1
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Amesaka H, Hara M, Sakai Y, Shintani A, Sue K, Yamanaka T, Tanaka S, Furukawa Y. Engineering a monobody specific to monomeric Cu/Zn-superoxide dismutase associated with amyotrophic lateral sclerosis. Protein Sci 2024; 33:e4961. [PMID: 38511674 PMCID: PMC10955725 DOI: 10.1002/pro.4961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024]
Abstract
Misfolding of mutant Cu/Zn-superoxide dismutase (SOD1) has been implicated in familial form of amyotrophic lateral sclerosis (ALS). A natively folded SOD1 forms a tight homodimer, and the dimer dissociation has been proposed to trigger the oligomerization/aggregation of SOD1. Besides increasing demand for probes allowing the detection of monomerized forms of SOD1 in various applications, the development of probes has been limited to conventional antibodies. Here, we have developed Mb(S4) monobody, a small synthetic binding protein based on the fibronectin type III scaffold, that recognizes a monomeric but not dimeric form of SOD1 by performing combinatorial library selections using phage and yeast-surface display methods. Although Mb(S4) was characterized by its excellent selectivity to the monomeric conformation of SOD1, the monomeric SOD1/Mb(S4) complex was not so stable (apparent Kd ~ μM) as to be detected in conventional pull-down experiments. Instead, the complex of Mb(S4) with monomeric but not dimeric SOD1 was successfully trapped by proximity-enabled chemical crosslinking even when reacted in the cell lysates. We thus anticipate that Mb(S4) binding followed by chemical crosslinking would be a useful strategy for in vitro and also ex vivo detection of the monomeric SOD1 proteins.
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Affiliation(s)
- Hiroshi Amesaka
- Department of Biomolecular ChemistryKyoto Prefectural UniversityKyotoJapan
| | - Mizuho Hara
- Department of Biomolecular ChemistryKyoto Prefectural UniversityKyotoJapan
| | - Yuki Sakai
- Department of Biomolecular ChemistryKyoto Prefectural UniversityKyotoJapan
| | | | - Kaori Sue
- Department of ChemistryKeio UniversityYokohamaJapan
| | - Tomoyuki Yamanaka
- Department of Neuroscience of DiseaseBrain Research Institute, Niigata UniversityNiigataJapan
| | - Shun‐ichi Tanaka
- Department of Biomolecular ChemistryKyoto Prefectural UniversityKyotoJapan
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2
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Nakamura I, Amesaka H, Hara M, Yonezawa K, Okamoto K, Kamikubo H, Tanaka S, Matsuo T. Conformation state-specific monobodies regulate the functions of flexible proteins through conformation trapping. Protein Sci 2023; 32:e4813. [PMID: 37861467 PMCID: PMC10659937 DOI: 10.1002/pro.4813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
Synthetic binding proteins have emerged as modulators of protein functions through protein-protein interactions (PPIs). Because PPIs are influenced by the structural dynamics of targeted proteins, investigating whether the synthetic-binders-based strategy is applicable for proteins with large conformational changes is important. This study demonstrates the applicability of monobodies (fibronectin type-III domain-based synthetic binding proteins) in regulating the functions of proteins that undergo tens-of-angstroms-scale conformational changes, using an example of the A55C/C77S/V169C triple mutant (Adktm ; a phosphoryl transfer-catalyzing enzyme with a conformational change between OPEN/CLOSED forms). Phage display successfully developed monobodies that recognize the OPEN form (substrate-unbound form), but not the CLOSED form of Adktm . Two OPEN form-specific clones (OP-2 and OP-4) inhibited Adktm kinase activity. Epitope mapping with a yeast-surface display/flow cytometry indicated that OP-2 binds to the substrate-entry side of Adktm , whereas OP-4 binding occurs at another site. Small angle X-ray scattering coupled with size-exclusion chromatography (SEC-SAXS) indicated that OP-4 binds to the hinge side opposite to the substrate-binding site of Adktm , retaining the whole OPEN-form structure of Adktm . Titration of the OP-4-Adktm complex with Ap5 A, a transition-state analog of Adktm , showed that the conformational shift to the CLOSED form was suppressed although Adktm retained the OPEN-form (i.e., substrate-binding ready form). These results show that OP-4 captures and stabilizes the OPEN-form state, thereby affecting the hinge motion. These experimental results indicate that monobody-based modulators can regulate the functions of proteins that show tens-of-angstroms-scale conformational changes, by trapping specific conformational states generated during large conformational change process that is essential for function exertion.
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Affiliation(s)
- Ibuki Nakamura
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
| | - Hiroshi Amesaka
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Mizuho Hara
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Kento Yonezawa
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
- Center for Digital Green‐innovationNara Institute of Science and Technology (NAIST)NaraJapan
| | - Keisuke Okamoto
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
- Center for Digital Green‐innovationNara Institute of Science and Technology (NAIST)NaraJapan
| | - Shun‐ichi Tanaka
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
- Department of Biotechnology, College of Life SciencesRitsumeikan UniversityKusatsuJapan
| | - Takashi Matsuo
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
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3
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Mizuno A, Toyama T, Ichikawa A, Sakai N, Yoshioka Y, Nishito Y, Toga R, Amesaka H, Kaneko T, Arisawa K, Tsutsumi R, Mita Y, Tanaka SI, Noguchi N, Saito Y. An efficient selenium transport pathway of selenoprotein P utilizing a high-affinity ApoER2 receptor variant and being independent of selenocysteine lyase. J Biol Chem 2023; 299:105009. [PMID: 37406814 PMCID: PMC10407282 DOI: 10.1016/j.jbc.2023.105009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023] Open
Abstract
Selenoprotein P (SeP, encoded by the SELENOP gene) is a plasma protein that contains selenium in the form of selenocysteine residues (Sec, a cysteine analog containing selenium instead of sulfur). SeP functions for the transport of selenium to specific tissues in a receptor-dependent manner. Apolipoprotein E receptor 2 (ApoER2) has been identified as a SeP receptor. However, diverse variants of ApoER2 have been reported, and the details of its tissue specificity and the molecular mechanism of its efficiency remain unclear. In the present study, we found that human T lymphoma Jurkat cells have a high ability to utilize selenium via SeP, while this ability was low in human rhabdomyosarcoma cells. We identified an ApoER2 variant with a high affinity for SeP in Jurkat cells. This variant had a dissociation constant value of 0.67 nM and a highly glycosylated O-linked sugar domain. Moreover, the acidification of intracellular vesicles was necessary for selenium transport via SeP in both cell types. In rhabdomyosarcoma cells, SeP underwent proteolytic degradation in lysosomes and transported selenium in a Sec lyase-dependent manner. However, in Jurkat cells, SeP transported selenium in Sec lyase-independent manner. These findings indicate a preferential selenium transport pathway involving SeP and high-affinity ApoER2 in a Sec lyase-independent manner. Herein, we provide a novel dynamic transport pathway for selenium via SeP.
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Affiliation(s)
- Ayako Mizuno
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Takashi Toyama
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Atsuya Ichikawa
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Naoko Sakai
- The Systems Life Sciences Laboratory, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Yuya Yoshioka
- The Systems Life Sciences Laboratory, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Yukina Nishito
- The Systems Life Sciences Laboratory, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Renya Toga
- Laboratory of Biostructural Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Hiroshi Amesaka
- Laboratory of Biostructural Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Takayuki Kaneko
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kotoko Arisawa
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Ryouhei Tsutsumi
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yuichiro Mita
- The Systems Life Sciences Laboratory, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Shun-Ichi Tanaka
- Laboratory of Biostructural Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan; Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Shiga, Japan
| | - Noriko Noguchi
- The Systems Life Sciences Laboratory, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Yoshiro Saito
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan; The Systems Life Sciences Laboratory, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan.
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4
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Wallon L, Khan I, Teng KW, Koide A, Zuberi M, Li J, Ketavarapu G, Traaseth NJ, O’Bryan JP, Koide S. Inhibition of RAS-driven signaling and tumorigenesis with a pan-RAS monobody targeting the Switch I/II pocket. Proc Natl Acad Sci U S A 2022; 119:e2204481119. [PMID: 36252024 PMCID: PMC9618066 DOI: 10.1073/pnas.2204481119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
RAS mutants are major therapeutic targets in oncology with few efficacious direct inhibitors available. The identification of a shallow pocket near the Switch II region on RAS has led to the development of small-molecule drugs that target this site and inhibit KRAS(G12C) and KRAS(G12D). To discover other regions on RAS that may be targeted for inhibition, we have employed small synthetic binding proteins termed monobodies that have a strong propensity to bind to functional sites on a target protein. Here, we report a pan-RAS monobody, termed JAM20, that bound to all RAS isoforms with nanomolar affinity and demonstrated limited nucleotide-state specificity. Upon intracellular expression, JAM20 potently inhibited signaling mediated by all RAS isoforms and reduced oncogenic RAS-mediated tumorigenesis in vivo. NMR and mutation analysis determined that JAM20 bound to a pocket between Switch I and II, which is similarly targeted by low-affinity, small-molecule inhibitors, such as BI-2852, whose in vivo efficacy has not been demonstrated. Furthermore, JAM20 directly competed with both the RAF(RBD) and BI-2852. These results provide direct validation of targeting the Switch I/II pocket for inhibiting RAS-driven tumorigenesis. More generally, these results demonstrate the utility of tool biologics as probes for discovering and validating druggable sites on challenging targets.
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Affiliation(s)
- Lauren Wallon
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | - Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Kai Wen Teng
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
- Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Mariyam Zuberi
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Jianping Li
- Department of Chemistry, New York University, New York, NY 10003
| | - Gayatri Ketavarapu
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | | | - John P. O’Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016
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5
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Ishikawa E, Ikeda M, Sotoya H, Anbe M, Matsumoto H, Kiwaki M, Hatano H. Molecular characterization and secreted production of basidiomycetous cell-bound β-glycosidases applicable to production of galactooligosaccharides. J Ind Microbiol Biotechnol 2021; 49:6456355. [PMID: 34878143 PMCID: PMC9142197 DOI: 10.1093/jimb/kuab087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022]
Abstract
Cell-bound β-glycosidases of basidiomycetous yeasts show promise as biocatalysts in galactooligosaccharide (GOS) production. Using degenerated primers designed from Hamamotoa singularis (Hs) bglA gene, we newly identified three genes that encode cell-bound β-glycosidase from Sirobasidium magnum (Sm), Rhodotorula minuta (Rm), and Sterigmatomyces elviae (Se). These three genes, also named bglA, encoded family 1 glycosyl hydrolases with molecular masses of 67‒77 kDa. The BglA enzymes were approximately 44% identical to the Hs-BglA enzyme and possessed a unique domain at the N-terminus comprising 110 or 210 amino acids. The Sm-, Rm-, and Se-BglA enzymes as well as the Hs-BglA enzyme were successfully produced by recombinant Aspergillus oryzae, and all enzymes were entirely secreted to the supernatants. Furthermore, addition of some nonionic detergents (e.g. 0.4% [v/v] Triton-X) increased the production, especially of the Hs- or Se-BglA enzyme. Out of the BglA enzymes, the Se-BglA enzyme showed remarkable thermostability (∼70°C). Additionally, the Sm- and Se-BglA enzymes had better GOS yields, so there was less residual lactose than in others. Accordingly, the basidiomycetous BglA enzymes produced by recombinant A. oryzae would be applicable to GOS production, and the Se-BglA enzyme appeared to be the most promising enzyme for industrial uses.
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Affiliation(s)
- Eiji Ishikawa
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo, 186-8650, Japan
| | - Masakazu Ikeda
- Yakult Pharmaceutical Industry Co., Ltd., 5-11 Izumi, Kunitachi-shi, Tokyo, 156-8502, Japan
| | - Hidetsugu Sotoya
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo, 186-8650, Japan
| | - Minako Anbe
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo, 186-8650, Japan
| | | | - Mayumi Kiwaki
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo, 186-8650, Japan
| | - Hiroshi Hatano
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo, 186-8650, Japan
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6
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Li D, Xiong Q, Liang L, Duan H. Multienzyme nanoassemblies: from rational design to biomedical applications. Biomater Sci 2021; 9:7323-7342. [PMID: 34647942 DOI: 10.1039/d1bm01106e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multienzyme nanoassemblies (MENAs) that combine the functions of several enzymes into one entity have attracted widespread research interest due to their improved enzymatic performance and great potential for multiple applications. Considerable progress has been made to design and fabricate MENAs in recent years. This review begins with an introduction of the up-to-date strategies in designing MENAs, mainly including substrate channeling, compartmentalization and control of enzyme stoichiometry. The desirable properties that endow MENAs with important applications are also discussed in detail. Then, the recent advances in utilizing MENAs in the biomedical field are reviewed, with a particular focus on biosensing, tumor therapy, antioxidant and drug delivery. Finally, the challenges and perspectives for development of versatile MENAs are summarized.
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Affiliation(s)
- Di Li
- State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. .,School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qirong Xiong
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
| | - Li Liang
- State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hongwei Duan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
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7
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Yasui N, Nakamura K, Yamashita A. A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins. J Biochem 2021; 169:585-599. [PMID: 33386843 DOI: 10.1093/jb/mvaa147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
Synthetic binding proteins that have the ability to bind with molecules can be generated using various protein domains as non-antibody scaffolds. These designer proteins have been used widely in research studies, as their properties overcome the disadvantages of using antibodies. Here, we describe the first application of a phage display to generate synthetic binding proteins using a sweet protein, monellin, as a non-antibody scaffold. Single-chain monellin (scMonellin), in which two polypeptide chains of natural monellin are connected by a short linker, has two loops on one side of the molecule. We constructed phage display libraries of scMonellin, in which the amino acid sequence of the two loops is diversified. To validate the performance of these libraries, we sorted them against the folding mutant of the green fluorescent protein variant (GFPuv) and yeast small ubiquitin-related modifier. We successfully obtained scMonellin variants exhibiting moderate but significant affinities for these target proteins. Crystal structures of one of the GFPuv-binding variants in complex with GFPuv revealed that the two diversified loops were involved in target recognition. scMonellin, therefore, represents a promising non-antibody scaffold in the design and generation of synthetic binding proteins. We termed the scMonellin-derived synthetic binding proteins 'SWEEPins'.
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Affiliation(s)
- Norihisa Yasui
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuaki Nakamura
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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8
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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9
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Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly. Nat Commun 2021; 12:3805. [PMID: 34155202 PMCID: PMC8217511 DOI: 10.1038/s41467-021-23897-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
Centrioles are evolutionarily conserved multi-protein organelles essential for forming cilia and centrosomes. Centriole biogenesis begins with self-assembly of SAS-6 proteins into 9-fold symmetrical ring polymers, which then stack into a cartwheel that scaffolds organelle formation. The importance of this architecture has been difficult to decipher notably because of the lack of precise tools to modulate the underlying assembly reaction. Here, we developed monobodies against Chlamydomonas reinhardtii SAS-6, characterizing three in detail with X-ray crystallography, atomic force microscopy and cryo-electron microscopy. This revealed distinct monobody-target interaction modes, as well as specific consequences on ring assembly and stacking. Of particular interest, monobody MBCRS6-15 induces a conformational change in CrSAS-6, resulting in the formation of a helix instead of a ring. Furthermore, we show that this alteration impairs centriole biogenesis in human cells. Overall, our findings identify monobodies as powerful molecular levers to alter the architecture of multi-protein complexes and tune centriole assembly.
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10
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Movahedpour A, Ahmadi N, Ghalamfarsa F, Ghesmati Z, Khalifeh M, Maleksabet A, Shabaninejad Z, Taheri-Anganeh M, Savardashtaki A. β-Galactosidase: From its source and applications to its recombinant form. Biotechnol Appl Biochem 2021; 69:612-628. [PMID: 33656174 DOI: 10.1002/bab.2137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Carbohydrate-active enzymes are a group of important enzymes playing a critical role in the degradation and synthesis of carbohydrates. Glycosidases can hydrolyze glycosides into oligosaccharides, polysaccharides, and glycoconjugates via a cost-effective approach. Lactase is an important member of β-glycosidases found in higher plants, animals, and microorganisms. β-Galactosidases can be used to degrade the milk lactose for making lactose-free milk, which is sweeter than regular milk and is suitable for lactose-intolerant people. β-Galactosidase is employed by many food industries to degrade lactose and improve the digestibility, sweetness, solubility, and flavor of dairy products. β-Galactosidase enzymes have various families and are applied in the food-processing industries such as hydrolyzed-milk products, whey, and galactooligosaccharides. Thus, this enzyme is a valuable protein which is now produced by recombinant technology. In this review, origins, structure, recombinant production, and critical modifications of β-galactosidase for improving the production process are discussed. Since β-galactosidase is a valuable enzyme in industry and health care, a study of its various aspects is important in industrial biotechnology and applied biochemistry.
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Affiliation(s)
- Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahid Ahmadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farideh Ghalamfarsa
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Ghesmati
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoomeh Khalifeh
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mortaza Taheri-Anganeh
- Shahid Arefian Hospital, Urmia, Iran.,Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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11
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Tanaka SI, Tsutaki M, Yamamoto S, Mizutani H, Kurahashi R, Hirata A, Takano K. Exploring mutable conserved sites and fatal non-conserved sites by random mutation of esterase from Sulfolobus tokodaii and subtilisin from Thermococcus kodakarensis. Int J Biol Macromol 2020; 170:343-353. [PMID: 33383075 DOI: 10.1016/j.ijbiomac.2020.12.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
Homologous proteins differ in their amino acid sequences at several positions. Generally, conserved sites are recognized as not suitable for amino acid substitution, and thus in evolutionary protein engineering, non-conserved sites are often selected as mutation sites. However, there have also been reports of possible mutations in conserved sites. In this study, we explored mutable conserved sites and immutable non-conserved sites by testing random mutations of two thermostable proteins, an esterase from Sulfolobus tokodaii (Sto-Est) and a subtilisin from Thermococcus kodakarensis (Tko-Sub). The subtilisin domain of Tko-Sub needs Ca2+ ions and the propeptide domain for stability, folding and maturation. The results from the two proteins showed that about one-third of the mutable sites were detected in conserved sites and some non-conserved sites lost enzymatic activity at high temperatures due to mutation. Of the conserved sites in Sto-Est, the sites on the loop, on the surface, and far from the active site are more resistant to mutation. In Tko-Sub, the sites flanking Ca2+-binding sites and propeptide were undesirable for mutation. The results presented here serve as an index for selecting mutation sites and contribute to the expansion of available sequence range by introducing mutations at conserved sites.
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Affiliation(s)
- Shun-Ichi Tanaka
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Minami Tsutaki
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Seira Yamamoto
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hayate Mizutani
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Ryo Kurahashi
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Azumi Hirata
- Department of Anatomy and Cell Biology, Osaka Medical College, Daigaku-machi, Takatsuki, Osaka 569-8686, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.
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12
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β-Galactosidases: A great tool for synthesizing galactose-containing carbohydrates. Biotechnol Adv 2020; 39:107465. [DOI: 10.1016/j.biotechadv.2019.107465] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/26/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022]
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13
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Benkoulouche M, Fauré R, Remaud-Siméon M, Moulis C, André I. Harnessing glycoenzyme engineering for synthesis of bioactive oligosaccharides. Interface Focus 2019; 9:20180069. [PMID: 30842872 DOI: 10.1098/rsfs.2018.0069] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2018] [Indexed: 12/13/2022] Open
Abstract
Combined with chemical synthesis, the use of glycoenzyme biocatalysts has shown great synthetic potential over recent decades owing to their remarkable versatility in terms of substrates and regio- and stereoselectivity that allow structurally controlled synthesis of carbohydrates and glycoconjugates. Nonetheless, the lack of appropriate enzymatic tools with requisite properties in the natural diversity has hampered extensive exploration of enzyme-based synthetic routes to access relevant bioactive oligosaccharides, such as cell-surface glycans or prebiotics. With the remarkable progress in enzyme engineering, it has become possible to improve catalytic efficiency and physico-chemical properties of enzymes but also considerably extend the repertoire of accessible catalytic reactions and tailor novel substrate specificities. In this review, we intend to give a brief overview of the advantageous use of engineered glycoenzymes, sometimes in combination with chemical steps, for the synthesis of natural bioactive oligosaccharides or their precursors. The focus will be on examples resulting from the three main classes of glycoenzymes specialized in carbohydrate synthesis: glycosyltransferases, glycoside hydrolases and glycoside phosphorylases.
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Affiliation(s)
- Mounir Benkoulouche
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
| | - Régis Fauré
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
| | - Magali Remaud-Siméon
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
| | - Claire Moulis
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
| | - Isabelle André
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
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14
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Affiliation(s)
- Ariel L. Furst
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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15
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Lancaster L, Abdallah W, Banta S, Wheeldon I. Engineering enzyme microenvironments for enhanced biocatalysis. Chem Soc Rev 2018; 47:5177-5186. [PMID: 29796541 DOI: 10.1039/c8cs00085a] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein engineering provides a means to alter protein structure leading to new functions. Much work has focused on the engineering of enzyme active sites to enhance catalytic activity, however there is an increasing trend towards engineering other aspects of biocatalysts as these efforts can also lead to useful improvements. This tutorial discusses recent advances in engineering an enzyme's local chemical and physical environment, with the goal of enhancing enzyme reaction kinetics, substrate selectivity, and activity in harsh conditions (e.g., low or high pH). By introducing stimuli-responsiveness to these enzyme modifications, dynamic control of activity also becomes possible. These new biomolecular and protein engineering techniques are separate and independent from traditional active site engineering and can therefore be applied synergistically to create new biocatalyst technologies with novel functions.
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Affiliation(s)
- Louis Lancaster
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA.
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16
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Tanaka SI, Takahashi T, Koide A, Iwamoto R, Koikeda S, Koide S. Monobody-Mediated Alteration of Lipase Substrate Specificity. ACS Chem Biol 2018; 13:1487-1492. [PMID: 29757606 DOI: 10.1021/acschembio.8b00384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Controlling the catalytic properties of enzymes remain an important challenge in chemistry and biotechnology. We have recently established a strategy for altering enzyme specificity in which the addition of proxy monobodies, synthetic binding proteins, modulates the specificity of an otherwise unmodified enzyme. Here, in order to examine its broader applicability, we employed the strategy on Candida rugosa lipase 1 (CRL1), an enzyme with a tunnel-like substrate binding site. We successfully identified proxy monobodies that restricted the substrate specificity of CRL1 toward short-chain fatty acids. The successes with this enzyme system and a β-galactosidase used in the previous work suggest that our strategy can be applied to diverse enzymes with distinct architectures of substrate binding sites.
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Affiliation(s)
- Shun-ichi Tanaka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu 509-0109, Japan
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-higashi, Shiga 525-8577, Japan
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Shiga 525-8577, Japan
| | - Tetsuya Takahashi
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu 509-0109, Japan
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York 10016, United States
- Department of Medicine, New York University School of Medicine, New York, New York 10016, United States
| | - Riki Iwamoto
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Shiga 525-8577, Japan
| | - Satoshi Koikeda
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu 509-0109, Japan
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York 10016, United States
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, United States
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17
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Abstract
Over the past two decades, hundreds of new somatic mutations have been identified in tumours, and a few dozen novel cancer therapeutics that selectively target these mutated oncoproteins have entered clinical practice. This development has resulted in clinical breakthroughs for a few tumour types, but more commonly patients' overall survival has not improved because of the development of drug resistance. Furthermore, only a very limited number of oncoproteins, largely protein kinases, are successfully targeted, whereas most non-kinase oncoproteins inside cancer cells remain untargeted. Engineered small protein inhibitors offer great promise in targeting a larger variety of oncoproteins with better efficacy and higher selectivity. In this article, I focus on a promising class of synthetic binding proteins, termed monobodies, that we have shown to inhibit previously untargetable protein-protein interactions in different oncoproteins. I will discuss the great promise alongside the technical challenges inherent in converting monobodies from potent pre-clinical target validation tools to next-generation protein-based therapeutics.
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Affiliation(s)
- Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
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18
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Yin H, Pijning T, Meng X, Dijkhuizen L, van Leeuwen SS. Biochemical Characterization of the Functional Roles of Residues in the Active Site of the β-Galactosidase from Bacillus circulans ATCC 31382. Biochemistry 2017; 56:3109-3118. [PMID: 28538097 PMCID: PMC5481816 DOI: 10.1021/acs.biochem.7b00207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/14/2017] [Indexed: 12/29/2022]
Abstract
The β-galactosidase enzyme from Bacillus circulans ATCC 31382 BgaD is widely used in the food industry to produce prebiotic galactooligosaccharides (GOS). Recently, the crystal structure of a C-terminally truncated version of the enzyme (BgaD-D) has been elucidated. The roles of active site amino acid residues in β-galactosidase enzyme reaction and product specificity have remained unknown. On the basis of a structural alignment of the β-galactosidase enzymes BgaD-D from B. circulans and BgaA from Streptococcus pneumoniae, and the complex of BgaA with LacNAc, we identified eight active site amino acid residues (Arg185, Asp481, Lys487, Tyr511, Trp570, Trp593, Glu601, and Phe616) in BgaD-D. This study reports an investigation of the functional roles of these residues, using site-directed mutagenesis, and a detailed biochemical characterization and product profile analysis of the mutants obtained. The data show that these residues are involved in binding and positioning of the substrate and thus determine the BgaD-D activity and product linkage specificity. This study provides detailed insights into the structure-function relationships of the B. circulans BgaD-D enzyme, especially regarding GOS product linkage specificity, allowing the rational mutation of β-galactosidase enzymes to produce specific mixtures of GOS structures.
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Affiliation(s)
- Huifang Yin
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tjaard Pijning
- Biophysical
Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xiangfeng Meng
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sander S. van Leeuwen
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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19
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Rizk SS, Mukherjee S, Koide A, Koide S, Kossiakoff AA. Targeted rescue of cancer-associated IDH1 mutant activity using an engineered synthetic antibody. Sci Rep 2017; 7:556. [PMID: 28373671 PMCID: PMC5429742 DOI: 10.1038/s41598-017-00728-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/10/2017] [Indexed: 01/01/2023] Open
Abstract
We have utilized a high-diversity phage display library to engineer antibody fragments (Fabs) that can modulate the activity of the enzyme isocitrate dehydrogenase 1 (IDH1). We show that a conformation-specific Fab can reactivate an IDH1 mutant associated with brain tumors. The results show that this strategy is a first step towards developing "activator drugs" for a large number of genetic disorders where mutations have disrupted protein function.
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Affiliation(s)
- Shahir S Rizk
- Department of Chemistry and Biochemistry, Indiana University South Bend, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, South Bend, Indiana, USA.
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Akiko Koide
- Perlmutter Cancer Cener, New York University Langone Medical Center, New York, USA.,Department of Medicine, New York University School of Medicine, New York, USA
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Perlmutter Cancer Cener, New York University Langone Medical Center, New York, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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20
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Chavan T, Maduke M, Swartz K. Protein ligands for studying ion channel proteins. J Gen Physiol 2017; 149:407-411. [PMID: 28270405 PMCID: PMC5379924 DOI: 10.1085/jgp.201711776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chavan et al. highlight work showing that a monobody can inhibit a fluoride channel using a mechanism similar to that of a scorpion toxin blocker of potassium channels.
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Affiliation(s)
- Tanmay Chavan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Kenton Swartz
- Molecular Physiology and Biophysics Section, John Edward Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
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21
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Kükenshöner T, Schmit NE, Bouda E, Sha F, Pojer F, Koide A, Seeliger M, Koide S, Hantschel O. Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. J Mol Biol 2017; 429:1364-1380. [PMID: 28347651 PMCID: PMC5417323 DOI: 10.1016/j.jmb.2017.03.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/20/2017] [Accepted: 03/20/2017] [Indexed: 12/17/2022]
Abstract
The binding of Src-homology 2 (SH2) domains to phosphotyrosine (pY) sites is critical for the autoinhibition and substrate recognition of the eight Src family kinases (SFKs). The high sequence conservation of the 120 human SH2 domains poses a significant challenge to selectively perturb the interactions of even the SFK SH2 family against the rest of the SH2 domains. We have developed synthetic binding proteins, termed monobodies, for six of the SFK SH2 domains with nanomolar affinity. Most of these monobodies competed with pY ligand binding and showed strong selectivity for either the SrcA (Yes, Src, Fyn, Fgr) or SrcB subgroup (Lck, Lyn, Blk, Hck). Interactome analysis of intracellularly expressed monobodies revealed that they bind SFKs but no other SH2-containing proteins. Three crystal structures of monobody-SH2 complexes unveiled different and only partly overlapping binding modes, which rationalized the observed selectivity and enabled structure-based mutagenesis to modulate inhibition mode and selectivity. In line with the critical roles of SFK SH2 domains in kinase autoinhibition and T-cell receptor signaling, monobodies binding the Src and Hck SH2 domains selectively activated respective recombinant kinases, whereas an Lck SH2-binding monobody inhibited proximal signaling events downstream of the T-cell receptor complex. Our results show that SFK SH2 domains can be targeted with unprecedented potency and selectivity using monobodies. They are excellent tools for dissecting SFK functions in normal development and signaling and to interfere with aberrant SFK signaling networks in cancer cells.
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Affiliation(s)
- Tim Kükenshöner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Nadine Eliane Schmit
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Emilie Bouda
- Department of Pharmacological Sciences, Stony Brook University, BST 8-140, Stony Brook, NY 11794-8651, USA
| | - Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Florence Pojer
- Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, 430 East 29th Street, New York, NY 10016, USA; Department of Medicine, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA
| | - Markus Seeliger
- Department of Pharmacological Sciences, Stony Brook University, BST 8-140, Stony Brook, NY 11794-8651, USA
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, 430 East 29th Street, New York, NY 10016, USA; Department of Medicine, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA.
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland.
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22
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Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci 2017; 26:910-924. [PMID: 28249355 PMCID: PMC5405424 DOI: 10.1002/pro.3148] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/20/2023]
Abstract
Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in‐depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, often leading to new mechanistic insights. We propose that synthetic proteins will become powerful standard tools in diverse areas of protein science, biotechnology and medicine.
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Affiliation(s)
- Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016.,Department of Biochemistry and Molecular Pharmacology New York University School of Medicine, New York, NY, 10016
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23
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Yin H, Pijning T, Meng X, Dijkhuizen L, van Leeuwen SS. Engineering of the Bacillus circulans β-Galactosidase Product Specificity. Biochemistry 2017; 56:704-711. [PMID: 28092444 PMCID: PMC5330655 DOI: 10.1021/acs.biochem.7b00032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/22/2022]
Abstract
Microbial β-galactosidase enzymes are widely used as biocatalysts in industry to produce prebiotic galactooligosaccharides (GOS) from lactose. GOS mixtures are used as beneficial additives in infant formula to mimic the prebiotic effects of human milk oligosaccharides (hMOS). The structural variety in GOS mixtures is significantly lower than in hMOS. Since this structural complexity is considered as the basis for the multiple biological functions of hMOS, it is important to broaden the variety of GOS structures. In this study, residue R484 near +1 subsite of the C-terminally truncated β-galactosidase from Bacillus circulans (BgaD-D) was subjected to site saturation mutagenesis. Especially the R484S and R484H mutant enzymes displayed significantly altered enzyme specificity, leading to a new type of GOS mixture with altered structures and linkage types. The GOS mixtures produced by these mutant enzymes contained 14 structures that were not present in the wild-type enzyme GOS mixture; 10 of these are completely new structures. The GOS produced by these mutant enzymes contained a combination of (β1 → 3) and (β1 → 4) linkages, while the wild-type enzyme has a clear preference toward (β1 → 4) linkages. The yield of the trisaccharide β-d-Galp-(1 → 3)-β-d-Galp-(1 → 4)-d-Glcp produced by mutants R484S and R484H increased 50 times compared to that of the wild-type enzyme. These results indicate that residue R484 is crucial for the linkage specificity of BgaD-D. This is the first study showing that β-galactosidase enzyme engineering results in an altered GOS linkage specificity and product mixture. The more diverse GOS mixtures produced by these engineered enzymes may find industrial applications.
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Affiliation(s)
- Huifang Yin
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tjaard Pijning
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xiangfeng Meng
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sander S. van Leeuwen
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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24
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Bowman A, Koide A, Goodman JS, Colling ME, Zinne D, Koide S, Ladurner AG. sNASP and ASF1A function through both competitive and compatible modes of histone binding. Nucleic Acids Res 2016; 45:643-656. [PMID: 28123037 PMCID: PMC5314797 DOI: 10.1093/nar/gkw892] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/19/2016] [Accepted: 10/04/2016] [Indexed: 02/07/2023] Open
Abstract
Histone chaperones are proteins that interact with histones to regulate the thermodynamic process of nucleosome assembly. sNASP and ASF1 are conserved histone chaperones that interact with histones H3 and H4 and are found in a multi-chaperoning complex in vivo. Previously we identified a short peptide motif within H3 that binds to the TPR domain of sNASP with nanomolar affinity. Interestingly, this peptide motif is sequestered within the known ASF1–H3–H4 interface, raising the question of how these two proteins are found in complex together with histones when they share the same binding site. Here, we show that sNASP contains at least two additional histone interaction sites that, unlike the TPR–H3 peptide interaction, are compatible with ASF1A binding. These surfaces allow ASF1A to form a quaternary complex with both sNASP and H3–H4. Furthermore, we demonstrate that sNASP makes a specific complex with H3 on its own in vitro, but not with H4, suggesting that it could work upstream of ASF1A. Further, we show that sNASP and ASF1A are capable of folding an H3–H4 dimer in vitro under native conditions. These findings reveal a network of binding events that may promote the entry of histones H3 and H4 into the nucleosome assembly pathway.
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Affiliation(s)
- Andrew Bowman
- Biomedical Center Munich, Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Jay S Goodman
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Meaghan E Colling
- Biomedical Center Munich, Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Daria Zinne
- Biomedical Center Munich, Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Andreas G Ladurner
- Biomedical Center Munich, Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Butenandt Str. 5-13, 81377 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, Feodor Lynen Str. 17, 81377 Munich, Germany
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25
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Bruce VJ, Ta AN, McNaughton BR. Minimalist Antibodies and Mimetics: An Update and Recent Applications. Chembiochem 2016; 17:1892-1899. [DOI: 10.1002/cbic.201600303] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Virginia J. Bruce
- Department of Chemistry; Colorado State University; Fort Collins CO 80523 USA
| | - Angeline N. Ta
- Department of Chemistry; Colorado State University; Fort Collins CO 80523 USA
| | - Brian R. McNaughton
- Department of Chemistry; Colorado State University; Fort Collins CO 80523 USA
- Department of Biochemistry and Molecular Biology; Colorado State University; Fort Collins CO 80523 USA
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