1
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Yeshaya N, Gupta PK, Dym O, Morgenstern D, Major DT, Fass D. VWD domain stabilization by autocatalytic Asp-Pro cleavage. Protein Sci 2024; 33:e4929. [PMID: 38380729 PMCID: PMC10880436 DOI: 10.1002/pro.4929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/17/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
Domains known as von Willebrand factor type D (VWD) are found in extracellular and cell-surface proteins including von Willebrand factor, mucins, and various signaling molecules and receptors. Many VWD domains have a glycine-aspartate-proline-histidine (GDPH) amino-acid sequence motif, which is hydrolytically cleaved post-translationally between the aspartate (Asp) and proline (Pro). The Fc IgG binding protein (FCGBP), found in intestinal mucus secretions and other extracellular environments, contains 13 VWD domains, 11 of which have a GDPH cleavage site. In this study, we investigated the structural and biophysical consequences of Asp-Pro peptide cleavage in a representative FCGBP VWD domain. We found that endogenous Asp-Pro cleavage increases the resistance of the domain to exogenous proteolytic degradation. Tertiary structural interactions made by the newly generated chain termini, as revealed by a crystal structure of an FCGBP segment containing the VWD domain, may explain this observation. Notably, the Gly-Asp peptide bond, upstream of the cleavage site, assumed the cis configuration in the structure. In addition to these local features of the cleavage site, a global organizational difference was seen when comparing the FCGBP segment structure with the numerous other structures containing the same set of domains. Together, these data illuminate the outcome of GDPH cleavage and demonstrate the plasticity of proteins with VWD domains, which may contribute to their evolution for function in a dynamic extracellular environment.
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Affiliation(s)
- Noa Yeshaya
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Prashant Kumar Gupta
- Department of Chemistry and Institute for Nanotechnology & Advanced MaterialsBar‐Ilan UniversityRamat‐GanIsrael
| | - Orly Dym
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - David Morgenstern
- De Botton Institute for Protein Profiling, Nancy and Stephen Grand Israel National Center for Personalized MedicineWeizmann Institute of ScienceRehovotIsrael
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced MaterialsBar‐Ilan UniversityRamat‐GanIsrael
| | - Deborah Fass
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
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2
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Tennenhouse A, Khmelnitsky L, Khalaila R, Yeshaya N, Noronha A, Lindzen M, Makowski EK, Zaretsky I, Sirkis YF, Galon-Wolfenson Y, Tessier PM, Abramson J, Yarden Y, Fass D, Fleishman SJ. Computational optimization of antibody humanness and stability by systematic energy-based ranking. Nat Biomed Eng 2024; 8:30-44. [PMID: 37550425 PMCID: PMC10842793 DOI: 10.1038/s41551-023-01079-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 07/13/2023] [Indexed: 08/09/2023]
Abstract
Conventional methods for humanizing animal-derived antibodies involve grafting their complementarity-determining regions onto homologous human framework regions. However, this process can substantially lower antibody stability and antigen-binding affinity, and requires iterative mutational fine-tuning to recover the original antibody properties. Here we report a computational method for the systematic grafting of animal complementarity-determining regions onto thousands of human frameworks. The method, which we named CUMAb (for computational human antibody design; available at http://CUMAb.weizmann.ac.il ), starts from an experimental or model antibody structure and uses Rosetta atomistic simulations to select designs by energy and structural integrity. CUMAb-designed humanized versions of five antibodies exhibited similar affinities to those of the parental animal antibodies, with some designs showing marked improvement in stability. We also show that (1) non-homologous frameworks are often preferred to highest-homology frameworks, and (2) several CUMAb designs that differ by dozens of mutations and that use different human frameworks are functionally equivalent.
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Affiliation(s)
- Ariel Tennenhouse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Razi Khalaila
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Yeshaya
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ashish Noronha
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Moshit Lindzen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emily K Makowski
- Biointerfaces Institute and Departments of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ira Zaretsky
- Antibody Engineering Unit, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Peter M Tessier
- Biointerfaces Institute and Departments of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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3
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Khmelnitsky L, Milo A, Dym O, Fass D. Diversity of CysD domains in gel-forming mucins. FEBS J 2023; 290:5196-5203. [PMID: 37526947 DOI: 10.1111/febs.16918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023]
Abstract
CysD domains are disulfide-rich modules embedded within long O-glycosylated regions of mucin glycoproteins. CysD domains are thought to mediate intermolecular adhesion during the intracellular bioassembly of mucin polymers and perhaps also after secretion in extracellular mucus hydrogels. The human genome encodes 18 CysD domains distributed across three different mucins. To date, experimental structural information is available only for the first CysD domain (CysD1) of the intestinal mucin MUC2, which is one of the most divergent of the CysDs. To provide experimental data on a CysD that is representative of a larger branch of the fold family, we determined the crystal structure of the seventh CysD domain (CysD7) from MUC5AC, a mucin found in the respiratory tract and stomach. The MUC5AC CysD7 structure revealed a single calcium-binding site, contrasting with the two sites in MUC2 CysD1. The MUC5AC CysD7 structure also contained an additional α-helix absent from MUC2 CysD1, with potential functional implications for intermolecular interactions. Lastly, the experimental structure emphasized the flexibility of the loop analogous to the main adhesion loop of MUC2 CysD1, suggesting that both sequence divergence and physical plasticity in this region may contribute to the adaptation of mucin CysD domains.
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Affiliation(s)
- Lev Khmelnitsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ayala Milo
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Orly Dym
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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4
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Greenberg LJ, Fass D. Shearing of surface mucin saps tumor cell strength. Trends Pharmacol Sci 2023; 44:755-757. [PMID: 37679271 DOI: 10.1016/j.tips.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Aberrant expression of transmembrane mucins promotes tumor progression and interferes with immunological and medicinal elimination of cancer cells. In a recent article, Pedram et al. directed an attenuated bacterial mucin-specific protease to HER2-positive tumor cells and observed decreased tumor growth rates and extended survival of mice bearing HER2-positive tumors.
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Affiliation(s)
| | - Deborah Fass
- Weizmann Institute of Science, Rehovot 7610001, Israel.
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5
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Fass D, Xu Y. Macromolecular assemblies: Molecular mechanisms abound. Curr Opin Struct Biol 2023; 81:102639. [PMID: 37369162 DOI: 10.1016/j.sbi.2023.102639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Affiliation(s)
- Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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6
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Fass D, Thornton DJ. Mucin networks: Dynamic structural assemblies controlling mucus function. Curr Opin Struct Biol 2023; 79:102524. [PMID: 36753925 DOI: 10.1016/j.sbi.2022.102524] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/01/2022] [Accepted: 12/11/2022] [Indexed: 02/08/2023]
Abstract
Contrary to first appearances, mucus structural biology is not an oxymoron. Though mucus hydrogels derive their characteristics largely from intrinsically disordered, heavily glycosylated polypeptide segments, the secreted mucin glycoproteins that constitute mucus undergo an orderly assembly process controlled by folded domains at their termini. Recent structural studies revealed how mucin complexes promote disulphide-mediated polymerization to produce the mucus gel scaffold. Additional protein-protein and protein-glycan interactions likely tune the mesoscale properties, stability, and activities of mucins. Evidence is emerging that even intrinsically disordered glycosylated segments have specific structural roles in the production and properties of mucus. Though soft-matter biophysical approaches to understanding mucus remain highly relevant, high-resolution structural studies of mucins and other mucus components are providing new perspectives on these vital, protective hydrogels.
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Affiliation(s)
- Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David J Thornton
- Wellcome Centre for Cell-Matrix Research and the Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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7
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Ilani T, Reznik N, Yeshaya N, Feldman T, Vilela P, Lansky Z, Javitt G, Shemesh M, Brenner O, Elkis Y, Varsano N, Jaramillo AM, Evans CM, Fass D. The disulfide catalyst QSOX1 maintains the colon mucosal barrier by regulating Golgi glycosyltransferases. EMBO J 2023; 42:e111869. [PMID: 36245281 PMCID: PMC9841341 DOI: 10.15252/embj.2022111869] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 01/27/2023] Open
Abstract
Mucus is made of enormous mucin glycoproteins that polymerize by disulfide crosslinking in the Golgi apparatus. QSOX1 is a catalyst of disulfide bond formation localized to the Golgi. Both QSOX1 and mucins are highly expressed in goblet cells of mucosal tissues, leading to the hypothesis that QSOX1 catalyzes disulfide-mediated mucin polymerization. We found that knockout mice lacking QSOX1 had impaired mucus barrier function due to production of defective mucus. However, an investigation on the molecular level revealed normal disulfide-mediated polymerization of mucins and related glycoproteins. Instead, we detected a drastic decrease in sialic acid in the gut mucus glycome of the QSOX1 knockout mice, leading to the discovery that QSOX1 forms regulatory disulfides in Golgi glycosyltransferases. Sialylation defects in the colon are known to cause colitis in humans. Here we show that QSOX1 redox control of sialylation is essential for maintaining mucosal function.
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Affiliation(s)
- Tal Ilani
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nava Reznik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Yeshaya
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Feldman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Patrick Vilela
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zipora Lansky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gabriel Javitt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Shemesh
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | | | - Neta Varsano
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Ana M Jaramillo
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Christopher M Evans
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, USA.,Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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8
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Javitt G, Yeshaya N, Khmelnitsky L, Fass D. Assembly of von Willebrand factor tubules with in vivo helical parameters requires A1 domain insertion. Blood 2022; 140:2835-2843. [PMID: 36179246 PMCID: PMC10653096 DOI: 10.1182/blood.2022017153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/02/2022] [Accepted: 09/23/2022] [Indexed: 01/05/2023] Open
Abstract
The von Willebrand factor (VWF) glycoprotein is stored in tubular form in Weibel-Palade bodies (WPBs) before secretion from endothelial cells into the bloodstream. The organization of VWF in the tubules promotes formation of covalently linked VWF polymers and enables orderly secretion without polymer tangling. Recent studies have described the high-resolution structure of helical tubular cores formed in vitro by the D1D2 and D'D3 amino-terminal protein segments of VWF. Here we show that formation of tubules with the helical geometry observed for VWF in intracellular WPBs requires also the VWA1 (A1) domain. We reconstituted VWF tubules from segments containing the A1 domain and discovered it to be inserted between helical turns of the tubule, altering helical parameters and explaining the increased robustness of tubule formation when A1 is present. The conclusion from this observation is that the A1 domain has a direct role in VWF assembly, along with its known activity in hemostasis after secretion.
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Affiliation(s)
- Gabriel Javitt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Yeshaya
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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9
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Reznik N, Gallo AD, Rush KW, Javitt G, Fridmann-Sirkis Y, Ilani T, Nairner NA, Fishilevich S, Gokhman D, Chacón KN, Franz KJ, Fass D. Intestinal mucin is a chaperone of multivalent copper. Cell 2022; 185:4206-4215.e11. [PMID: 36206754 DOI: 10.1016/j.cell.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/21/2022] [Accepted: 09/09/2022] [Indexed: 01/26/2023]
Abstract
Mucus protects the epithelial cells of the digestive and respiratory tracts from pathogens and other hazards. Progress in determining the molecular mechanisms of mucus barrier function has been limited by the lack of high-resolution structural information on mucins, the giant, secreted, gel-forming glycoproteins that are the major constituents of mucus. Here, we report how mucin structures we determined enabled the discovery of an unanticipated protective role of mucus: managing the toxic transition metal copper. Using two juxtaposed copper binding sites, one for Cu2+ and the other for Cu1+, the intestinal mucin, MUC2, prevents copper toxicity by blocking futile redox cycling and the squandering of dietary antioxidants, while nevertheless permitting uptake of this important trace metal into cells. These findings emphasize the value of molecular structure in advancing mucosal biology, while introducing mucins, produced in massive quantities to guard extensive mucosal surfaces, as extracellular copper chaperones.
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Affiliation(s)
- Nava Reznik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Annastassia D Gallo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Katherine W Rush
- Department of Chemistry, Reed College, Portland, Oregon 97202, United States; Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Gabriel Javitt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael Fridmann-Sirkis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Ilani
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noa A Nairner
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Gokhman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kelly N Chacón
- Department of Chemistry, Reed College, Portland, Oregon 97202, United States
| | - Katherine J Franz
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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10
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Reznik N, Fass D. Disulfide Bond Formation and Redox Regulation in the Golgi Apparatus. FEBS Lett 2022; 596:2859-2872. [PMID: 36214053 DOI: 10.1002/1873-3468.14510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/06/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022]
Abstract
Formation of disulfide bonds in secreted and cell-surface proteins involves numerous enzymes and chaperones abundant in the endoplasmic reticulum (ER), the first and main site for disulfide bonding in the secretory pathway. Although the Golgi apparatus is the major station after the ER, little is known about thiol-based redox activity in this compartment. QSOX1 and its paralog QSOX2 are the only known Golgi-resident enzymes catalyzing disulfide bonding. Their conservation in animal cells and localization in an organelle downstream of the ER in the secretory pathway has long been puzzling. Recently, it has emerged that QSOX1 regulates particular glycosyltransferases, thereby influencing a central activity of the Golgi. Surprisingly, a few important disulfide-mediated multimerization events occurring in the Golgi were found to be independent of QSOX1. These multimerization events depend, however, on the low pH of the Golgi lumen and secretory granules. We compare and contrast disulfide-mediated multimerization in the ER vs. the Golgi to illustrate the variety of mechanisms controlling covalent supramolecular assembly of secreted proteins.
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Affiliation(s)
- Nava Reznik
- Weizmann Institute of Science, Rehovot, Israel
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11
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Javitt G, Kinzel A, Reznik N, Fass D. Conformational switches and redox properties of the colon cancer-associated human lectin ZG16. FEBS J 2021; 288:6465-6475. [PMID: 34077620 PMCID: PMC9291870 DOI: 10.1111/febs.16044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/16/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022]
Abstract
Zymogen granule membrane protein 16 (ZG16) is produced in organs that secrete large quantities of enzymes and other proteins into the digestive tract. ZG16 binds microbial pathogens, and lower ZG16 expression levels correlate with colorectal cancer, but the physiological function of the protein is poorly understood. One prominent attribute of ZG16 is its ability to bind glycans, but other aspects of the protein may also contribute to activity. An intriguing feature of ZG16 is a CXXC motif at the carboxy terminus. Here, we describe crystal structures and biochemical studies showing that the CXXC motif is on a flexible tail, where it contributes little to structure or stability but is available to engage in redox reactions. Specifically, we demonstrate that the ZG16 cysteine thiols can be oxidized to a disulfide by quiescin sulfhydryl oxidase 1, which is a sulfhydryl oxidase present together with ZG16 in the Golgi apparatus and in mucus, as well as by protein disulfide isomerase. ZG16 crystal structures also draw attention to a nonproline cis peptide bond that can isomerize within the protein and to the mobility of glycine‐rich loops in the glycan‐binding site. An understanding of the properties of the ZG16 CXXC motif and the discovery of internal conformational switches extend existing knowledge relating to the glycan‐binding activity of the protein.
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Affiliation(s)
- Gabriel Javitt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alisa Kinzel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nava Reznik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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12
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13
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Javitt G, Khmelnitsky L, Albert L, Bigman LS, Elad N, Morgenstern D, Ilani T, Levy Y, Diskin R, Fass D. Assembly Mechanism of Mucin and von Willebrand Factor Polymers. Cell 2020; 183:717-729.e16. [PMID: 33031746 PMCID: PMC7599080 DOI: 10.1016/j.cell.2020.09.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/25/2020] [Accepted: 09/08/2020] [Indexed: 12/11/2022]
Abstract
The respiratory and intestinal tracts are exposed to physical and biological hazards accompanying the intake of air and food. Likewise, the vasculature is threatened by inflammation and trauma. Mucin glycoproteins and the related von Willebrand factor guard the vulnerable cell layers in these diverse systems. Colon mucins additionally house and feed the gut microbiome. Here, we present an integrated structural analysis of the intestinal mucin MUC2. Our findings reveal the shared mechanism by which complex macromolecules responsible for blood clotting, mucociliary clearance, and the intestinal mucosal barrier form protective polymers and hydrogels. Specifically, cryo-electron microscopy and crystal structures show how disulfide-rich bridges and pH-tunable interfaces control successive assembly steps in the endoplasmic reticulum and Golgi apparatus. Remarkably, a densely O-glycosylated mucin domain performs an organizational role in MUC2. The mucin assembly mechanism and its adaptation for hemostasis provide the foundation for rational manipulation of barrier function and coagulation.
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Affiliation(s)
- Gabriel Javitt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lev Khmelnitsky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lis Albert
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lavi Shlomo Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nadav Elad
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Morgenstern
- De Botton Institute for Protein Profiling, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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14
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Warszawski S, Borenstein Katz A, Lipsh R, Khmelnitsky L, Ben Nissan G, Javitt G, Dym O, Unger T, Knop O, Albeck S, Diskin R, Fass D, Sharon M, Fleishman SJ. Correction: Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces. PLoS Comput Biol 2020; 16:e1008382. [PMID: 33085658 PMCID: PMC7577468 DOI: 10.1371/journal.pcbi.1008382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Feldman T, Grossman-Haham I, Elkis Y, Vilela P, Moskovits N, Barshack I, Salame TM, Fass D, Ilani T. Correction: Inhibition of fibroblast secreted QSOX1 perturbs extracellular matrix in the tumor microenvironment and decreases tumor growth and metastasis in murine cancer models. Oncotarget 2020; 11:3687. [PMID: 33088428 PMCID: PMC7546759 DOI: 10.18632/oncotarget.27764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Tal Feldman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Iris Grossman-Haham
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Elkis
- Almog Diagnostic, Shoham 6081513, Israel
| | - Patrick Vilela
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Neta Moskovits
- Felsenstein Medical Research Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Iris Barshack
- Institute of Pathology, Sheba Medical Center Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tomer M Salame
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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16
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Abstract
Aims: The post-translational oxidation of methionine to methionine sulfoxide (MetSO) is a reversible process, enabling the repair of oxidative damage to proteins and the use of sulfoxidation as a regulatory switch. MetSO reductases catalyze the stereospecific reduction of MetSO. One of the mammalian MetSO reductases, MsrB3, has a signal sequence for entry into the endoplasmic reticulum (ER). In the ER, MsrB3 is expected to encounter a distinct redox environment compared with its paralogs in the cytosol, nucleus, and mitochondria. We sought to determine the location and arrangement of MsrB3 redox-active cysteines, which may couple MsrB3 activity to other redox events in the ER. Results: We determined the human MsrB3 structure by using X-ray crystallography. The structure revealed that a disulfide bond near the protein amino terminus is distant in space from the active site. Nevertheless, biochemical assays showed that these amino-terminal cysteines are oxidized by the MsrB3 active site after its reaction with MetSO. Innovation: This study reveals a mechanism to shuttle oxidizing equivalents from the primary MsrB3 active site toward the enzyme surface, where they would be available for further dithiol-disulfide exchange reactions. Conclusion: Conformational changes must occur during the MsrB3 catalytic cycle to transfer oxidizing equivalents from the active site to the amino-terminal redox-active disulfide. The accessibility of this exposed disulfide may help couple MsrB3 activity to other dithiol-disulfide redox events in the secretory pathway.
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Affiliation(s)
- Gabriel Javitt
- Department of Structural Biology and Weizmann Institute of Science, Rehovot, Israel
| | - Zhenbo Cao
- Institute of Molecular, Cellular and Systems Biology, CMVLS, University of Glasgow, Glasgow, United Kingdom
| | - Efrat Resnick
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ronen Gabizon
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Neil J Bulleid
- Institute of Molecular, Cellular and Systems Biology, CMVLS, University of Glasgow, Glasgow, United Kingdom
| | - Deborah Fass
- Department of Structural Biology and Weizmann Institute of Science, Rehovot, Israel
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17
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Carter SD, Hampton CM, Langlois R, Melero R, Farino ZJ, Calderon MJ, Li W, Wallace CT, Tran NH, Grassucci RA, Siegmund SE, Pemberton J, Morgenstern TJ, Eisenman L, Aguilar JI, Greenberg NL, Levy ES, Yi E, Mitchell WG, Rice WJ, Wigge C, Pilli J, George EW, Aslanoglou D, Courel M, Freyberg RJ, Javitch JA, Wills ZP, Area-Gomez E, Shiva S, Bartolini F, Volchuk A, Murray SA, Aridor M, Fish KN, Walter P, Balla T, Fass D, Wolf SG, Watkins SC, Carazo JM, Jensen GJ, Frank J, Freyberg Z. Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells. Sci Adv 2020; 6:eaay9572. [PMID: 32270040 PMCID: PMC7112762 DOI: 10.1126/sciadv.aay9572] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/13/2020] [Indexed: 05/21/2023]
Abstract
The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo-electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic β-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells.
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Affiliation(s)
- Stephen D. Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cheri M. Hampton
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Robert Langlois
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Roberto Melero
- Biocomputing Unit, Centro Nacional de Biotecnología–CSIC, Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Zachary J. Farino
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michael J. Calderon
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Callen T. Wallace
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ngoc Han Tran
- HHMI, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert A. Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stephanie E. Siegmund
- Department of Cellular, Molecular and Biophysical Studies, Columbia University Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Joshua Pemberton
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Travis J. Morgenstern
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Leanna Eisenman
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jenny I. Aguilar
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Nili L. Greenberg
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Elana S. Levy
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Edward Yi
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - William G. Mitchell
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | | | | | - Jyotsna Pilli
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Emily W. George
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Despoina Aslanoglou
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maïté Courel
- CNRS-UMR7622, Institut de Biologie Paris-Seine, Université Pierre & Marie Curie, 75252 Paris, France
| | - Robin J. Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jonathan A. Javitch
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Zachary P. Wills
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Allen Volchuk
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sandra A. Murray
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Meir Aridor
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kenneth N. Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Peter Walter
- HHMI, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon G. Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - José María Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología–CSIC, Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Grant J. Jensen
- HHMI, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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18
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Feldman T, Grossman-Haham I, Elkis Y, Vilela P, Moskovits N, Barshack I, Salame TM, Fass D, Ilani T. Inhibition of fibroblast secreted QSOX1 perturbs extracellular matrix in the tumor microenvironment and decreases tumor growth and metastasis in murine cancer models. Oncotarget 2020; 11:386-398. [PMID: 32064042 PMCID: PMC6996906 DOI: 10.18632/oncotarget.27438] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/29/2019] [Indexed: 12/20/2022] Open
Abstract
Extracellular matrix (ECM) plays an important role in tumor development and dissemination, but few points of therapeutic intervention targeting ECM of the tumor microenvironment have been exploited to date. Recent observations suggest that the enzymatic introduction of disulfide bond cross-links into the ECM may be modulated to affect cancer progression. Specifically, the disulfide bond-forming activity of the enzyme Quiescin sulfhydryl oxidase 1 (QSOX1) is required by fibroblasts to assemble ECM components for adhesion and migration of cancer cells. Based on this finding and the increased QSOX1 expression in the stroma of aggressive breast carcinomas, we developed monoclonal antibody inhibitors with the aim of preventing QSOX1 from participating in pro-metastatic ECM remodeling. Here we show that QSOX1 inhibitory antibodies decreased tumor growth and metastasis in murine cancer models and had added benefits when provided together with chemotherapy. Mechanistically, the inhibitors dampened stromal participation in tumor development, as the tumors of treated animals showed fewer myofibroblasts and poorer ECM organization. Thus, our findings demonstrate that specifically targeting excess stromal QSOX1 secreted in response to tumor-cell signaling provides a means to modulate the tumor microenvironment and may complement other therapeutic approaches in cancer.
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Affiliation(s)
- Tal Feldman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Iris Grossman-Haham
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Elkis
- Almog Diagnostic, Shoham 6081513, Israel
| | - Patrick Vilela
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Neta Moskovits
- Felsenstein Medical Research Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Iris Barshack
- Institute of Pathology, Sheba Medical Center Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tomer M Salame
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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19
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Warszawski S, Borenstein Katz A, Lipsh R, Khmelnitsky L, Ben Nissan G, Javitt G, Dym O, Unger T, Knop O, Albeck S, Diskin R, Fass D, Sharon M, Fleishman SJ. Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces. PLoS Comput Biol 2019; 15:e1007207. [PMID: 31442220 PMCID: PMC6728052 DOI: 10.1371/journal.pcbi.1007207] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 09/05/2019] [Accepted: 06/21/2019] [Indexed: 11/18/2022] Open
Abstract
Antibodies developed for research and clinical applications may exhibit suboptimal stability, expressibility, or affinity. Existing optimization strategies focus on surface mutations, whereas natural affinity maturation also introduces mutations in the antibody core, simultaneously improving stability and affinity. To systematically map the mutational tolerance of an antibody variable fragment (Fv), we performed yeast display and applied deep mutational scanning to an anti-lysozyme antibody and found that many of the affinity-enhancing mutations clustered at the variable light-heavy chain interface, within the antibody core. Rosetta design combined enhancing mutations, yielding a variant with tenfold higher affinity and substantially improved stability. To make this approach broadly accessible, we developed AbLIFT, an automated web server that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains (http://AbLIFT.weizmann.ac.il). We applied AbLIFT to two unrelated antibodies targeting the human antigens VEGF and QSOX1. Strikingly, the designs improved stability, affinity, and expression yields. The results provide proof-of-principle for bypassing laborious cycles of antibody engineering through automated computational affinity and stability design. Antibodies are highly important in research, biotechnology, and medical applications. Despite their great utility, however, many antibodies exhibit suboptimal stability and affinity, raising production costs and limiting their practical usefulness. To tackle this general limitation, we used deep mutational scanning to characterize the effects of mutations in an antibody variable fragment on its antigen-binding affinity. Surprisingly, many of the affinity-enhancing mutations clustered at the variable light-heavy chain interface. We, therefore, developed an automated method, called AbLIFT (http://AbLIFT.weizmann.ac.il) to optimize this interface through design. Two unrelated antibodies were tested and showed improvements in expression levels, stability, and antigen-binding affinity. Since AbLIFT requires testing of only a few dozen specific designs, it may dramatically accelerate the development of promising antibodies into useful research and clinical tools.
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Affiliation(s)
- Shira Warszawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rosalie Lipsh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gabriel Javitt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Orly Dym
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Orli Knop
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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20
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Abstract
ATF6 is a major signal transducer for cellular reprogramming in response to protein mis-folding in the endoplasmic reticulum. However, the mechanism by which ATF6 senses unfolded proteins and becomes activated is not yet known. In this issue of The EMBO Journal, Oka et al show that ERp18, a single-domain member of the protein disulfide isomerase family, interacts preferentially with ATF6 under stress conditions and regulates ATF6 transport to the Golgi apparatus. Furthermore, ERp18 impacts the ATF6 cleavage product generated in the Golgi, ultimately determining whether or not ATF6 becomes a functional transcription factor and induces the unfolded protein response.
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Affiliation(s)
- Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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21
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Javitt G, Calvo MLG, Albert L, Reznik N, Ilani T, Diskin R, Fass D. Intestinal Gel-Forming Mucins Polymerize by Disulfide-Mediated Dimerization of D3 Domains. J Mol Biol 2019; 431:3740-3752. [PMID: 31310764 PMCID: PMC6739602 DOI: 10.1016/j.jmb.2019.07.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/03/2019] [Accepted: 07/09/2019] [Indexed: 01/06/2023]
Abstract
The mucin 2 glycoprotein assembles into a complex hydrogel that protects intestinal epithelia and houses the gut microbiome. A major step in mucin 2 assembly is further multimerization of preformed mucin dimers, thought to produce a honeycomb-like arrangement upon hydrogel expansion. Important open questions are how multiple mucin 2 dimers become covalently linked to one another and how mucin 2 multimerization compares with analogous processes in related polymers such as respiratory tract mucins and the hemostasis protein von Willebrand factor. Here we report the x-ray crystal structure of the mucin 2 multimerization module, found to form a dimer linked by two intersubunit disulfide bonds. The dimer structure calls into question the current model for intestinal mucin assembly, which proposes disulfide-mediated trimerization of the same module. Key residues making interactions across the dimer interface are highly conserved in intestinal mucin orthologs, supporting the physiological relevance of the observed quaternary structure. With knowledge of the interface residues, it can be demonstrated that many of these amino acids are also present in other mucins and in von Willebrand factor, further indicating that the stable dimer arrangement reported herein is likely to be shared across this functionally broad protein family. The mucin 2 module structure thus reveals the manner by which both mucins and von Willebrand factor polymerize, drawing deep structural parallels between macromolecular assemblies critical to mucosal epithelia and the vasculature.
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Affiliation(s)
- Gabriel Javitt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Lis Albert
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nava Reznik
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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22
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Lansky Z, Mutsafi Y, Houben L, Ilani T, Armony G, Wolf SG, Fass D. 3D mapping of native extracellular matrix reveals cellular responses to the microenvironment. J Struct Biol X 2019; 1:100002. [PMID: 32055794 PMCID: PMC7001979 DOI: 10.1016/j.yjsbx.2018.100002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/23/2018] [Accepted: 12/07/2018] [Indexed: 01/23/2023]
Abstract
Cells and extracellular matrix (ECM) are mutually interdependent: cells guide self-assembly of ECM precursors, and the resulting ECM architecture supports and instructs cells. Though bidirectional signaling between ECM and cells is fundamental to cell biology, it is challenging to gain high-resolution structural information on cellular responses to the matrix microenvironment. Here we used cryo-scanning transmission electron tomography (CSTET) to reveal the nanometer- to micron-scale organization of major fibroblast ECM components in a native-like context, while simultaneously visualizing internal cell ultrastructure including organelles and cytoskeleton. In addition to extending current models for collagen VI fibril organization, three-dimensional views of thick cell regions and surrounding matrix showed how ECM networks impact the structures and dynamics of intracellular organelles and how cells remodel ECM. Collagen VI and fibronectin were seen to distribute in fundamentally different ways in the cell microenvironment and perform distinct roles in supporting and interacting with cells. This work demonstrates that CSTET provides a new perspective for the study of ECM in cell biology, highlighting labeled extracellular elements against a backdrop of unlabeled but morphologically identifiable cellular features with nanometer resolution detail.
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Affiliation(s)
- Zipora Lansky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Mutsafi
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lothar Houben
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gad Armony
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon G. Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
- Corresponding author.
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23
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Javitt G, Grossman‐Haham I, Alon A, Resnick E, Mutsafi Y, Ilani T, Fass D. cis-Proline mutants of quiescin sulfhydryl oxidase 1 with altered redox properties undermine extracellular matrix integrity and cell adhesion in fibroblast cultures. Protein Sci 2019; 28:228-238. [PMID: 30367560 PMCID: PMC6295897 DOI: 10.1002/pro.3537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 11/13/2022]
Abstract
The thioredoxin superfamily has expanded and diverged extensively throughout evolution such that distant members no longer show appreciable sequence homology. Nevertheless, redox-active thioredoxin-fold proteins functioning in diverse physiological contexts often share canonical amino acids near the active-site (di-)cysteine motif. Quiescin sulfhydryl oxidase 1 (QSOX1), a catalyst of disulfide bond formation secreted by fibroblasts, is a multi-domain thioredoxin superfamily enzyme with certain similarities to the protein disulfide isomerase (PDI) enzymes. Among other potential functions, QSOX1 supports extracellular matrix assembly in fibroblast cultures. We introduced mutations at a cis-proline in QSOX1 that is conserved across the thioredoxin superfamily and was previously observed to modulate redox interactions of the bacterial enzyme DsbA. The resulting QSOX1 variants showed a striking detrimental effect when added exogenously to fibroblasts: they severely disrupted the extracellular matrix and cell adhesion, even in the presence of naturally secreted, wild-type QSOX1. The specificity of this phenomenon for particular QSOX1 mutants inspired an investigation of the effects of mutation on catalytic and redox properties. For a series of QSOX1 mutants, the detrimental effect correlated with the redox potential of the first redox-active site, and an X-ray crystal structure of one of the mutants revealed the reorganization of the cis-proline loop caused by the mutations. Due to the conservation of the mutated residues across the PDI family and beyond, insights obtained in this study may be broadly applicable to a variety of physiologically important redox-active enzymes. IMPACT STATEMENT: We show that mutation of a conserved cis-proline amino acid, analogous to a mutation used to trap substrates of a bacterial disulfide catalyst, has a dramatic effect on the physiological function of the mammalian disulfide catalyst QSOX1. As the active-site region of QSOX1 is shared with the large family of protein disulfide isomerases in humans, the effects of such mutations on redox properties, enzymatic activity, and biological targeting may be relevant across the family.
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Affiliation(s)
- Gabriel Javitt
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Iris Grossman‐Haham
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Assaf Alon
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Efrat Resnick
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Yael Mutsafi
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Tal Ilani
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Deborah Fass
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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24
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Horowitz B, Javitt G, Ilani T, Gat Y, Morgenstern D, Bard FA, Fass D. Quiescin sulfhydryl oxidase 1 (QSOX1) glycosite mutation perturbs secretion but not Golgi localization. Glycobiology 2018; 28:580-591. [PMID: 29757379 DOI: 10.1093/glycob/cwy044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/08/2018] [Indexed: 12/13/2022] Open
Abstract
Quiescin sulfhydryl oxidase 1 (QSOX1) catalyzes the formation of disulfide bonds in protein substrates. Unlike other enzymes with related activities, which are commonly found in the endoplasmic reticulum, QSOX1 is localized to the Golgi apparatus or secreted. QSOX1 is upregulated in quiescent fibroblast cells and secreted into the extracellular environment, where it contributes to extracellular matrix assembly. QSOX1 is also upregulated in adenocarcinomas, though the extent to which it is secreted in this context is currently unknown. To achieve a better understanding of factors that dictate QSOX1 localization and function, we aimed to determine how post-translational modifications affect QSOX1 trafficking and activity. We found a highly conserved N-linked glycosylation site to be required for QSOX1 secretion from fibroblasts and other cell types. Notably, QSOX1 lacking a glycan at this site arrives at the Golgi, suggesting that it passes endoplasmic reticulum quality control but is not further transported to the cell surface for secretion. The QSOX1 transmembrane segment is dispensable for Golgi localization and secretion, as fully luminal and transmembrane variants displayed the same trafficking behavior. This study provides a key example of the effect of glycosylation on Golgi exit and contributes to an understanding of late secretory sorting and quality control.
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Affiliation(s)
- Ben Horowitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gabriel Javitt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yair Gat
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Morgenstern
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Frederic A Bard
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Proteos, Singapore
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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25
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Szekely O, Armony G, Olsen GL, Bigman LS, Levy Y, Fass D, Frydman L. Identification and Rationalization of Kinetic Folding Intermediates for a Low-Density Lipoprotein Receptor Ligand-Binding Module. Biochemistry 2018; 57:4776-4787. [PMID: 29979586 DOI: 10.1021/acs.biochem.8b00466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many mutations that cause familial hypercholesterolemia localize to ligand-binding domain 5 (LA5) of the low-density lipoprotein receptor, motivating investigation of the folding and misfolding of this small, disulfide-rich, calcium-binding domain. LA5 folding is known to involve non-native disulfide isomers, yet these folding intermediates have not been structurally characterized. To provide insight into these intermediates, we used nuclear magnetic resonance (NMR) to follow LA5 folding in real time. We demonstrate that misfolded or partially folded disulfide intermediates are indistinguishable from the unfolded state when focusing on the backbone NMR signals, which provide information on the formation of only the final, native state. However, 13C labeling of cysteine side chains differentiated transient intermediates from the unfolded and native states and reported on disulfide bond formation in real time. The cysteine pairings in a dominant intermediate were identified using 13C-edited three-dimensional NMR, and coarse-grained molecular dynamics simulations were used to investigate the preference of this disulfide set over other non-native arrangements. The transient population of LA5 species with particular non-native cysteine connectitivies during folding supports the conclusion that cysteine pairing is not random and that there is a bias toward certain structural ensembles during the folding process, even prior to the binding of calcium.
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Affiliation(s)
- Or Szekely
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Gad Armony
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Gregory Lars Olsen
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Lavi S Bigman
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Yaakov Levy
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Deborah Fass
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Lucio Frydman
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
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26
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Wolf SG, Mutsafi Y, Dadosh T, Ilani T, Lansky Z, Horowitz B, Rubin S, Elbaum M, Fass D. 3D visualization of mitochondrial solid-phase calcium stores in whole cells. eLife 2017; 6:29929. [PMID: 29106371 PMCID: PMC5703638 DOI: 10.7554/elife.29929] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
The entry of calcium into mitochondria is central to metabolism, inter-organelle communication, and cell life/death decisions. Long-sought transporters involved in mitochondrial calcium influx and efflux have recently been identified. To obtain a unified picture of mitochondrial calcium utilization, a parallel advance in understanding the forms and quantities of mitochondrial calcium stores is needed. We present here the direct 3D visualization of mitochondrial calcium in intact mammalian cells using cryo-scanning transmission electron tomography (CSTET). Amorphous solid granules containing calcium and phosphorus were pervasive in the mitochondrial matrices of a variety of mammalian cell types. Analysis based on quantitative electron scattering revealed that these repositories are equivalent to molar concentrations of dissolved ions. These results demonstrate conclusively that calcium buffering in the mitochondrial matrix in live cells occurs by phase separation, and that solid-phase stores provide a major ion reservoir that can be mobilized for bioenergetics and signaling.
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Affiliation(s)
- Sharon Grayer Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Mutsafi
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zipora Lansky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ben Horowitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Rubin
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Elbaum
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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27
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Abstract
Cysteine thiols are among the most reactive functional groups in proteins, and their pairing in disulfide linkages is a common post-translational modification in proteins entering the secretory pathway. This modest amino acid alteration, the mere removal of a pair of hydrogen atoms from juxtaposed cysteine residues, contrasts with the substantial changes that characterize most other post-translational reactions. However, the wide variety of proteins that contain disulfides, the profound impact of cross-linking on the behavior of the protein polymer, the numerous and diverse players in intracellular pathways for disulfide formation, and the distinct biological settings in which disulfide bond formation can take place belie the simplicity of the process. Here we lay the groundwork for appreciating the mechanisms and consequences of disulfide bond formation in vivo by reviewing chemical principles underlying cysteine pairing and oxidation. We then show how enzymes tune redox-active cofactors and recruit oxidants to improve the specificity and efficiency of disulfide formation. Finally, we discuss disulfide bond formation in a cellular context and identify important principles that contribute to productive thiol oxidation in complex, crowded, dynamic environments.
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Affiliation(s)
- Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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28
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Zhang L, Cheng Q, Zhang L, Wang Y, Merrill GF, Ilani T, Fass D, Arnér ESJ, Zhang J. Serum thioredoxin reductase is highly increased in mice with hepatocellular carcinoma and its activity is restrained by several mechanisms. Free Radic Biol Med 2016; 99:426-435. [PMID: 27581528 DOI: 10.1016/j.freeradbiomed.2016.08.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 02/02/2023]
Abstract
Increased thioredoxin reductase (TrxR) levels in serum were recently identified as possible prognostic markers for human prostate cancer or hepatocellular carcinoma. We had earlier shown that serum levels of TrxR protein are very low in healthy mice, but can in close correlation to alanine aminotransferase (ALT) increase more than 200-fold upon chemically induced liver damage. We also found that enzymatic TrxR activity in serum is counteracted by a yet unidentified oxidase activity in serum. In the present study we found that mice carrying H22 hepatocellular carcinoma tumors present highly increased levels of TrxR in serum, similarly to that reported in human patients. In this case ALT levels did not parallel those of TrxR. We also discovered here that the TrxR-antagonistic oxidase activity in serum is due to the presence of quiescin Q6 sulfhydryl oxidase 1 (QSOX1). We furthermore found that the chemotherapeutic agents cisplatin or auranofin, when given systemically to H22 tumor bearing mice, can further inhibit TrxR activities in serum. The TrxR serum activity was also inhibited by endogenous electrophilic inhibitors, found to increase in tumor-bearing mice and to include protoporphyrin IX (PpIX) and 4-hydroxynonenal (HNE). Thus, hepatocellular carcinoma triggers high levels of serum TrxR that are not paralleled by ALT, and TrxR enzyme activity in serum is counteracted by several different mechanisms. The physiological role of TrxR in serum, if any, as well as its potential value as a prognostic marker for tumor progression, needs to be studied further.
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Affiliation(s)
- Le Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Longjie Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Yijun Wang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Gary F Merrill
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jinsong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China.
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29
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Grossman I, Ilani T, Fleishman SJ, Fass D. Overcoming a species-specificity barrier in development of an inhibitory antibody targeting a modulator of tumor stroma. Protein Eng Des Sel 2016; 29:135-47. [PMID: 26819240 PMCID: PMC4795942 DOI: 10.1093/protein/gzv067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 09/19/2015] [Accepted: 12/14/2015] [Indexed: 12/26/2022] Open
Abstract
The secreted disulfide catalyst Quiescin sulfhydryl oxidase-1 (QSOX1) affects extracellular matrix organization and is overexpressed in various adenocarcinomas and associated stroma. Inhibition of extracellular human QSOX1 by a monoclonal antibody decreased tumor cell migration in a cell co-culture model and hence may have therapeutic potential. However, the species specificity of the QSOX1 monoclonal antibody has been a setback in assessing its utility as an anti-metastatic agent in vivo, a common problem in the antibody therapy industry. We therefore used structurally guided engineering to expand the antibody species specificity, improving its affinity toward mouse QSOX1 by at least four orders of magnitude. A crystal structure of the re-engineered variant, complexed with its mouse antigen, revealed that the antibody accomplishes dual-species targeting through altered contacts between its heavy and light chains, plus replacement of bulky aromatics by flexible side chains and versatile water-bridged polar interactions. In parallel, we produced a surrogate antibody targeting mouse QSOX1 that exhibits a new QSOX1 inhibition mode. This set of three QSOX1 inhibitory antibodies is compatible with various mouse models for pre-clinical trials and biotechnological applications. In this study we provide insights into structural blocks to cross-reactivity and set up guideposts for successful antibody design and re-engineering.
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Affiliation(s)
- Iris Grossman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel Jacob Fleishman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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30
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Wolf SG, Mutsafi Y, Horowitz B, Elbaum M, Fass D. Cryo-Stem Tomography Provides Morphological and Chemical Characterization of Precipitated Calcium-Phosphate Clusters Sequestered in Mitochondria of Intact Vitrified Fibroblasts. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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31
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Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 2015; 84 Suppl 1:34-50. [PMID: 26473983 PMCID: PMC4834066 DOI: 10.1002/prot.24942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/17/2015] [Accepted: 10/11/2015] [Indexed: 11/17/2022]
Abstract
The Critical Assessment of protein Structure Prediction (CASP) experiment would not have been possible without the prediction targets provided by the experimental structural biology community. In this article, selected crystallographers providing targets for the CASP11 experiment discuss the functional and biological significance of the target proteins, highlight their most interesting structural features, and assess whether these features were correctly reproduced in the predictions submitted to CASP11. Proteins 2016; 84(Suppl 1):34–50. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Alex Burgin
- Broad Institute, Cambridge, Massachusetts, 02142
| | | | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, California, 92182.,Department of Computer Science, San Diego State University, San Diego, California, 92182
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Mateusz Korycinski
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | | | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Janet Newman
- Biomedical Manufacturing Program, CSIRO, Parkville, VIC, Australia
| | - Thomas S Peat
- Biomedical Manufacturing Program, CSIRO, Parkville, VIC, Australia
| | - Kurt H Piepenbrink
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Janani Prahlad
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Mark J van Raaij
- Centro Nactional De Biotecnologia (CNB-CSIC), Madrid, E-28049, Spain
| | - Forest Rohwer
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, California, 92182
| | - Anca M Segall
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, California, 92182
| | | | - Eric J Sundberg
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, 21201.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, 21201.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Abhimanyu K Singh
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, 4056, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland.
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32
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Moran T, Gat Y, Fass D. Laminin L4 domain structure resembles adhesion modules in ephrin receptor and other transmembrane glycoproteins. FEBS J 2015; 282:2746-57. [PMID: 25962468 DOI: 10.1111/febs.13319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/07/2015] [Accepted: 05/07/2015] [Indexed: 12/12/2022]
Abstract
UNLABELLED The ~ 800 kDa laminin heterotrimer forms a distinctive cross-shaped structure that further self-assembles into networks within the extracellular matrix. The domains at the laminin chain termini, which engage in network formation and cell-surface interaction, are well understood both structurally and functionally. By contrast, the structures and roles of additional domains embedded within the limbs of the laminin cross have remained obscure. Here, we report the X-ray crystal structure, determined to 1.2 Å resolution, of the human laminin α2 subunit L4b domain, site of an inframe deletion mutation associated with mild congenital muscular dystrophy. The α2 L4b domain is an irregular β-sandwich with many short and broken strands linked by extended loops. The most similar known structures are the carbohydrate-binding domains of bacterial cellulases, the ephrin-binding domain of ephrin receptors, and MAM adhesion domains in various other eukaryotic cell-surface proteins. This similarity to mammalian adhesion modules, which was not predicted on the basis of amino acid sequence alone due to lack of detectable homology, suggests that laminin internal domains evolved from a progenitor adhesion molecule and may retain a role in cell adhesion in the context of the laminin trimer. DATABASE The atomic coordinates and structure factors have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ, USA (http://www.rcsb.org/) under codes 4YEP and 4YEQ.
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Affiliation(s)
- Toot Moran
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yair Gat
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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33
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Kirchenbuechler D, Mutsafi Y, Horowitz B, Levin-Zaidman S, Fass D, G. Wolf S, Elbaum M. Cryo-STEM Tomography of Intact Vitrified Fibroblasts. AIMS Biophysics 2015. [DOI: 10.3934/biophy.2015.3.259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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34
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Fass D, Rittinger K. Editorial overview: Multi-protein assemblies in signaling. Curr Opin Struct Biol 2014; 29:vi-viii. [PMID: 25497899 DOI: 10.1016/j.sbi.2014.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Katrin Rittinger
- National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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35
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Biran S, Gat Y, Fass D. The Eps1p protein disulfide isomerase conserves classic thioredoxin superfamily amino acid motifs but not their functional geometries. PLoS One 2014; 9:e113431. [PMID: 25437863 PMCID: PMC4249923 DOI: 10.1371/journal.pone.0113431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/24/2014] [Indexed: 02/04/2023] Open
Abstract
The widespread thioredoxin superfamily enzymes typically share the following features: a characteristic α-β fold, the presence of a Cys-X-X-Cys (or Cys-X-X-Ser) redox-active motif, and a proline in the cis configuration abutting the redox-active site in the tertiary structure. The Cys-X-X-Cys motif is at the solvent-exposed amino terminus of an α-helix, allowing the first cysteine to engage in nucleophilic attack on substrates, or substrates to attack the Cys-X-X-Cys disulfide, depending on whether the enzyme functions to reduce, isomerize, or oxidize its targets. We report here the X-ray crystal structure of an enzyme that breaks many of our assumptions regarding the sequence-structure relationship of thioredoxin superfamily proteins. The yeast Protein Disulfide Isomerase family member Eps1p has Cys-X-X-Cys motifs and proline residues at the appropriate primary structural positions in its first two predicted thioredoxin-fold domains. However, crystal structures show that the Cys-X-X-Cys of the second domain is buried and that the adjacent proline is in the trans, rather than the cis isomer. In these configurations, neither the “active-site” disulfide nor the backbone carbonyl preceding the proline is available to interact with substrate. The Eps1p structures thus expand the documented diversity of the PDI oxidoreductase family and demonstrate that conserved sequence motifs in common folds do not guarantee structural or functional conservation.
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Affiliation(s)
- Shai Biran
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yair Gat
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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36
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Gat Y, Vardi-Kilshtain A, Grossman I, Major DT, Fass D. Enzyme structure captures four cysteines aligned for disulfide relay. Protein Sci 2014; 23:1102-12. [PMID: 24888638 PMCID: PMC4116658 DOI: 10.1002/pro.2496] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/28/2014] [Accepted: 05/28/2014] [Indexed: 11/09/2022]
Abstract
Thioredoxin superfamily proteins introduce disulfide bonds into substrates, catalyze the removal of disulfides, and operate in electron relays. These functions rely on one or more dithiol/disulfide exchange reactions. The flavoenzyme quiescin sulfhydryl oxidase (QSOX), a catalyst of disulfide bond formation with an interdomain electron transfer step in its catalytic cycle, provides a unique opportunity for exploring the structural environment of enzymatic dithiol/disulfide exchange. Wild-type Rattus norvegicus QSOX1 (RnQSOX1) was crystallized in a conformation that juxtaposes the two redox-active di-cysteine motifs in the enzyme, presenting the entire electron-transfer pathway and proton-transfer participants in their native configurations. As such a state cannot generally be enriched and stabilized for analysis, RnQSOX1 gives unprecedented insight into the functional group environments of the four cysteines involved in dithiol/disulfide exchange and provides the framework for analysis of the energetics of electron transfer in the presence of the bound flavin adenine dinucleotide cofactor. Hybrid quantum mechanics/molecular mechanics (QM/MM) free energy simulations based on the X-ray crystal structure suggest that formation of the interdomain disulfide intermediate is highly favorable and secures the flexible enzyme in a state from which further electron transfer via the flavin can occur.
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Affiliation(s)
- Yair Gat
- Department of Structural Biology, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Alexandra Vardi-Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar Ilan UniversityRamat Gan, 52900, Israel
| | - Iris Grossman
- Department of Structural Biology, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar Ilan UniversityRamat Gan, 52900, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of ScienceRehovot, 76100, Israel
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37
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Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins 2014; 82 Suppl 2:26-42. [PMID: 24318984 PMCID: PMC4072496 DOI: 10.1002/prot.24489] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 11/01/2013] [Accepted: 11/09/2013] [Indexed: 11/12/2022]
Abstract
For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616,
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - Patrick Bales
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - J. Fernando Bazan
- (1) Departments of Protein Engineering and (2) Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, (3) Present address: 44th & Aspen Life Sciences, 924 4th St. N., Stillwater, MN 55082,
| | - Marco Biasini
- (1) Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (2) SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, 4056 Basel, Switzerland;
| | - Alex Burgin
- Broad Institute, 5 Cambridge Center, Cambridge, MA 02142, USA;
| | - Chen Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - Frank V. Cochran
- Department of Biochemistry, Stanford University, Stanford, California, 94305, USA;
| | | | - Rhiju Das
- (1) Department of Biochemistry, Stanford University, Stanford, California, 94305, USA; (2) Department of Physics, Stanford University, Stanford, California, 94305, USA,
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100 Israel, Tel: +972-8-934-3214; Fax: +972-8-934-4136;
| | - Carmela Garcia-Doval
- Centro Nactional de Biotecnologia (CNB-CSIC), calle Darwin 3, E-28049 Madrid, Spain.
| | - Osnat Herzberg
- (1) Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA; (2) Department of Chemistry and Biochemistry, University of Maryland, College Park;
| | - Donald Lorimer
- Emerald Bio, 7869 NE Day Rd W, Bainbridge Isle, WA 98110, USA;
| | - Hartmut Luecke
- Center for Biomembrane Systems and Depts. of Biochemistry, Biophysics & Computer Science, 3205 McGaugh Hall, University of California, Irvine, CA 92697-3900, USA;
| | - Xiaolei Ma
- (1) Departments of Protein Engineering and (2) Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080 (3) Present address: Novartis Institutes for Biomedical Research, 4560 Horton St., Emeryville, CA 94608, USA;
| | - Daniel C. Nelson
- (1) Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA; (2) Department of Veterinary Medicine, University of Maryland, College Park,
| | - Mark J. van Raaij
- Centro Nactional de Biotecnologia (CNB-CSIC), calle Darwin 3, E-28049 Madrid, Spain.
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
| | - Anca Segall
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
| | - Victor Seguritan
- Department of Biology, San Diego State University, San Diego, CA 9218
| | - Kornelius Zeth
- Unidad de Biofisica (CSIC-UPV/EHU), Barrio Sarriena s/n 48940, Leioa, Vizcaya, SPAIN, and IKERBASQUE, Basque Foundation for Science, Bilbao, Spain;
| | - Torsten Schwede
- (1) Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (2) SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, 4056 Basel, Switzerland;
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38
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Abstract
In this issue, Lee et al. (2013) exhibit methionine sulfoxidation in a new light. By bringing together two antagonistic enzymes affecting methionine redox state, the authors demonstrate that methionine oxidation constitutes a reversible, posttranslational regulatory mechanism, akin to protein phosphorylation.
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Affiliation(s)
- Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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39
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Grossman I, Alon A, Ilani T, Fass D. An inhibitory antibody blocks the first step in the dithiol/disulfide relay mechanism of the enzyme QSOX1. J Mol Biol 2013; 425:4366-78. [PMID: 23867277 DOI: 10.1016/j.jmb.2013.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/09/2013] [Indexed: 01/01/2023]
Abstract
Quiescin sulfhydryl oxidase 1 (QSOX1) is a catalyst of disulfide bond formation that undergoes regulated secretion from fibroblasts and is over-produced in adenocarcinomas and other cancers. We have recently shown that QSOX1 is required for incorporation of particular laminin isoforms into the extracellular matrix (ECM) of cultured fibroblasts and, as a consequence, for tumor cell adhesion to and penetration of the ECM. The known role of laminins in integrin-mediated cell survival and motility suggests that controlling QSOX1 activity may provide a novel means of combating metastatic disease. With this motivation, we developed a monoclonal antibody that inhibits the activity of human QSOX1. Here, we present the biochemical and structural characterization of this antibody and demonstrate that it is a tight-binding inhibitor that blocks one of the redox-active sites in the enzyme, but not the site at which de novo disulfides are generated catalytically. Sulfhydryl oxidase activity is thus prevented without direct binding of the sulfhydryl oxidase domain, confirming the model for the interdomain QSOX1 electron transfer mechanism originally surmised based on mutagenesis and protein dissection. In addition, we developed a single-chain variant of the antibody and show that it is a potent QSOX1 inhibitor. The QSOX1 inhibitory antibody will be a valuable tool in studying the role of ECM composition and architecture in cell migration, and the recombinant version may be further developed for potential therapeutic applications based on manipulation of the tumor microenvironment.
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Affiliation(s)
- Iris Grossman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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40
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Ilani T, Alon A, Grossman I, Horowitz B, Kartvelishvily E, Cohen SR, Fass D. A secreted disulfide catalyst controls extracellular matrix composition and function. Science 2013; 341:74-6. [PMID: 23704371 DOI: 10.1126/science.1238279] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Disulfide bond formation in secretory proteins occurs primarily in the endoplasmic reticulum (ER), where multiple enzyme families catalyze cysteine cross-linking. Quiescin sulfhydryl oxidase 1 (QSOX1) is an atypical disulfide catalyst, localized to the Golgi apparatus or secreted from cells. We examined the physiological function for extracellular catalysis of de novo disulfide bond formation by QSOX1. QSOX1 activity was required for incorporation of laminin into the extracellular matrix (ECM) synthesized by fibroblasts, and ECM produced without QSOX1 was defective in supporting cell-matrix adhesion. We developed an inhibitory monoclonal antibody against QSOX1 that could modulate ECM properties and undermine cell migration.
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Affiliation(s)
- Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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41
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Abstract
It has been known for many decades that cell surface, soluble-secreted, and extracellular matrix proteins are generally rich in disulfide bonds, but only more recently has the functional diversity of disulfide bonding in extracellular proteins been appreciated. In addition to the classic mechanisms by which disulfide bonds enhance protein thermodynamic stability, disulfides in certain configurations contribute particular mechanical properties to proteins that sense and respond to tensile forces. Disulfides may help warp protein folds for the evolution of new functions, or they may fasten aggregation-prone flaps of polypeptide to protein surfaces to prevent fibrilization or oligomerization. Disulfides can also be used to package and secure macromolecular cargo for intercellular transport. A series of case studies illustrating diverse biophysical roles of disulfide bonding are reviewed, with a focus on proteins functioning in the extracellular environment.
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Affiliation(s)
- Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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42
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Limor-Waisberg K, Ben-Dor S, Fass D. Diversification of quiescin sulfhydryl oxidase in a preserved framework for redox relay. BMC Evol Biol 2013; 13:70. [PMID: 23510202 PMCID: PMC3616962 DOI: 10.1186/1471-2148-13-70] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/07/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The enzyme family Quiescin Sulfhydryl Oxidase (QSOX) is defined by the presence of an amino-terminal thioredoxin-fold (Trx) domain and a carboxy-terminal Erv family sulfhydryl oxidase domain. QSOX enzymes, which generate disulfide bonds and transfer them to substrate proteins, are present in a wide variety of eukaryotic species including metazoans and plants, but are absent from fungi. Plant and animal QSOXs differ in their active-site amino acid sequences and content of non-catalytic domains. The question arises, therefore, whether the Trx-Erv fusion has the same mechanistic significance in all QSOX enzymes, and whether shared features distinguish the functional domains of QSOX from other instances in which these domains occur independently. Through a study of QSOX phylogeny and an analysis of QSOX sequence diversity in light of recently determined three-dimensional structures, we sought insight into the origin and evolution of this multi-domain redox alliance. RESULTS An updated collection of QSOX enzymes was used to confirm and refine the differences in domain composition and active-site sequence motif patterns of QSOXs belonging to various eukaryotic phyla. Beyond the expected phylogenetic distinction of animal and plant QSOX enzymes, trees based on individual redox-active QSOX domains show a particular distinction of the Trx domain early in plant evolution. A comparison of QSOX domains with Trx and Erv domains from outside the QSOX family revealed several sequence and structural features that clearly differentiate QSOXs from other enzymes containing either of these domains. Notably, these features, present in QSOXs of various phyla, localize to the interface between the Trx and Erv domains observed in structures of QSOX that model interdomain redox communication. CONCLUSIONS The infrastructure for interdomain electron relay, previously identified for animal and parasite QSOXs, is found broadly across the QSOX family, including the plant enzymes. We conclude that the conserved three-dimensional framework of the QSOX catalytic domains accommodates lineage-specific differences and paralog diversification in the amino acid residues surrounding the redox-active cysteines. Our findings indicate that QSOX enzymes are characterized not just by the presence of the two defining domain folds but also by features that promote coordinated activity.
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Affiliation(s)
- Keren Limor-Waisberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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43
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Hakim M, Ezerina D, Alon A, Vonshak O, Fass D. Exploring ORFan domains in giant viruses: structure of mimivirus sulfhydryl oxidase R596. PLoS One 2012; 7:e50649. [PMID: 23209798 PMCID: PMC3509050 DOI: 10.1371/journal.pone.0050649] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/22/2012] [Indexed: 11/25/2022] Open
Abstract
The mimivirus genome contains many genes that lack homologs in the sequence database and are thus known as ORFans. In addition, mimivirus genes that encode proteins belonging to known fold families are in some cases fused to domain-sized segments that cannot be classified. One such ORFan region is present in the mimivirus enzyme R596, a member of the Erv family of sulfhydryl oxidases. We determined the structure of a variant of full-length R596 and observed that the carboxy-terminal region of R596 assumes a folded, compact domain, demonstrating that these ORFan segments can be stable structural units. Moreover, the R596 ORFan domain fold is novel, hinting at the potential wealth of protein structural innovation yet to be discovered in large double-stranded DNA viruses. In the context of the R596 dimer, the ORFan domain contributes to formation of a broad cleft enriched with exposed aromatic groups and basic side chains, which may function in binding target proteins or localization of the enzyme within the virus factory or virions. Finally, we find evidence for an intermolecular dithiol/disulfide relay within the mimivirus R596 dimer, the first such extended, intersubunit redox-active site identified in a viral sulfhydryl oxidase.
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Affiliation(s)
- Motti Hakim
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daria Ezerina
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Alon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ohad Vonshak
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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44
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Limor-Waisberg K, Alon A, Mehlman T, Fass D. Phylogenetics and enzymology of plant quiescin sulfhydryl oxidase. FEBS Lett 2012; 586:4119-25. [PMID: 23068612 DOI: 10.1016/j.febslet.2012.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/30/2012] [Accepted: 10/03/2012] [Indexed: 11/29/2022]
Abstract
Quiescin Sulfhydryl Oxidase (QSOX), a catalyst of disulfide bond formation, is found in both plants and animals. Mammalian, avian, and trypanosomal QSOX enzymes have been studied in detail, but plant QSOX has yet to be characterized. Differences between plant and animal QSOXs in domain composition and active-site sequences raise the question of whether these QSOXs function by the same mechanism. We demonstrate that Arabidopsis thaliana QSOX produced in bacteria is folded and functional as a sulfhydryl oxidase but does not exhibit the interdomain electron transfer observed for its animal counterpart. Based on this finding, further exploration into the respective roles of the redox-active sites in plant QSOX and the reason for their concatenation is warranted.
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Affiliation(s)
- Keren Limor-Waisberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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45
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Moran MS, Yang J, Ma S, Gaudreau B, Higgins SA, Weidhaas JB, Wilson LD, Peschel R, Fass D, Rockwell S. A prospective, multicenter trial of complementary and alternative medicine (CAM) utilization by patients undergoing definitive breast radiotherapy. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.27_suppl.241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
241 Background: A substantial number of breast cancer (BC) pts use complementary and alternative medicines (CAM), but there is a paucity of data on CAM specifically during radiation therapy (RT). The purpose of this study was to prospectively assess the utilization of CAM during RT for BC pts. Methods: 456 pts w/stage 0-III BC were accrued from 5 RT centers from 9/07-2/09. Participating MDs were advised not to discuss CAM. A validated survey instrument was administered during the last week of RT under guidance of a study nurse, which included demographics, details regarding types/doses/frequency of CAM and skin assessments by pt and nurse. Results: 360 pts were eligible for analysis (79%); median age 57 yrs; stage 0-II, 91%; white race 89%; chemotherapy 39%; hormone therapy (HT) w/ RT, 26%; > college education, 59%. CAM was reported in 54% (n = 195), of which 72% reported programs/activities (i.e., Reiki, healing touch, visualization, etc.), and 66% oral/topical CAM. Only 16% reported counseling prior to starting CAM. CAM use did not differ by ethnicity, chemotherapy or stage (all p > 0.05), but correlated significantly with higher education level (p = 0.0001) and inversely correlated w/ HT/RT (p = 0.015). There was a trend towards CAM use in younger pts (p = 0.069). On MVA, education (RC: 1.859; OR: 6.417, 95% CI: 2.023, 20.357, p = 0.002) and HT/RT (RC: -0.530, OR: 0.589, 95% CI: 0.357, 0.970, p = 0.038) independently predicted for CAM use. Rationale for oral/topical: 32% “improve their chance of cure”; 24% “provide treatment-related symptom relief”. For programs/activities: 31% “relaxation/stress reduction”; 11% “reduces treatment-related symptoms”. Despite these beliefs, there were no significant differences between the perception of the pts to nursing skin assessment score as a function of CAM use (p = 0.497). Conclusions: To our knowledge, this is the first and largest prospective study of CAM during RT for BC pts. Given the high prevalence of undocumented CAM use during RT, questions regarding CAM should be considered during consultation and weekly tx visits. A better understanding of CAM practices during RT will facilitate evaluation of potential interactions of CAM and RT for BC.
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Affiliation(s)
- M. S. Moran
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - J. Yang
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - S. Ma
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - B. Gaudreau
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - S. A. Higgins
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - J. B. Weidhaas
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - L. D. Wilson
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - R. Peschel
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - D. Fass
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
| | - S. Rockwell
- Yale University School of Medicine, New Haven, CT; Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT; University of Connecticut, Farmington, CT; Greenwich Hospital, Greenwich, CT
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46
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DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D. Improved molecular replacement by density- and energy-guided protein structure optimization. Nature 2011; 473:540-3. [PMID: 21532589 DOI: 10.1038/nature09964] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 02/22/2011] [Indexed: 11/10/2022]
Abstract
Molecular replacement procedures, which search for placements of a starting model within the crystallographic unit cell that best account for the measured diffraction amplitudes, followed by automatic chain tracing methods, have allowed the rapid solution of large numbers of protein crystal structures. Despite extensive work, molecular replacement or the subsequent rebuilding usually fail with more divergent starting models based on remote homologues with less than 30% sequence identity. Here we show that this limitation can be substantially reduced by combining algorithms for protein structure modelling with those developed for crystallographic structure determination. An approach integrating Rosetta structure modelling with Autobuild chain tracing yielded high-resolution structures for 8 of 13 X-ray diffraction data sets that could not be solved in the laboratories of expert crystallographers and that remained unsolved after application of an extensive array of alternative approaches. We estimate that the new method should allow rapid structure determination without experimental phase information for over half the cases where current methods fail, given diffraction data sets of better than 3.2 Å resolution, four or fewer copies in the asymmetric unit, and the availability of structures of homologous proteins with >20% sequence identity.
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Affiliation(s)
- Frank DiMaio
- University of Washington, Department of Biochemistry and HHMI, Seattle, Washington 98195, USA
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Heldman N, Vonshak O, Sevier CS, Vitu E, Mehlman T, Fass D. Steps in reductive activation of the disulfide-generating enzyme Ero1p. Protein Sci 2011; 19:1863-76. [PMID: 20669236 DOI: 10.1002/pro.473] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ero1p is the primary catalyst of disulfide bond formation in the yeast endoplasmic reticulum (ER). Ero1p contains a pair of essential disulfide bonds that participate directly in the electron transfer pathway from substrate thiol groups to oxygen. Remarkably, elimination of certain other Ero1p disulfides by mutation enhances enzyme activity. In particular, the C150A/C295A Ero1p mutant exhibits increased thiol oxidation in vitro and in vivo and interferes with redox homeostasis in yeast cells by hyperoxidizing the ER. Inhibitory disulfides of Ero1p are thus important for enzyme regulation. To visualize the differences between de-regulated and wild-type Ero1p, we determined the crystal structure of Ero1p C150A/C295A. The structure revealed local changes compared to the wild-type enzyme around the sites of mutation, but no conformational transitions within 25 A of the active site were observed. To determine how the C150--C295 disulfide nonetheless participates in redox regulation of Ero1p, we analyzed using mass spectrometry the changes in Ero1p disulfide connectivity as a function of time after encounter with reducing substrates. We found that the C150--C295 disulfide sets a physiologically appropriate threshold for enzyme activation by guarding a key neighboring disulfide from reduction. This study illustrates the diverse and interconnected roles that disulfides can play in redox regulation of protein activity.
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Affiliation(s)
- Nimrod Heldman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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48
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Abstract
Proteins that have evolved to contain stabilizing disulfide bonds generally fold in a membrane-delimited compartment in the cell [i.e., the endoplasmic reticulum (ER) or the mitochondrial intermembrane space (IMS)]. These compartments contain sulfhydryl oxidase enzymes that catalyze the pairing and oxidation of cysteine residues. In contrast, most proteins in a healthy cytosol are maintained in reduced form through surveillance by NADPH-dependent reductases and the lack of sulfhydryl oxidases. Nevertheless, one of the core functionalities that unify the broad and diverse set of nucleocytoplasmic large DNA viruses (NCLDVs) is the ability to catalyze disulfide formation in the cytosol. The substrates of this activity are proteins that contribute to the assembly, structure, and infectivity of the virions. If the last common ancestor of NCLDVs was present during eukaryogenesis as has been proposed, it is interesting to speculate that viral disulfide bond formation pathways may have predated oxidative protein folding in intracellular organelles.
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Affiliation(s)
- Motti Hakim
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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49
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Kogan K, Spear ED, Kaiser CA, Fass D. Structural conservation of components in the amino acid sensing branch of the TOR pathway in yeast and mammals. J Mol Biol 2010; 402:388-98. [PMID: 20655927 DOI: 10.1016/j.jmb.2010.07.034] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
Abstract
The highly conserved Rag family GTPases have a role in reporting amino acid availability to the TOR (target of rapamycin) signaling complex, which regulates cell growth and metabolism in response to environmental cues. The yeast Rag proteins Gtr1p and Gtr2p were shown in multiple independent studies to interact with the membrane-associated proteins Gse1p (Ego3p) and Gse2p (Ego1p). However, mammalian orthologs of Gse1p and Gse2p could not be identified. We determined the crystal structure of Gse1p and found it to match the fold of two mammalian proteins, MP1 (mitogen-activated protein kinase scaffold protein 1) and p14, which form a heterodimeric complex that had been assigned a scaffolding function in mitogen-activated protein kinase pathways. The significance of this structural similarity is validated by the recent identification of a physical and functional association between mammalian Rag proteins and MP1/p14. Together, these findings reveal that key components of the TOR signaling pathway are structurally conserved between yeast and mammals, despite divergence of sequence to a degree that thwarts detection through simple homology searches.
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Affiliation(s)
- Konstantin Kogan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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50
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Blais JD, Chin KT, Zito E, Zhang Y, Heldman N, Harding HP, Fass D, Thorpe C, Ron D. A small molecule inhibitor of endoplasmic reticulum oxidation 1 (ERO1) with selectively reversible thiol reactivity. J Biol Chem 2010; 285:20993-1003. [PMID: 20442408 PMCID: PMC2898301 DOI: 10.1074/jbc.m110.126599] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/28/2010] [Indexed: 01/29/2023] Open
Abstract
Endoplasmic reticulum oxidation 1 (ERO1) is a conserved eukaryotic flavin adenine nucleotide-containing enzyme that promotes disulfide bond formation by accepting electrons from reduced protein disulfide isomerase (PDI) and passing them on to molecular oxygen. Although disulfide bond formation is an essential process, recent experiments suggest a surprisingly broad tolerance to genetic manipulations that attenuate the rate of disulfide bond formation and that a hyperoxidizing ER may place stressed cells at a disadvantage. In this study, we report on the development of a high throughput in vitro assay for mammalian ERO1alpha activity and its application to identify small molecule inhibitors. The inhibitor EN460 (IC(50), 1.9 mum) interacts selectively with the reduced, active form of ERO1alpha and prevents its reoxidation. Despite rapid and promiscuous reactivity with thiolates, EN460 exhibits selectivity for ERO1. This selectivity is explained by the rapid reversibility of the reaction of EN460 with unstructured thiols, in contrast to the formation of a stable bond with ERO1alpha followed by displacement of bound flavin adenine dinucleotide from the active site of the enzyme. Modest concentrations of EN460 and a functionally related inhibitor, QM295, promote signaling in the unfolded protein response and precondition cells against severe ER stress. Together, these observations point to the feasibility of targeting the enzymatic activity of ERO1alpha with small molecule inhibitors.
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Affiliation(s)
- Jaime D. Blais
- From the Kimmel Center for Biology and Medicine of the Skirball Institute and the Departments of Cell Biology and Medicine, New York University School of Medicine, New York, New York 10016
| | - King-Tung Chin
- From the Kimmel Center for Biology and Medicine of the Skirball Institute and the Departments of Cell Biology and Medicine, New York University School of Medicine, New York, New York 10016
| | - Ester Zito
- From the Kimmel Center for Biology and Medicine of the Skirball Institute and the Departments of Cell Biology and Medicine, New York University School of Medicine, New York, New York 10016
| | - Yuhong Zhang
- From the Kimmel Center for Biology and Medicine of the Skirball Institute and the Departments of Cell Biology and Medicine, New York University School of Medicine, New York, New York 10016
| | - Nimrod Heldman
- the Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, and
| | - Heather P. Harding
- From the Kimmel Center for Biology and Medicine of the Skirball Institute and the Departments of Cell Biology and Medicine, New York University School of Medicine, New York, New York 10016
- the Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Deborah Fass
- the Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, and
| | - Colin Thorpe
- the Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - David Ron
- From the Kimmel Center for Biology and Medicine of the Skirball Institute and the Departments of Cell Biology and Medicine, New York University School of Medicine, New York, New York 10016
- the Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
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