTM Cawangan Selangor, Bandar Puncak Alam, Selangor, Malaysia
| | - Ruzianisra Mohamed
- Bioinformatics Unit, Faculty of Pharmacy, UiTM Cawangan Selangor, Bandar Puncak Alam, Selangor, Malaysia
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, UiTM Puncak Alam Campus, Bandar Puncak Alam, Selangor, Malaysia
| | - Khairul Bariyyah Abd Halim
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Siti Syairah Mohd Mutalip
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, UiTM Puncak Alam Campus, Bandar Puncak Alam, Selangor, Malaysia
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2
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Estavoyer B, Messmer C, Echbicheb M, Rudd CE, Milot E, Affar EB. Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases. J Biol Chem 2022; 298:102198. [PMID: 35764170 PMCID: PMC9356280 DOI: 10.1016/j.jbc.2022.102198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
Deubiquitinases (DUBs) are required for the reverse reaction of ubiquitination and act as major regulators of ubiquitin signaling processes. Emerging evidence suggests that these enzymes are regulated at multiple levels in order to ensure proper and timely substrate targeting and to prevent the adverse consequences of promiscuous deubiquitination. The importance of DUB regulation is highlighted by disease-associated mutations that inhibit or activate DUBs, deregulating their ability to coordinate cellular processes. Here, we describe the diverse mechanisms governing protein stability, enzymatic activity, and function of DUBs. In particular, we outline how DUBs are regulated by their protein domains and interacting partners. Intramolecular interactions can promote protein stability of DUBs, influence their subcellular localization, and/or modulate their enzymatic activity. Remarkably, these intramolecular interactions can induce self-deubiquitination to counteract DUB ubiquitination by cognate E3 ubiquitin ligases. In addition to intramolecular interactions, DUBs can also oligomerize and interact with a wide variety of cellular proteins, thereby forming obligate or facultative complexes that regulate their enzymatic activity and function. The importance of signaling and post-translational modifications in the integrated control of DUB function will also be discussed. While several DUBs are described with respect to the multiple layers of their regulation, the tumor suppressor BAP1 will be outlined as a model enzyme whose localization, stability, enzymatic activity, and substrate recognition are highly orchestrated by interacting partners and post-translational modifications.
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Affiliation(s)
- Benjamin Estavoyer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Clémence Messmer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Mohamed Echbicheb
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Christopher E Rudd
- Laboratory for Cell Signaling in Immunotherapy, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Laboratory for Malignant Hematopoiesis and Epigenetic Regulation of Gene Expression, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - El Bachir Affar
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada.
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3
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Fieulaine S, Witte MD, Theile CS, Ayach M, Ploegh HL, Jupin I, Bressanelli S. Turnip yellow mosaic virus protease binds ubiquitin suboptimally to fine-tune its deubiquitinase activity. J Biol Chem 2020; 295:13769-13783. [PMID: 32732284 PMCID: PMC7535911 DOI: 10.1074/jbc.ra120.014628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/27/2020] [Indexed: 11/21/2022] Open
Abstract
Single-stranded, positive-sense RNA viruses assemble their replication complexes in infected cells from a multidomain replication polyprotein. This polyprotein usually contains at least one protease, the primary function of which is to process the polyprotein into mature proteins. Such proteases also may have other functions in the replication cycle. For instance, cysteine proteases (PRO) frequently double up as ubiquitin hydrolases (DUB), thus interfering with cellular processes critical for virus replication. We previously reported the crystal structures of such a PRO/DUB from Turnip yellow mosaic virus (TYMV) and of its complex with one of its PRO substrates. Here we report the crystal structure of TYMV PRO/DUB in complex with ubiquitin. We find that PRO/DUB recognizes ubiquitin in an unorthodox way: It interacts with the body of ubiquitin through a split recognition motif engaging both the major and the secondary recognition patches of ubiquitin (Ile44 patch and Ile36 patch, respectively, including Leu8, which is part of the two patches). However, the contacts are suboptimal on both sides. Introducing a single-point mutation in TYMV PRO/DUB aimed at improving ubiquitin-binding led to a much more active DUB. Comparison with other PRO/DUBs from other viral families, particularly coronaviruses, suggests that low DUB activities of viral PRO/DUBs may generally be fine-tuned features of interaction with host factors.
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Affiliation(s)
- Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Martin D Witte
- Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher S Theile
- Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Maya Ayach
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Hidde L Ploegh
- Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Isabelle Jupin
- Laboratory of Molecular Virology, Jacques Monod Institute, CNRS, UMR, Université de Paris, Paris, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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4
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Berk JM, Lim C, Ronau JA, Chaudhuri A, Chen H, Beckmann JF, Loria JP, Xiong Y, Hochstrasser M. A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi. Nat Commun 2020; 11:2343. [PMID: 32393759 PMCID: PMC7214410 DOI: 10.1038/s41467-020-15985-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/02/2020] [Indexed: 01/07/2023] Open
Abstract
Ubiquitin mediated signaling contributes critically to host cell defenses during pathogen infection. Many pathogens manipulate the ubiquitin system to evade these defenses. Here we characterize a likely effector protein bearing a deubiquitylase (DUB) domain from the obligate intracellular bacterium Orientia tsutsugamushi, the causative agent of scrub typhus. The Ulp1-like DUB prefers ubiquitin substrates over ubiquitin-like proteins and efficiently cleaves polyubiquitin chains of three or more ubiquitins. The co-crystal structure of the DUB (OtDUB) domain with ubiquitin revealed three bound ubiquitins: one engages the S1 site, the second binds an S2 site contributing to chain specificity and the third binds a unique ubiquitin-binding domain (UBD). The UBD modulates OtDUB activity, undergoes a pronounced structural transition upon binding ubiquitin, and binds monoubiquitin with an unprecedented ~5 nM dissociation constant. The characterization and high-resolution structure determination of this enzyme should aid in its development as a drug target to counter Orientia infections.
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Affiliation(s)
- Jason M Berk
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Christopher Lim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Discovery, Research and Development, AbbVie, Inc., North Chicago, IL, 60064, USA
| | - Apala Chaudhuri
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Hongli Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36830, USA
| | - J Patrick Loria
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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5
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Ubiquitin recognition of BAP1: understanding its enzymatic function. Biosci Rep 2017; 37:BSR20171099. [PMID: 28935764 PMCID: PMC5665613 DOI: 10.1042/bsr20171099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 09/01/2017] [Accepted: 09/19/2017] [Indexed: 01/10/2023] Open
Abstract
BRCA1-associated protein 1 (BAP1) is a nuclear localizing UCH, having tumor suppressor activity and is widely involved in many crucial cellular processes. BAP1 has garnered attention for its links with cancer, however, the molecular mechanism in the regulation of cancer by BAP1 has not been established. Amongst the four UCHs, only BAP1 and UCHL5 are able to hydrolyze small and large ubiquitin adducts but UCHL5 hydrolyzes only when it is present in the PA700 complex of the proteasome. The ability of BAP1 to cleave large ubiquitin derivatives is because of its relatively longer active-site crossover loop than other UCHs. The mechanism of ubiquitin recognition has not been studied for BAP1. The comparative enzymatic analysis of ubiquitin C-terminal hydrolase L1 (UCHL1), ubiquitin C-terminal hydrolase L3 (UCHL3), ubiquitin C-terminal hydrolase L5 (UCHL5N), and BAP1N has confirmed that enzymatically BAP1 is similar to UCHL5, which corroborates with the bioinformatics analysis done earlier. We have undertaken extensive mutational approaches to gain mechanistic insight into BAP1–ubiquitin interaction. Based on the homology-modeled BAP1 structure, we have identified a few BAP1 residues which possibly play a crucial role in ubiquitin interaction of which a few mutations have been identified in many cancers. Our comparative thermodynamic analysis reveals that BAP1–ubiquitin interaction is majorly driven by entropy factor which is unique amongst UCHs. Our study sheds light on BAP1 interaction with ubiquitin, which will be useful in understanding its enzymatic function.
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6
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Molecular architecture of polycomb repressive complexes. Biochem Soc Trans 2017; 45:193-205. [PMID: 28202673 PMCID: PMC5310723 DOI: 10.1042/bst20160173] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/24/2016] [Accepted: 12/02/2016] [Indexed: 01/05/2023]
Abstract
The polycomb group (PcG) proteins are a large and diverse family that epigenetically repress the transcription of key developmental genes. They form three broad groups of polycomb repressive complexes (PRCs) known as PRC1, PRC2 and Polycomb Repressive DeUBiquitinase, each of which modifies and/or remodels chromatin by distinct mechanisms that are tuned by having variable compositions of core and accessory subunits. Until recently, relatively little was known about how the various PcG proteins assemble to form the PRCs; however, studies by several groups have now allowed us to start piecing together the PcG puzzle. Here, we discuss some highlights of recent PcG structures and the insights they have given us into how these complexes regulate transcription through chromatin.
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7
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Lee YTC, Chang CY, Chen SY, Pan YR, Ho MR, Hsu STD. Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome. Sci Rep 2017; 7:45174. [PMID: 28338014 PMCID: PMC5364529 DOI: 10.1038/srep45174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023] Open
Abstract
Human ubiquitin C-terminal hydrolyase UCH-L5 is a topologically knotted deubiquitinase that is activated upon binding to the proteasome subunit Rpn13. The length of its intrinsically disordered cross-over loop is essential for substrate recognition. Here, we showed that the catalytic domain of UCH-L5 exhibits higher equilibrium folding stability with an unfolding rate on the scale of 10−8 s−1, over four orders of magnitudes slower than its paralogs, namely UCH-L1 and -L3, which have shorter cross-over loops. NMR relaxation dynamics analysis confirmed the intrinsic disorder of the cross-over loop. Hydrogen deuterium exchange analysis further revealed a positive correlation between the length of the cross-over loop and the degree of local fluctuations, despite UCH-L5 being thermodynamically and kinetically more stable than the shorter UCHs. Considering the role of UCH-L5 in removing K48-linked ubiquitin to prevent proteasomal degradation of ubiquitinated substrates, our findings offered mechanistic insights into the evolution of UCH-L5. Compared to its paralogs, it is entropically stabilized to withstand mechanical unfolding by the proteasome while maintaining structural plasticity. It can therefore accommodate a broad range of substrate geometries at the cost of unfavourable entropic loss.
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Affiliation(s)
- Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Chia-Yun Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Szu-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Ru Pan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
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8
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A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility. Nat Microbiol 2017; 2:17007. [PMID: 28248294 PMCID: PMC5336136 DOI: 10.1038/nmicrobiol.2017.7] [Citation(s) in RCA: 250] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/10/2017] [Indexed: 12/29/2022]
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9
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White RR, Ponsford AH, Weekes MP, Rodrigues RB, Ascher DB, Mol M, Selkirk ME, Gygi SP, Sanderson CM, Artavanis-Tsakonas K. Ubiquitin-Dependent Modification of Skeletal Muscle by the Parasitic Nematode, Trichinella spiralis. PLoS Pathog 2016; 12:e1005977. [PMID: 27870901 PMCID: PMC5117777 DOI: 10.1371/journal.ppat.1005977] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022] Open
Abstract
Trichinella spiralis is a muscle-specific parasitic worm that is uniquely intracellular. T. spiralis reprograms terminally differentiated skeletal muscle cells causing them to de-differentiate and re-enter the cell cycle, a process that cannot occur naturally in mammalian skeletal muscle cells, but one that holds great therapeutic potential. Although the host ubiquitin pathway is a common target for viruses and bacteria during infection, its role in parasite pathogenesis has been largely overlooked. Here we demonstrate that the secreted proteins of T. spiralis contain E2 Ub-conjugating and E3 Ub-ligase activity. The E2 activity is attributed to TsUBE2L3, a novel and conserved T. spiralis enzyme located in the secretory organ of the parasite during the muscle stages of infection. TsUBE2L3 cannot function with any T.spiralis secreted E3, but specifically binds to a panel of human RING E3 ligases, including the RBR E3 ARIH2 with which it interacts with a higher affinity than the mammalian ortholog UbcH7/UBE2L3. Expression of TsUBE2L3 in skeletal muscle cells causes a global downregulation in protein ubiquitination, most predominantly affecting motor, sarcomeric and extracellular matrix proteins, thus mediating their stabilization with regards to proteasomal degradation. This effect is not observed in the presence of the mammalian ortholog, suggesting functional divergence in the evolution of the parasite protein. These findings demonstrate the first example of host-parasite interactions via a parasite-derived Ub conjugating enzyme; an E2 that demonstrates a novel muscle protein stabilization function. Parasitic worms often establish long-lasting infections in their hosts; tightly regulating their surroundings to strike a delicate balance between host cell modulation and protection that will ensure their replication. This is accomplished via the active secretion of parasite glycolipids and glycoproteins into the host. Trichinella spiralis, a parasitic nematode that infects skeletal muscle of mammals, birds and reptiles, is the only parasitic worm with a true intracellular stage. T. spiralis invade terminally differentiated myotubes, reprogramming them to de-differentiate and re-enter the cell cycle, a process that cannot occur naturally in mammalian skeletal muscle cells, but one that holds great therapeutic potential. We have identified and characterized a novel T. spiralis secreted protein that, despite a high level of sequence identity, appears to have evolved a different function to its host ortholog. This protein is an active Ub conjugating enzyme that binds to a panel of human E3 Ub ligases with higher affinity than the host ortholog. Furthermore, when expressed in skeletal muscle cells in culture, its presence uniquely leads to the stabilization of muscle-specific proteins via the downregulation of their ubiquitination.
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Affiliation(s)
- Rhiannon R. White
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Amy H. Ponsford
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Department of Cell Biology, Harvard Medical School, Boston, United States of America
| | - Rachel B. Rodrigues
- Department of Cell Biology, Harvard Medical School, Boston, United States of America
| | - David B. Ascher
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Melbourne, Melbourne, Australia
| | - Marco Mol
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Murray E. Selkirk
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, United States of America
| | - Christopher M. Sanderson
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Katerina Artavanis-Tsakonas
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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10
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Vreven T, Pierce BG, Borrman TM, Weng Z. Performance of ZDOCK and IRAD in CAPRI rounds 28-34. Proteins 2016; 85:408-416. [PMID: 27718275 DOI: 10.1002/prot.25186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 11/11/2022]
Abstract
We report the performance of our protein-protein docking pipeline, including the ZDOCK rigid-body docking algorithm, on 19 targets in CAPRI rounds 28-34. Following the docking step, we reranked the ZDOCK predictions using the IRAD scoring function, pruned redundant predictions, performed energy landscape analysis, and utilized our interface prediction approach RCF. In addition, we applied constraints to the search space based on biological information that we culled from the literature, which increased the chance of making a correct prediction. For all but two targets we were able to find and apply biological information and we found the information to be highly accurate, indicating that effective incorporation of biological information is an important component for protein-protein docking. Proteins 2017; 85:408-416. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Brian G Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Tyler M Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
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11
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van Tilburg GB, Elhebieshy AF, Ovaa H. Synthetic and semi-synthetic strategies to study ubiquitin signaling. Curr Opin Struct Biol 2016; 38:92-101. [PMID: 27315041 PMCID: PMC7125694 DOI: 10.1016/j.sbi.2016.05.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 01/30/2023]
Abstract
The post-translational modification ubiquitin can be attached to the ɛ-amino group of lysine residues or to a protein's N-terminus as a mono ubiquitin moiety. Via its seven intrinsic lysine residues and its N-terminus, it can also form ubiquitin chains on substrates in many possible ways. To study ubiquitin signals, many synthetic and semi-synthetic routes have been developed for generation of ubiquitin-derived tools and conjugates. The strength of these methods lies in their ability to introduce chemo-selective ligation handles at sites that currently cannot be enzymatically modified. Here, we review the different synthetic and semi-synthetic methods available for ubiquitin conjugate synthesis and their contribution to how they have helped investigating conformational diversity of diubiquitin signals. Next, we discuss how these methods help understanding the ubiquitin conjugation-deconjugation system by recent advances in ubiquitin ligase probes and diubiquitin-based DUB probes. Lastly, we discuss how these methods help studying post-translational modification of ubiquitin itself.
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Affiliation(s)
- Gabriëlle Ba van Tilburg
- Department of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Angela F Elhebieshy
- Department of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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12
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Ronau JA, Beckmann JF, Hochstrasser M. Substrate specificity of the ubiquitin and Ubl proteases. Cell Res 2016; 26:441-56. [PMID: 27012468 PMCID: PMC4822132 DOI: 10.1038/cr.2016.38] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Conjugation and deconjugation of ubiquitin and ubiquitin-like proteins (Ubls) to cellular proteins are highly regulated processes integral to cellular homeostasis. Most often, the C-termini of these small polypeptides are attached to lysine side chains of target proteins by an amide (isopeptide) linkage. Deubiquitinating enzymes (DUBs) and Ubl-specific proteases (ULPs) comprise a diverse group of proteases that recognize and remove ubiquitin and Ubls from their substrates. How DUBs and ULPs distinguish among different modifiers, or different polymeric forms of these modifiers, remains poorly understood. The specificity of ubiquitin/Ubl-deconjugating enzymes for particular substrates depends on multiple factors, ranging from the topography of specific substrate features, as in different polyubiquitin chain types, to structural elements unique to each enzyme. Here we summarize recent structural and biochemical studies that provide insights into mechanisms of substrate specificity among various DUBs and ULPs. We also discuss the unexpected specificities of non-eukaryotic proteases in these families.
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Affiliation(s)
- Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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13
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Daou S, Hammond-Martel I, Mashtalir N, Barbour H, Gagnon J, Iannantuono NVG, Nkwe NS, Motorina A, Pak H, Yu H, Wurtele H, Milot E, Mallette FA, Carbone M, Affar EB. The BAP1/ASXL2 Histone H2A Deubiquitinase Complex Regulates Cell Proliferation and Is Disrupted in Cancer. J Biol Chem 2015; 290:28643-63. [PMID: 26416890 DOI: 10.1074/jbc.m115.661553] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Indexed: 01/03/2023] Open
Abstract
The deubiquitinase (DUB) and tumor suppressor BAP1 catalyzes ubiquitin removal from histone H2A Lys-119 and coordinates cell proliferation, but how BAP1 partners modulate its function remains poorly understood. Here, we report that BAP1 forms two mutually exclusive complexes with the transcriptional regulators ASXL1 and ASXL2, which are necessary for maintaining proper protein levels of this DUB. Conversely, BAP1 is essential for maintaining ASXL2, but not ASXL1, protein stability. Notably, cancer-associated loss of BAP1 expression results in ASXL2 destabilization and hence loss of its function. ASXL1 and ASXL2 use their ASXM domains to interact with the C-terminal domain (CTD) of BAP1, and these interactions are required for ubiquitin binding and H2A deubiquitination. The deubiquitination-promoting effect of ASXM requires intramolecular interactions between catalytic and non-catalytic domains of BAP1, which generate a composite ubiquitin-binding interface (CUBI). Notably, the CUBI engages multiple interactions with ubiquitin involving (i) the ubiquitin carboxyl hydrolase catalytic domain of BAP1, which interacts with the hydrophobic patch of ubiquitin, and (ii) the CTD domain, which interacts with a charged patch of ubiquitin. Significantly, we identified cancer-associated mutations of BAP1 that disrupt the CUBI and notably an in-frame deletion in the CTD that inhibits its interaction with ASXL1/2 and DUB activity and deregulates cell proliferation. Moreover, we demonstrated that BAP1 interaction with ASXL2 regulates cell senescence and that ASXL2 cancer-associated mutations disrupt BAP1 DUB activity. Thus, inactivation of the BAP1/ASXL2 axis might contribute to cancer development.
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Affiliation(s)
- Salima Daou
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Ian Hammond-Martel
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Nazar Mashtalir
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Haithem Barbour
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Jessica Gagnon
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Nicholas V G Iannantuono
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Nadine Sen Nkwe
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Alena Motorina
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Helen Pak
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Helen Yu
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Hugo Wurtele
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Eric Milot
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Frédérick A Mallette
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Michele Carbone
- the Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813
| | - El Bachir Affar
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
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14
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Abstract
Two studies in this issue of Molecular Cell,VanderLinden et al. (2015) and Sahtoe et al. (2015),report crystal structures that define how deubiquitinating enzyme UCH37 is switched on or off by proteasome ubiquitin receptor RPN13 or chromatin remodeler component INO80G.
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15
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Shih PM, Wang I, Lee YTC, Hsieh SJ, Chen SY, Wang LW, Huang CT, Chien CT, Chang CY, Hsu STD. Random-Coil Behavior of Chemically Denatured Topologically Knotted Proteins Revealed by Small-Angle X-ray Scattering. J Phys Chem B 2015; 119:5437-43. [DOI: 10.1021/acs.jpcb.5b01984] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Po-Min Shih
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Iren Wang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Yun-Tzai Cloud Lee
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Shu-Ju Hsieh
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Szu-Yu Chen
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Liang-Wei Wang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Chih-Ting Huang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Chih-Ta Chien
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Department
of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Chia-Yun Chang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Shang-Te Danny Hsu
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
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16
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Vander Linden RT, Hemmis CW, Schmitt B, Ndoja A, Whitby FG, Robinson H, Cohen RE, Yao T, Hill CP. Structural basis for the activation and inhibition of the UCH37 deubiquitylase. Mol Cell 2015; 57:901-911. [PMID: 25702872 DOI: 10.1016/j.molcel.2015.01.016] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022]
Abstract
The UCH37 deubiquitylase functions in two large and very different complexes, the 26S proteasome and the INO80 chromatin remodeler. We have performed biochemical characterization and determined crystal structures of UCH37 in complexes with RPN13 and NFRKB, which mediate its recruitment to the proteasome and INO80, respectively. RPN13 and NFRKB make similar contacts to the UCH37 C-terminal domain but quite different contacts to the catalytic UCH domain. RPN13 can activate UCH37 by disrupting dimerization, although physiologically relevant activation likely results from stabilization of a surface competent for ubiquitin binding and modulation of the active-site crossover loop. In contrast, NFRKB inhibits UCH37 by blocking the ubiquitin-binding site and by disrupting the enzyme active site. These findings reveal remarkable commonality in mechanisms of recruitment, yet very different mechanisms of regulating enzyme activity, and provide a foundation for understanding the roles of UCH37 in the unrelated proteasome and INO80 complexes.
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Affiliation(s)
- Ryan T Vander Linden
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Casey W Hemmis
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Benjamin Schmitt
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Ada Ndoja
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Frank G Whitby
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
| | - Howard Robinson
- Biology Department Brookhaven National Laboratory, Upton, NY, 11973 USA
| | - Robert E Cohen
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology Colorado State University, Fort Collins, CO 80523 USA
| | - Christopher P Hill
- Department of Biochemistry University of Utah School of Medicine, Salt Lake City, UT 84112-5650 USA
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17
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Sahtoe DD, van Dijk WJ, El Oualid F, Ekkebus R, Ovaa H, Sixma TK. Mechanism of UCH-L5 activation and inhibition by DEUBAD domains in RPN13 and INO80G. Mol Cell 2015; 57:887-900. [PMID: 25702870 PMCID: PMC4352763 DOI: 10.1016/j.molcel.2014.12.039] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/16/2014] [Accepted: 12/24/2014] [Indexed: 12/15/2022]
Abstract
Deubiquitinating enzymes (DUBs) control vital processes in eukaryotes by hydrolyzing ubiquitin adducts. Their activities are tightly regulated, but the mechanisms remain elusive. In particular, the DUB UCH-L5 can be either activated or inhibited by conserved regulatory proteins RPN13 and INO80G, respectively. Here we show how the DEUBAD domain in RPN13 activates UCH-L5 by positioning its C-terminal ULD domain and crossover loop to promote substrate binding and catalysis. The related DEUBAD domain in INO80G inhibits UCH-L5 by exploiting similar structural elements in UCH-L5 to promote a radically different conformation, and employs molecular mimicry to block ubiquitin docking. In this process, large conformational changes create small but highly specific interfaces that mediate activity modulation of UCH-L5 by altering the affinity for substrates. Our results establish how related domains can exploit enzyme conformational plasticity to allosterically regulate DUB activity. These allosteric sites may present novel insights for pharmaceutical intervention in DUB activity. The RPN13 DEUBAD domain activates UCH-L5 by positioning its CL and ULD domain The INO80G DEUBAD domain inhibits UCH-L5 by blocking ubiquitin binding The FRF hairpin in the DEUBAD domain of INO80G drives UCH-L5 inhibition DEUBAD domains regulate UCH-L5 activity by tuning UCH-L5 substrate affinity
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Affiliation(s)
- Danny D Sahtoe
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Farid El Oualid
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; UbiQ, Science Park 408, 1098XH Amsterdam, the Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Huib Ovaa
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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18
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Abstract
Electron-hole separation following hard X-ray absorption during diffraction analysis of soft materials under cryogenic conditions produces substantial local electric fields visualizable by second harmonic generation (SHG) microscopy. Monte Carlo simulations of X-ray photoelectron trajectories suggest the formation of substantial local electric fields in the regions adjacent to those exposed to X-rays, indicating a possible electric-field-induced SHG (EFISH) mechanism for generating the observed signal. In studies of amorphous vitreous solvents, analysis of the SHG spatial profiles following X-ray microbeam exposure was consistent with an EFISH mechanism. Within protein crystals, exposure to 12-keV (1.033-Å) X-rays resulted in increased SHG in the region extending ∼ 3 μm beyond the borders of the X-ray beam. Moderate X-ray exposures typical of those used for crystal centering by raster scanning through an X-ray beam were sufficient to produce static electric fields easily detectable by SHG. The X-ray-induced SHG activity was observed with no measurable loss for longer than 2 wk while maintained under cryogenic conditions, but disappeared if annealed to room temperature for a few seconds. These results provide direct experimental observables capable of validating simulations of X-ray-induced damage within soft materials. In addition, X-ray-induced local fields may potentially impact diffraction resolution through localized piezoelectric distortions of the lattice.
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