1
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Raut KK, Pandey S, Kharel G, Pascal SM. Evidence of direct interaction between cisplatin and the caspase-cleaved prostate apoptosis response-4 tumor suppressor. Protein Sci 2024; 33:e4867. [PMID: 38093605 PMCID: PMC10868438 DOI: 10.1002/pro.4867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 02/16/2024]
Abstract
Prostate apoptosis response-4 (Par-4) tumor suppressor protein has gained attention as a potential therapeutic target owing to its unique ability to selectively induce apoptosis in cancer cells, sensitize them to chemotherapy and radiotherapy, and mitigate drug resistance. It has recently been reported that Par-4 interacts synergistically with cisplatin, a widely used anticancer drug. However, the mechanistic details underlying this relationship remain elusive. In this investigation, we employed an array of biophysical techniques, including circular dichroism spectroscopy, dynamic light scattering, and UV-vis absorption spectroscopy, to characterize the interaction between the active caspase-cleaved Par-4 (cl-Par-4) fragment and cisplatin. Additionally, elemental analysis was conducted to quantitatively assess the binding of cisplatin to the protein, utilizing inductively coupled plasma-optical emission spectroscopy and atomic absorption spectroscopy. Our findings provide evidence of direct interaction between cl-Par-4 and cisplatin, and reveal a binding stoichiometry of 1:1. This result provides insights that could be useful in enhancing the efficacy of cisplatin-based and tumor suppressor-based cancer therapies.
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Affiliation(s)
- Krishna K. Raut
- Department of Chemistry and BiochemistryOld Dominion UniversityNorfolkVirginiaUSA
| | - Samjhana Pandey
- Biomedical Sciences ProgramOld Dominion UniversityNorfolkVirginiaUSA
| | - Gyanendra Kharel
- Department of Chemistry and BiochemistryOld Dominion UniversityNorfolkVirginiaUSA
| | - Steven M. Pascal
- Department of Chemistry and BiochemistryOld Dominion UniversityNorfolkVirginiaUSA
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2
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Pandey S, Raut KK, Clark AM, Baudin A, Djemri L, Libich DS, Ponniah K, Pascal SM. Enhancing the Conformational Stability of the cl-Par-4 Tumor Suppressor via Site-Directed Mutagenesis. Biomolecules 2023; 13:biom13040667. [PMID: 37189414 DOI: 10.3390/biom13040667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Intrinsically disordered proteins play important roles in cell signaling, and dysregulation of these proteins is associated with several diseases. Prostate apoptosis response-4 (Par-4), an approximately 40 kilodalton proapoptotic tumor suppressor, is a predominantly intrinsically disordered protein whose downregulation has been observed in various cancers. The caspase-cleaved fragment of Par-4 (cl-Par-4) is active and plays a role in tumor suppression by inhibiting cell survival pathways. Here, we employed site-directed mutagenesis to create a cl-Par-4 point mutant (D313K). The expressed and purified D313K protein was characterized using biophysical techniques, and the results were compared to that of the wild-type (WT). We have previously demonstrated that WT cl-Par-4 attains a stable, compact, and helical conformation in the presence of a high level of salt at physiological pH. Here, we show that the D313K protein attains a similar conformation as the WT in the presence of salt, but at an approximately two times lower salt concentration. This establishes that the substitution of a basic residue for an acidic residue at position 313 alleviates inter-helical charge repulsion between dimer partners and helps to stabilize the structural conformation.
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Affiliation(s)
- Samjhana Pandey
- Biomedical Sciences Program, Old Dominion University, Norfolk, VA 23529, USA
| | - Krishna K Raut
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Andrea M Clark
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Antoine Baudin
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lamya Djemri
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - David S Libich
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
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3
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Structural Analysis of the cl-Par-4 Tumor Suppressor as a Function of Ionic Environment. Biomolecules 2021; 11:biom11030386. [PMID: 33807852 PMCID: PMC7998163 DOI: 10.3390/biom11030386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/09/2023] Open
Abstract
Prostate apoptosis response-4 (Par-4) is a proapoptotic tumor suppressor protein that has been linked to a large number of cancers. This 38 kilodalton (kDa) protein has been shown to be predominantly intrinsically disordered in vitro. In vivo, Par-4 is cleaved by caspase-3 at Asp-131 to generate the 25 kDa functionally active cleaved Par-4 protein (cl-Par-4) that inhibits NF-κB-mediated cell survival pathways and causes selective apoptosis in tumor cells. Here, we have employed circular dichroism (CD) spectroscopy and dynamic light scattering (DLS) to assess the effects of various monovalent and divalent salts upon the conformation of cl-Par-4 in vitro. We have previously shown that high levels of sodium can induce the cl-Par-4 fragment to form highly compact, highly helical tetramers in vitro. Spectral characteristics suggest that most or at least much of the helical content in these tetramers are non-coiled coils. Here, we have shown that potassium produces a similar effect as was previously reported for sodium and that magnesium salts also produce a similar conformation effect, but at an approximately five times lower ionic concentration. We have also shown that anion identity has far less influence than does cation identity. The degree of helicity induced by each of these salts suggests that the "Selective for Apoptosis in Cancer cells" (SAC) domain-the region of Par-4 that is most indispensable for its apoptotic function-is likely to be helical in cl-Par-4 under the studied high salt conditions. Furthermore, we have shown that under medium-strength ionic conditions, a combination of high molecular weight aggregates and smaller particles form and that the smaller particles are also highly helical, resembling at least in secondary structure, the tetramers found at high salt.
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4
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Cheratta AR, Thayyullathil F, Pallichankandy S, Subburayan K, Alakkal A, Galadari S. Prostate apoptosis response-4 and tumor suppression: it's not just about apoptosis anymore. Cell Death Dis 2021; 12:47. [PMID: 33414404 PMCID: PMC7790818 DOI: 10.1038/s41419-020-03292-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023]
Abstract
The tumor suppressor prostate apoptosis response-4 (Par-4) has recently turned ‘twenty-five’. Beyond its indisputable role as an apoptosis inducer, an increasing and sometimes bewildering, new roles for Par-4 are being reported. These roles include its ability to regulate autophagy, senescence, and metastasis. This growing range of responses to Par-4 is reflected by our increasing understanding of the various mechanisms through which Par-4 can function. In this review, we summarize the existing knowledge on Par-4 tumor suppressive mechanisms, and discuss how the interaction of Par-4 with different regulators influence cell fate. This review also highlights the new secretory pathway that has emerged and the likely discussion on its clinical implications.
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Affiliation(s)
- Anees Rahman Cheratta
- Cell Death Signaling Laboratory, Division of Science, Experimental Research Building, New York University Abu Dhabi, PO Box 129188, Saadiyat Island Campus, Abu Dhabi, UAE
| | - Faisal Thayyullathil
- Cell Death Signaling Laboratory, Division of Science, Experimental Research Building, New York University Abu Dhabi, PO Box 129188, Saadiyat Island Campus, Abu Dhabi, UAE
| | - Siraj Pallichankandy
- Cell Death Signaling Laboratory, Division of Science, Experimental Research Building, New York University Abu Dhabi, PO Box 129188, Saadiyat Island Campus, Abu Dhabi, UAE
| | - Karthikeyan Subburayan
- Cell Death Signaling Laboratory, Division of Science, Experimental Research Building, New York University Abu Dhabi, PO Box 129188, Saadiyat Island Campus, Abu Dhabi, UAE
| | - Ameer Alakkal
- Cell Death Signaling Laboratory, Division of Science, Experimental Research Building, New York University Abu Dhabi, PO Box 129188, Saadiyat Island Campus, Abu Dhabi, UAE
| | - Sehamuddin Galadari
- Cell Death Signaling Laboratory, Division of Science, Experimental Research Building, New York University Abu Dhabi, PO Box 129188, Saadiyat Island Campus, Abu Dhabi, UAE.
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5
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Kapiainen E, Kihlström MK, Pietilä R, Kaakinen M, Ronkainen VP, Tu H, Heikkinen A, Devarajan R, Miinalainen I, Laitakari A, Ansarizadeh M, Zhang Q, Wei GH, Ruddock L, Pihlajaniemi T, Elamaa H, Eklund L. The Amino-Terminal Oligomerization Domain of Angiopoietin-2 Affects Vascular Remodeling, Mammary Gland Tumor Growth, and Lung Metastasis in Mice. Cancer Res 2020; 81:129-143. [PMID: 33037065 DOI: 10.1158/0008-5472.can-19-1904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 05/03/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
Angiopoietin-2 (ANGPT2) is a context-dependent TIE2 agonistic or antagonistic ligand that induces diverse responses in cancer. Blocking ANGPT2 provides a promising strategy for inhibiting tumor growth and metastasis, yet variable effects of targeting ANGPT2 have complicated drug development. ANGPT2443 is a naturally occurring, lower oligomeric protein isoform whose expression is increased in cancer. Here, we use a knock-in mouse line (mice expressing Angpt2443), a genetic model for breast cancer and metastasis (MMTV-PyMT), a syngeneic melanoma lung colonization model (B16F10), and orthotopic injection of E0771 breast cancer cells to show that alternative forms increase the diversity of Angpt2 function. In a mouse retina model of angiogenesis, expression of Angpt2443 caused impaired venous development, suggesting enhanced function as a competitive antagonist for Tie2. In mammary gland tumor models, Angpt2443 differentially affected primary tumor growth and vascularization; these varying effects were associated with Angpt2 protein localization in the endothelium or in the stromal extracellular matrix as well as the frequency of Tie2-positive tumor blood vessels. In the presence of metastatic cells, Angpt2443 promoted destabilization of pulmonary vasculature and lung metastasis. In vitro, ANGPT2443 was susceptible to proteolytical cleavage, resulting in a monomeric ligand (ANGPT2DAP) that inhibited ANGPT1- or ANGPT4-induced TIE2 activation but did not bind to alternative ANGPT2 receptor α5β1 integrin. Collectively, these data reveal novel roles for the ANGPT2 N-terminal domain in blood vessel remodeling, tumor growth, metastasis, integrin binding, and proteolytic regulation. SIGNIFICANCE: This study identifies the role of the N-terminal oligomerization domain of angiopoietin-2 in vascular remodeling and lung metastasis and provides new insights into mechanisms underlying the versatile functions of angiopoietin-2 in cancer.See related commentary by Kamiyama and Augustin, p. 35.
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Affiliation(s)
- Emmi Kapiainen
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Minna K Kihlström
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Riikka Pietilä
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | | | - Hongmin Tu
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anne Heikkinen
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Raman Devarajan
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Anna Laitakari
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mohammadhassan Ansarizadeh
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Qin Zhang
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lloyd Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Taina Pihlajaniemi
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Harri Elamaa
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lauri Eklund
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland. .,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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6
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Clark AM, Ponniah K, Warden MS, Raitt EM, Smith BG, Pascal SM. Tetramer formation by the caspase-activated fragment of the Par-4 tumor suppressor. FEBS J 2019; 286:4060-4073. [PMID: 31177609 DOI: 10.1111/febs.14955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/10/2019] [Accepted: 06/06/2019] [Indexed: 11/27/2022]
Abstract
The prostate apoptosis response-4 (Par-4) tumor suppressor can selectively kill cancer cells via apoptosis while leaving healthy cells unharmed. Full length Par-4 has been shown to be predominantly intrinsically disordered in vitro under neutral conditions. As part of the apoptotic process, cellular Par-4 is cleaved at D131 by caspase-3, which generates a 24 kDa C-terminal activated fragment (cl-Par-4) that enters the nucleus and inhibits pro-survival genes, thereby preventing cancer cell proliferation. Here, the structure of cl-Par-4 was investigated using CD spectroscopy, dynamic light scattering, intrinsic tyrosine fluorescence, and size exclusion chromatography with mutli-angle light scattering. Biophysical characterization shows that cl-Par-4 aggregates and is disordered at low ionic strength. However, with increasing ionic strength, cl-Par-4 becomes progressively more helical and less aggregated, ultimately forming largely ordered tetramers at high NaCl concentration. These results, together with previous results showing induced folding at acidic pH, suggest that the in vivo structure and self-association state of cl-Par-4 may be strongly dependent upon cellular environment.
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Affiliation(s)
- Andrea M Clark
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Emily M Raitt
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Benjamin G Smith
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
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7
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Clark AM, Ponniah K, Warden MS, Raitt EM, Yawn AC, Pascal SM. pH-Induced Folding of the Caspase-Cleaved Par-4 Tumor Suppressor: Evidence of Structure Outside of the Coiled Coil Domain. Biomolecules 2018; 8:biom8040162. [PMID: 30518159 PMCID: PMC6316887 DOI: 10.3390/biom8040162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022] Open
Abstract
Prostate apoptosis response-4 (Par-4) is a 38 kDa largely intrinsically disordered tumor suppressor protein that functions in cancer cell apoptosis. Par-4 down-regulation is often observed in cancer while up-regulation is characteristic of neurodegenerative conditions such as Alzheimer’s disease. Cleavage of Par-4 by caspase-3 activates tumor suppression via formation of an approximately 25 kDa fragment (cl-Par-4) that enters the nucleus and inhibits Bcl-2 and NF-ƙB, which function in pro-survival pathways. Here, we have investigated the structure of cl-Par-4 using biophysical techniques including circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and intrinsic tyrosine fluorescence. The results demonstrate pH-dependent folding of cl-Par-4, with high disorder and aggregation at neutral pH, but a largely folded, non-aggregated conformation at acidic pH.
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Affiliation(s)
- Andrea M Clark
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Emily M Raitt
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Andrea C Yawn
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
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8
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Bitard‐Feildel T, Lamiable A, Mornon J, Callebaut I. Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences. Proteomics 2018; 18:e1800054. [PMID: 30299594 PMCID: PMC7168002 DOI: 10.1002/pmic.201800054] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/29/2018] [Indexed: 12/17/2022]
Abstract
Hydrophobic cluster analysis (HCA) is an original approach for protein sequence analysis, which provides access to the foldable repertoire of the protein universe, including yet unannotated protein segments ("dark proteome"). Foldable segments correspond to ordered regions, as well as to intrinsically disordered regions (IDRs) undergoing disorder to order transitions. In this review, how HCA can be used to give insight into this last category of foldable segments is illustrated, with examples matching known 3D structures. After reviewing the HCA principles, examples of short foldable segments are given, which often contain short linear motifs, typically matching hydrophobic clusters. These segments become ordered upon contact with partners, with secondary structure preferences generally corresponding to those observed in the 3D structures within the complexes. Such small foldable segments are sometimes larger than the segments of known 3D structures, including flanking hydrophobic clusters that may be critical for interaction specificity or regulation, as well as intervening sequences allowing fuzziness. Cases of larger conditionally disordered domains are also presented, with lower density in hydrophobic clusters than well-folded globular domains or with exposed hydrophobic patches, which are stabilized by interaction with partners.
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Affiliation(s)
- Tristan Bitard‐Feildel
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
- Laboratoire de Biologie Computationnelle et Quantitative (LCQB)Institute of Biology Paris‐Seine (IBPS)Centre national de la recherche scientifique (CNRS)Sorbonne Université75005ParisFrance
| | - Alexis Lamiable
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
| | - Jean‐Paul Mornon
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
| | - Isabelle Callebaut
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
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9
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Abstract
Par-4 is a unique proapoptotic protein with the ability to induce apoptosis selectively in cancer cells. The X-ray crystal structure of the C-terminal domain of Par-4 (Par-4CC), which regulates its apoptotic function, was obtained by MAD phasing. Par-4 homodimerizes by forming a parallel coiled-coil structure. The N-terminal half of Par-4CC contains the homodimerization subdomain. This structure includes a nuclear export signal (Par-4NES) sequence, which is masked upon dimerization indicating a potential mechanism for nuclear localization. The heteromeric-interaction models specifically showed that charge interaction is an important factor in the stability of heteromers of the C-terminal leucine zipper subdomain of Par-4 (Par-4LZ). These heteromer models also displayed NES masking capacity and therefore the ability to influence intracellular localization.
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10
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Killoran RC, Sowole MA, Halim MA, Konermann L, Choy WY. Conformational characterization of the intrinsically disordered protein Chibby: Interplay between structural elements in target recognition. Protein Sci 2016; 25:1420-9. [PMID: 27082063 DOI: 10.1002/pro.2936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 04/09/2016] [Accepted: 04/11/2016] [Indexed: 11/12/2022]
Abstract
The protein Chibby (Cby) is an antagonist of the Wnt signaling pathway, where it inhibits the binding between the transcriptional coactivator β-catenin and the Tcf/Lef transcription factors. The 126 residue Cby is partially disordered; its N-terminal half is unstructured while its C-terminal half comprises a coiled-coil domain. Previous structural analyses of Cby using NMR spectroscopy suffered from severe line broadening for residues within the protein's C-terminal half, hindering detailed characterization of the coiled-coil domain. Here, we use hydrogen/deuterium exchange-mass spectrometry (HDX-MS) to examine Cby's C-terminal half. Results reveal that Cby is divided into three structural elements: a disordered N-terminal half, a coiled-coil domain, and a C-terminal unstructured extension consisting of the last ∼ 25 residues (which we term C-terminal extension). A series of truncation constructs were designed to assess the roles of individual structural elements in protein stability and Cby binding to TC-1, a positive regulator of the Wnt signaling pathway. CD and NMR data show that Cby maintains coiled-coil structure upon deletion of either disordered region. NMR and ITC binding experiments between Cby and TC-1 illustrate that the interaction is retained upon deletion of either Cby's N-terminal half or its C-terminal extension. Intriguingly, Cby's C-terminal half alone binds to TC-1 with significantly greater affinity compared to full-length Cby, implying that target binding of the coiled-coil domain is affected by the flanking disordered regions.
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Affiliation(s)
- Ryan C Killoran
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Mohammad A Halim
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Lars Konermann
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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11
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Treude F, Kappes F, Fahrenkamp D, Müller-Newen G, Dajas-Bailador F, Krämer OH, Lüscher B, Hartkamp J. Caspase-8-mediated PAR-4 cleavage is required for TNFα-induced apoptosis. Oncotarget 2015; 5:2988-98. [PMID: 24931006 PMCID: PMC4102785 DOI: 10.18632/oncotarget.1634] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The tumor suppressor protein prostate apoptosis response-4 (PAR-4) is silenced in a subset of human cancers and its down-regulation serves as a mechanism for cancer cell survival following chemotherapy. PAR-4 re-expression selectively causes apoptosis in cancer cells but how its pro-apoptotic functions are controlled and executed precisely is currently unknown. We demonstrate here that UV-induced apoptosis results in a rapid caspase-dependent PAR-4 cleavage at EEPD131G, a sequence that was preferentially recognized by caspase-8. To investigate the effect on cell growth for this cleavage event we established stable cell lines that express wild-type-PAR-4 or the caspase cleavage resistant mutant PAR-4 D131G under the control of a doxycycline-inducible promoter. Induction of the wild-type protein but not the mutant interfered with cell proliferation, predominantly through induction of apoptosis. We further demonstrate that TNFα-induced apoptosis leads to caspase-8-dependent PAR-4-cleavage followed by nuclear accumulation of the C-terminal PAR-4 (132-340) fragment, which then induces apoptosis. Taken together, our results indicate that the mechanism by which PAR-4 orchestrates the apoptotic process requires cleavage by caspase-8.
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Affiliation(s)
- Fabian Treude
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
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12
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Tiruttani Subhramanyam UK, Kubicek J, Eidhoff UB, Labahn J. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the C-terminal domain of Par-4 (PAWR). Acta Crystallogr F Struct Biol Commun 2014; 70:1224-7. [PMID: 25195896 PMCID: PMC4157423 DOI: 10.1107/s2053230x14014691] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/21/2014] [Indexed: 11/10/2022] Open
Abstract
Prostate apoptosis response-4 protein is an intrinsically disordered pro-apoptotic protein with tumour suppressor function. Par-4 is known for its selective induction of apoptosis in cancer cells only and its ability to interact with various apoptotic proteins via its C-terminus. Par-4, with its unique function and various interacting partners, has gained importance as a potential target for cancer therapy. The C-terminus of the rat homologue of Par-4 was crystallized and a 3.7 Å resolution X-ray diffraction data set was collected. Preliminary data analysis shows the space group to be P41212. The unit-cell parameters are a = b = 115.351, c = 123.663 Å, α = β = γ = 90°.
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Affiliation(s)
- Udaya Kumar Tiruttani Subhramanyam
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jan Kubicek
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Cube Biotech GmbH, Alfred-Nobel-Strasse 10, 40789 Monheim, Germany
| | - Ulf B. Eidhoff
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Joerg Labahn
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Forschungszentrum Jülich, 52425 Jülich, Germany
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13
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Resilience of death: intrinsic disorder in proteins involved in the programmed cell death. Cell Death Differ 2013; 20:1257-67. [PMID: 23764774 DOI: 10.1038/cdd.2013.65] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 05/09/2013] [Accepted: 05/14/2013] [Indexed: 11/08/2022] Open
Abstract
It is recognized now that intrinsically disordered proteins (IDPs), which do not have unique 3D structures as a whole or in noticeable parts, constitute a significant fraction of any given proteome. IDPs are characterized by an astonishing structural and functional diversity that defines their ability to be universal regulators of various cellular pathways. Programmed cell death (PCD) is one of the most intricate cellular processes where the cell uses specialized cellular machinery and intracellular programs to kill itself. This cell-suicide mechanism enables metazoans to control cell numbers and to eliminate cells that threaten the animal's survival. PCD includes several specific modules, such as apoptosis, autophagy, and programmed necrosis (necroptosis). These modules are not only tightly regulated but also intimately interconnected and are jointly controlled via a complex set of protein-protein interactions. To understand the role of the intrinsic disorder in controlling and regulating the PCD, several large sets of PCD-related proteins across 28 species were analyzed using a wide array of modern bioinformatics tools. This study indicates that the intrinsic disorder phenomenon has to be taken into consideration to generate a complete picture of the interconnected processes, pathways, and modules that determine the essence of the PCD. We demonstrate that proteins involved in regulation and execution of PCD possess substantial amount of intrinsic disorder. We annotate functional roles of disorder across and within apoptosis, autophagy, and necroptosis processes. Disordered regions are shown to be implemented in a number of crucial functions, such as protein-protein interactions, interactions with other partners including nucleic acids and other ligands, are enriched in post-translational modification sites, and are characterized by specific evolutionary patterns. We mapped the disorder into an integrated network of PCD pathways and into the interactomes of selected proteins that are involved in the p53-mediated apoptotic signaling pathway.
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Abstract
INTRODUCTION Despite extensive research, cancer continues to be a leading cause of death worldwide and is expected to continue to rise as a result of an aging population. Therefore, new therapies are constantly being developed. Par-4 is a naturally occurring tumor suppressor protein that is capable of inducing apoptosis in cancer, but not normal cells. For this reason, Par-4 offers an attractive target for development of cancer therapy, particularly of difficult to treat cancers. AREAS COVERED The mechanisms by which Par-4 induces cell death are summarized. The ways that Par-4 is controlled in cancer cells are discussed. We discuss how different research groups have developed ways to overexpress and/or activate Par-4 in vitro and in vivo. The studies described demonstrate that when Par-4 levels and/or activity are increased, susceptibility to apoptosis is enhanced and tumor growth is inhibited. EXPERT OPINION Par-4 is a promising therapeutic protein that can be overexpressed and/or activated to induce apoptosis in a cancer-selective manner. This cancer selectivity is important given that the side-effects of chemotherapeutics can be as debilitating as cancer itself. However, there are key issues that need to be addressed to optimize the effects of Par-4 in patients.
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Affiliation(s)
- Rosalyn B Irby
- Penn State Hershey Cancer Institute, 500 University Drive, Hershey, PA 17033, USA.
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15
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Nido GS, Méndez R, Pascual-García A, Abia D, Bastolla U. Protein disorder in the centrosome correlates with complexity in cell types number. MOLECULAR BIOSYSTEMS 2011; 8:353-67. [PMID: 22076659 DOI: 10.1039/c1mb05199g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we study the properties and the evolution of proteins that constitute the Centrosome, the complex molecular assembly that regulates the division and differentiation of animal cells. We found that centrosomal proteins are predicted to be significantly enriched in disordered and coiled-coil regions, more phosphorylated and longer than control proteins of the same organism. Interestingly, the ratio of these properties in centrosomal and control proteins tends to increase with the number of cell-types. We reconstructed indels evolution, finding that indels significantly increase disorder in both centrosomal and control proteins, at a rate that is typically larger along branches associated with a large growth in cell-types number, and larger for centrosomal than for control proteins. Substitutions show a similar trend for coiled-coil, but they contribute less to the evolution of disorder. Our results suggest that the increase in cell-types number in animal evolution is correlated with the gain of disordered and coiled-coil regions in centrosomal proteins, establishing a connection between organism and molecular complexity. We argue that the structural plasticity conferred to the Centrosome by disordered regions and phosphorylation plays an important role in its mechanical properties and its regulation in space and time.
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Affiliation(s)
- G S Nido
- Centro de Biología Molecular Severo Ochoa, (CSIC-UAM), Madrid, Spain
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16
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Kline CLB, Irby RB. The pro-apoptotic protein Prostate Apoptosis Response Protein-4 (Par-4) can be activated in colon cancer cells by treatment with Src inhibitor and 5-FU. Apoptosis 2011; 16:1285-94. [DOI: 10.1007/s10495-011-0648-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mokhtarzada S, Yu C, Brickenden A, Choy WY. Structural characterization of partially disordered human Chibby: insights into its function in the Wnt-signaling pathway. Biochemistry 2011; 50:715-26. [PMID: 21182262 PMCID: PMC3031990 DOI: 10.1021/bi101236z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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The Wnt/β-catenin signaling pathway is critical to embryonic development as well as adult tissue regeneration. Dysregulation of this pathway can lead to a variety of human diseases, in particular cancers. Chibby (Cby), a small and highly conserved protein, plays an antagonistic role in Wnt signaling by inhibiting the binding of β-catenin to Tcf/Lef family proteins, a protein interaction that is essential for the transcriptional activation of Wnt target genes. Cby is also involved in regulating intracellular distribution of β-catenin. Phosphorylated Cby forms a ternary complex with 14-3-3 protein and β-catenin, facilitating the export of β-catenin from the nucleus. On the other hand, the antagonistic function of Cby is inhibited upon binding to thyroid cancer-1 (TC-1). To dissect the structure−function relationship of Cby, we have used NMR spectroscopy, ESI-MS, CD, and DLS to extensively characterize the structure of human Cby. Our results show that the 126-residue Cby is partially disordered under nondenaturing conditions. While the N-terminal portion of the protein is predominantly unstructured in solution, the C-terminal half of Cby adopts a coiled-coil structure through self-association. Initial data for the binding studies of Cby to 14-3-3ζ (one of the isoforms in the 14-3-3 family) and TC-1 via these two distinct structural modules have also been obtained. It is noteworthy that in a recent large-scale analysis of the intrinsically disordered proteome of mouse, a substantial number of disordered proteins are predicted to have coiled-coil motif presence in their sequences. The combination of these two molecular recognition features could facilitate disordered Cby in assembling protein complexes via different modes of interaction.
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Affiliation(s)
- Sulayman Mokhtarzada
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1
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18
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Schwalbe M, Dutta K, Libich DS, Venugopal H, Claridge JK, Gell DA, Mackay JP, Edwards PJB, Pascal SM. Two-state conformational equilibrium in the Par-4 leucine zipper domain. Proteins 2010; 78:2433-49. [PMID: 20602362 DOI: 10.1002/prot.22752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Prostate apoptosis response factor-4 (Par-4) is a pro-apoptotic and tumor-suppressive protein. A highly conserved heptad repeat sequence at the Par-4 C-terminus suggests the presence of a leucine zipper (LZ). This C-terminal region is essential for Par-4 self-association and interaction with various effector proteins. We have used nuclear magnetic resonance (NMR) spectroscopy to fully assign the chemical shift resonances of a peptide comprising the LZ domain of Par-4 at neutral pH. Further, we have investigated the properties of the Par-4 LZ domain and two point mutants under a variety of conditions using NMR, circular dichroism (CD), light scattering, and bioinformatics. Results indicate an environment-dependent conformational equilibrium between a partially ordered monomer (POM) and a predominantly coiled coil dimer (CCD). The combination of techniques used allows the time scales of the equilibrium to be probed and also helps to identify features of the amino acid sequence that may influence the equilibrium.
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Affiliation(s)
- Martin Schwalbe
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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19
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Filippakopoulos P, Low A, Sharpe TD, Uppenberg J, Yao S, Kuang Z, Savitsky P, Lewis RS, Nicholson SE, Norton RS, Bullock AN. Structural basis for Par-4 recognition by the SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4. J Mol Biol 2010; 401:389-402. [PMID: 20561531 PMCID: PMC2923778 DOI: 10.1016/j.jmb.2010.06.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 06/04/2010] [Accepted: 06/08/2010] [Indexed: 11/30/2022]
Abstract
The mammalian SPRY domain- and SOCS box-containing proteins, SPSB1 to SPSB4, belong to the SOCS box family of E3 ubiquitin ligases. Substrate recognition sites for the SPRY domain are identified only for human Par-4 (ELNNNL) and for the Drosophila orthologue GUSTAVUS binding to the DEAD-box RNA helicase VASA (DINNNN). To further investigate this consensus motif, we determined the crystal structures of SPSB1, SPSB2, and SPSB4, as well as their binding modes and affinities for both Par-4 and VASA. Mutation of each of the three Asn residues in Par-4 abrogated binding to all three SPSB proteins, while changing EL to DI enhanced binding. By comparison to SPSB1 and SPSB4, the more divergent protein SPSB2 showed only weak binding to Par-4 and was hypersensitive to DI substitution. Par-4(59–77) binding perturbed NMR resonances from a number of SPSB2 residues flanking the ELNNN binding site, including loop D, which binds the EL/DI sequence. Although interactions with the consensus peptide motif were conserved in all structures, flanking sites in SPSB2 were identified as sites of structural change. These structural changes limit high-affinity interactions for SPSB2 to aspartate-containing sequences, whereas SPSB1 and SPSB4 bind strongly to both Par-4 and VASA peptides.
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Affiliation(s)
- Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Andrew Low
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Timothy D. Sharpe
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jonas Uppenberg
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Shenggen Yao
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Zhihe Kuang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Pavel Savitsky
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Rowena S. Lewis
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Sandra E. Nicholson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Raymond S. Norton
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Corresponding authors.
| | - Alex N. Bullock
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
- Corresponding authors.
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