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Thapliyal C, Mishra R. The Chaperone-Active State of HdeB at pH 4 Arises from Its Conformational Rearrangement and Enhanced Stability Instead of Surface Hydrophobicity. Biochemistry 2024; 63:1147-1161. [PMID: 38640496 DOI: 10.1021/acs.biochem.4c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
HdeA and HdeB are dimeric ATP-independent acid-stress chaperones, which protect the periplasmic proteins of enteric bacteria at pH 2.0 and 4.0, respectively, during their passage through the acidic environment of the mammalian stomach. Despite being structurally similar, they exhibit distinct functional pH optima and conformational prerequisite for their chaperone action. HdeA undergoes a dimer-to-monomer transition at pH 2.0, whereas HdeB remains dimeric at pH 4.0. The monomerization of HdeA exposes its hydrophobic motifs, which facilitates its interaction with the partially folded substrates. How HdeB functions despite maintaining its dimeric conformation has been poorly elucidated in the literature. Herein, we characterized the conformational states and stability of HdeB at its physiologically relevant pH and compared the data with those of HdeA. At pH 4.0, HdeB exhibited distinct spectroscopic signatures and higher stability against heat and guanidine-HCl-induced denaturation than at pH 7.5. We affirm that the pH 4.0 conformer of HdeB was distinct from that at pH 7.5 and that these two conformational states were hierarchically unrelated. Salt-bridge mutations that perturbed HdeB's intersubunit interactions resulted in the loss of its stability and function at pH 4.0. In contrast, mutations affecting intrasubunit interactions enhanced its function, albeit with a reduction in stability. These findings suggest that, unlike HdeA, HdeB acts as a noncanonical chaperone, where pH-dependent stability and conformational rearrangement at pH 4.0 play a core role in its chaperone function rather than its surface hydrophobicity. Such rearrangement establishes a stability-function trade-off that allows HdeB to function while maintaining its stable dimeric state.
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Affiliation(s)
- Charu Thapliyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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2
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Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins. Mol Cell 2023; 83:1936-1952.e7. [PMID: 37267908 PMCID: PMC10281453 DOI: 10.1016/j.molcel.2023.05.006] [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: 04/12/2022] [Revised: 01/29/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
Non-native conformations drive protein-misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well suited for elucidating them and their phenotypic effects. Especially intractable are the transient conformations populated by intrinsically disordered proteins. We describe an approach to systematically discover, stabilize, and purify native and non-native conformations, generated in vitro or in vivo, and directly link conformations to molecular, organismal, or evolutionary phenotypes. This approach involves high-throughput disulfide scanning (HTDS) of the entire protein. To reveal which disulfides trap which chromatographically resolvable conformers, we devised a deep-sequencing method for double-Cys variant libraries of proteins that precisely and simultaneously locates both Cys residues within each polypeptide. HTDS of the abundant E. coli periplasmic chaperone HdeA revealed distinct classes of disordered hydrophobic conformers with variable cytotoxicity depending on where the backbone was cross-linked. HTDS can bridge conformational and phenotypic landscapes for many proteins that function in disulfide-permissive environments.
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Affiliation(s)
- Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Victor Y Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kibum Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amir Bitran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sunia A Trauger
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Bogdan Budnik
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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3
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Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep-sequencing of proteins. ARXIV 2023:2204.06159. [PMID: 36776823 PMCID: PMC9915745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Non-native conformations drive protein misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well-suited for elucidating them and their phenotypic effects. Especially intractable are the transient conformations populated by intrinsically disordered proteins. We describe an approach to systematically discover, stabilize, and purify native and non-native conformations, generated in vitro or in vivo, and directly link conformations to molecular, organismal, or evolutionary phenotypes. This approach involves high-throughput disulfide scanning (HTDS) of the entire protein. To reveal which disulfides trap which chromatographically resolvable conformers, we devised a deep-sequencing method for double-Cys variant libraries of proteins that precisely and simultaneously locates both Cys residues within each polypeptide. HTDS of the abundant E. coli periplasmic chaperone HdeA revealed distinct classes of disordered hydrophobic conformers with variable cytotoxicity depending on where the backbone was cross-linked. HTDS can bridge conformational and phenotypic landscapes for many proteins that function in disulfide-permissive environments.
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Affiliation(s)
- Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - Victor Y. Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - Kibum Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - Amir Bitran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | | | - Bogdan Budnik
- Center for Mass Spectrometry, Harvard University, Cambridge, MA
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4
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Nakata Y, Kitazaki Y, Kanaoka H, Shingen E, Uehara R, Hongo K, Kawata Y, Mizobata T. Formation of Fibrils by the Periplasmic Molecular Chaperone HdeB from Escherichia coli. Int J Mol Sci 2022; 23:ijms232113243. [PMID: 36362039 PMCID: PMC9657021 DOI: 10.3390/ijms232113243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
The molecular chaperones HdeA and HdeB of the Escherichia coli (E. coli) periplasm protect client proteins from acid denaturation through a unique mechanism that utilizes their acid denatured states to bind clients. We previously demonstrated that the active, acid-denatured form of HdeA is also prone to forming inactive, amyloid fibril-like aggregates in a pH-dependent, reversible manner. In this study, we report that HdeB also displays a similar tendency to form fibrils at low pH. HdeB fibrils were observed at pH < 3 in the presence of NaCl. Similar to HdeA, HdeB fibrils could be resolubilized by a simple shift to neutral pH. In the case of HdeB, however, we found that after extended incubation at low pH, HdeB fibrils were converted into a form that could not resolubilize at pH 7. Fresh fibrils seeded from these “transformed” fibrils were also incapable of resolubilizing at pH 7, suggesting that the transition from reversible to irreversible fibrils involved a specific conformational change that was transmissible through fibril seeds. Analyses of fibril secondary structure indicated that HdeB fibrils retained significant alpha helical content regardless of the conditions under which fibrils were formed. Fibrils that were formed from HdeB that had been treated to remove its intrinsic disulfide bond also were incapable of resolubilizing at pH 7, suggesting that certain residual structures that are retained in acid-denatured HdeB are important for this protein to recover its soluble state from the fibril form.
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Affiliation(s)
- Yui Nakata
- Department of Chemistry and Biotechnology, Tottori University, Tottori 680-8552, Japan
| | - Yuuto Kitazaki
- Department of Chemistry and Biotechnology, Tottori University, Tottori 680-8552, Japan
| | - Hitomi Kanaoka
- Department of Chemistry and Biotechnology, Tottori University, Tottori 680-8552, Japan
| | - Erika Shingen
- Department of Chemistry and Biotechnology, Tottori University, Tottori 680-8552, Japan
| | - Rina Uehara
- Course of Biotechnology, Graduate School of Sustainable Social Sciences, Tottori University, Tottori 680-8552, Japan
| | - Kunihiro Hongo
- Department of Chemistry and Biotechnology, Tottori University, Tottori 680-8552, Japan
- Course of Biotechnology, Graduate School of Sustainable Social Sciences, Tottori University, Tottori 680-8552, Japan
- Center for Green Sustainable Chemistry, Faculty of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Tottori University, Tottori 680-8552, Japan
- Course of Biotechnology, Graduate School of Sustainable Social Sciences, Tottori University, Tottori 680-8552, Japan
- Center for Green Sustainable Chemistry, Faculty of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Tomohiro Mizobata
- Department of Chemistry and Biotechnology, Tottori University, Tottori 680-8552, Japan
- Course of Biotechnology, Graduate School of Sustainable Social Sciences, Tottori University, Tottori 680-8552, Japan
- Center for Green Sustainable Chemistry, Faculty of Engineering, Tottori University, Tottori 680-8552, Japan
- Correspondence: ; Tel.: +81-857-31-5691
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Wu Q, Liu X, Chai Z, Cheng K, Xu G, Jiang L, Liu M, Li C. Lanmodulin Remains Unfold and Fails to Interact with Lanthanide Ions in Escherichia coli Cells. Chem Commun (Camb) 2022; 58:8230-8233. [DOI: 10.1039/d2cc02038f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the conformation of a newly discovered specific lanthanide ions (Ln3+) binding protein, Lanmodulin (LanM), and its inteaction with Ln3+ in Escherichia coli cells using In-cell NMR. We found...
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Aguirre-Cardenas MI, Geddes-Buehre DH, Crowhurst KA. Removal of disulfide from acid stress chaperone HdeA does not wholly eliminate structure or function at low pH. Biochem Biophys Rep 2021; 27:101064. [PMID: 34307907 PMCID: PMC8258783 DOI: 10.1016/j.bbrep.2021.101064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/10/2021] [Accepted: 06/24/2021] [Indexed: 11/29/2022] Open
Abstract
HdeA is an acid-stress chaperone that operates in the periplasm of various strains of pathogenic gram-negative bacteria. Its primary function is to prevent irreversible aggregation of other periplasmic proteins when the bacteria enter the acidic environment of the stomach after contaminated food is ingested; its role is therefore to help the bacteria survive long enough to enter and colonize the intestines. The mechanism of operation of HdeA is unusual in that this helical homodimer is inactive when folded at neutral pH but becomes activated at low pH after the dimer dissociates and partially unfolds. Studies with chemical reducing agents previously suggested that the intramolecular disulfide bond is important for maintaining residual structure in HdeA at low pH and may be responsible for positioning exposed hydrophobic residues together for the purpose of binding unfolded client proteins. In order to explore its role in HdeA structure and chaperone function we performed a conservative cysteine to serine mutation of the disulfide. We found that, although residual structure is greatly diminished at pH 2 without the disulfide, it is not completely lost; conversely, the mutant is almost completely random coil at pH 6. Aggregation assays showed that mutated HdeA, although less successful as a chaperone than wild type, still maintains a surprising level of function. These studies highlight that we still have much to learn about the factors that stabilize residual structure at low pH and the role of disulfide bonds.
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Affiliation(s)
- M. Imex Aguirre-Cardenas
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St., Northridge, CA, 91330-8262, USA
- Present address: Department of Chemistry, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Dane H. Geddes-Buehre
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St., Northridge, CA, 91330-8262, USA
| | - Karin A. Crowhurst
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St., Northridge, CA, 91330-8262, USA
- Corresponding author.
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7
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Detection of key sites of dimer dissociation and unfolding initiation during activation of acid-stress chaperone HdeA at low pH. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140576. [PMID: 33253897 DOI: 10.1016/j.bbapap.2020.140576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022]
Abstract
HdeA is a small acid-stress chaperone protein with a unique activity profile. At physiological pH, it forms a folded, but inactive, dimer. Below pH 3.0, HdeA unfolds and dissociates into disordered monomers, utilizing exposed hydrophobic patches to bind other unfolded proteins and prevent their irreversible aggregation. In this way, HdeA has a key role in helping pathogenic bacteria survive our acidic stomach and colonize our intestines, facilitating the spread of dysentery. Despite numerous publications on the topic, there remain questions about the mechanism by which HdeA unfolding and activation are triggered. Previous studies usually assessed HdeA unfolding over pH increments that are too far apart to gain fine detail of the process of unfolding and dimer dissociation, and often employed techniques that prevented thorough evaluation of specific regions of the protein. We used a variety of heteronuclear NMR experiments to investigate changes to backbone and side chain structure and dynamics of HdeA at four pHs between 3.0 and 2.0. We found that the long loop in the dimer interface is an early site of initiation of dimer dissociation, and that a molecular "clasp" near the disulfide bond is broken open at low pH as part, or as a trigger, of unfolding; this process also results in the separation of C-terminal helices and exposure of key hydrophobic client binding sites. Our results highlight important regions of HdeA that may have previously been overlooked because they lie too close to the disulfide bond or are thought to be too dynamic in the folded state to influence unfolding processes.
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8
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Pacheco S, Widjaja MA, Gomez JS, Crowhurst KA, Abrol R. The complex role of the N-terminus and acidic residues of HdeA as pH-dependent switches in its chaperone function. Biophys Chem 2020; 264:106406. [PMID: 32593908 PMCID: PMC8276670 DOI: 10.1016/j.bpc.2020.106406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/03/2020] [Accepted: 05/16/2020] [Indexed: 10/24/2022]
Abstract
HdeA is a small acid-stress chaperone protein found in the periplasm of several pathogenic gram-negative bacteria. In neutral pH environments HdeA is an inactive folded homodimer but when exposed to strong acidic environments it partially unfolds and, once activated, binds to other periplasmic proteins, protecting them from irreversible aggregation. Here we use a combination of hydrogen/deuterium exchange NMR experiments and constant pH molecular dynamics simulations to elucidate the role of HdeA's N-terminus in its activation mechanism. Previous work indicates that the N-terminus is flexible and unprotected at high pH while exhibiting interactions with some HdeA client binding site residues. It, however, becomes partially solvent-protected at pH 2.6 - 2.8 and then loses protection again at pH 2.0. This protection is not due to the appearance of new secondary structure, but rather increased contacts between N-terminal residues and the C-terminus of the other protomer in the dimer, as well as concurrent loosening of its hold on the client binding site residues, priming HdeA for interactions with periplasmic client proteins. This work also uncovers unusual protonation profiles of some titratable residues and suggests their complex role in chaperone function.
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Affiliation(s)
- Sayuri Pacheco
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America
| | - Marlyn A Widjaja
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America
| | - Jafaeth S Gomez
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America
| | - Karin A Crowhurst
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America.
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff St., Northridge, CA 91330, United States of America.
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9
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Hu Y, Li C, He L, Jin C, Liu M. Mechanisms of Chaperones as Active Assistant/Protector for Proteins: Insights from NMR Studies. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.201900441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, College of Life Sciences, Peking University Beijing 100871 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
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10
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Yu XC, Hu Y, Ding J, Li H, Jin C. Structural basis and mechanism of the unfolding-induced activation of HdeA, a bacterial acid response chaperone. J Biol Chem 2018; 294:3192-3206. [PMID: 30573682 DOI: 10.1074/jbc.ra118.006398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/17/2018] [Indexed: 11/06/2022] Open
Abstract
The role of protein structural disorder in biological functions has gained increasing attention in the past decade. The bacterial acid-resistant chaperone HdeA belongs to a group of "conditionally disordered" proteins, because it is inactive in its well-structured state and becomes activated via an order-to-disorder transition under acid stress. However, the mechanism for unfolding-induced activation remains unclear because of a lack of experimental information on the unfolded state conformation and the chaperone-client interactions. Herein, we used advanced solution NMR methods to characterize the activated-state conformation of HdeA under acidic conditions and identify its client-binding sites. We observed that the structure of activated HdeA becomes largely disordered and exposes two hydrophobic patches essential for client interactions. Furthermore, using the pH-dependent chemical exchange saturation transfer (CEST) NMR method, we identified three acid-sensitive regions that act as structural locks in regulating the exposure of the two client-binding sites during the activation process, revealing a multistep activation mechanism of HdeA's chaperone function at the atomic level. Our results highlight the role of intrinsic protein disorder in chaperone function and the self-inhibitory role of ordered structures under nonstress conditions, offering new insights for improving our understanding of protein structure-function paradigms.
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Affiliation(s)
- Xing-Chi Yu
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Yunfei Hu
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center
| | - Jienv Ding
- Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences
| | - Hongwei Li
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Changwen Jin
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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11
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Kim J, Choi D, Cha SY, Oh YM, Hwang E, Park C, Ryu KS. Zinc-mediated Reversible Multimerization of Hsp31 Enhances the Activity of Holding Chaperone. J Mol Biol 2018; 430:1760-1772. [PMID: 29709570 DOI: 10.1016/j.jmb.2018.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 04/10/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Abstract
Hsp31 protein, belonging to the DJ-1/ThiJ/PfpI superfamily, increases the survival of Escherichia coli under various stresses. While it was reported as a holding chaperone, Hsp31 was also shown to exhibit the glyoxalase III activity in subsequent study. Here, we describe our finding that Hsp31 undergoes a Zn+2-mediated multimerization (HMWZinc), resulting in an enhanced chaperone activity. Furthermore, it was shown that the formation of HMWZinc is reversible such that the oligomer dissociates into the native dimer by EDTA incubation. We attempted to determine the structural change involving the transition between the native dimer and HMWZinc by adding Ni+2, which is Zn+2-mimetic, producing a potential intermediate structure. An analysis of this intermediate revealed a structure with hydrophobic interior exposed, due to an unfolding of the N-terminal loop and the C-terminal β-to-α region. A treatment with hydrogen peroxide accelerated HMWZinc formation, so that the Hsp31C185E mutant rendered the formation of HMWZinc even at 45 °C. However, the presence of Zn+2 in the catalytic site antagonizes the oxidation of C185, implying a negative role. Our results suggest an unprecedented mechanism of the enhancing chaperone activity by Hsp31, in which the reversible formation of HMWZinc occurs in the presence of heat and Zn+2 ion.
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Affiliation(s)
- Jihong Kim
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea; Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, South Korea
| | - Dongwook Choi
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea; Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, South Korea
| | - So-Young Cha
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Young-Mee Oh
- Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, South Korea
| | - Eunha Hwang
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Chankyu Park
- Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, South Korea.
| | - Kyoung-Seok Ryu
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, South Korea.
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12
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Yu XC, Yang C, Ding J, Niu X, Hu Y, Jin C. Characterizations of the Interactions between Escherichia coli Periplasmic Chaperone HdeA and Its Native Substrates during Acid Stress. Biochemistry 2017; 56:5748-5757. [PMID: 29016106 DOI: 10.1021/acs.biochem.7b00724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial acid-resistant chaperone HdeA is a "conditionally disordered" protein that functions at low pH when it undergoes a transition from a well-folded dimer to an unfolded monomer. The dimer dissociation and unfolding processes result in exposure of hydrophobic surfaces that allows binding to a broad range of client proteins. To fully elucidate the chaperone mechanism of HdeA, it is crucial to understand how the activated HdeA interacts with its native substrates during acid stress. Herein, we present a nuclear magnetic resonance study of the pH-dependent HdeA-substrate interactions. Our results show that the activation of HdeA is not only induced by acidification but also regulated by the presence of unfolded substrates. The variable extent of unfolding of substrates differentially regulates the HdeA-substrate interaction, and the binding further affects the HdeA conformation. Finally, we show that HdeA binds its substrates heterogeneously, and the "amphiphilic" model for HdeA-substrate interaction is discussed.
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Affiliation(s)
- Xing-Chi Yu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Chengfeng Yang
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Jienv Ding
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Changwen Jin
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
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