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Ning J, Sala M, Reina J, Kalagiri R, Hunter T, McCullough BS. Histidine Phosphorylation: Protein Kinases and Phosphatases. Int J Mol Sci 2024; 25:7975. [PMID: 39063217 PMCID: PMC11277029 DOI: 10.3390/ijms25147975] [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: 06/07/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Phosphohistidine (pHis) is a reversible protein post-translational modification (PTM) that is currently poorly understood. The P-N bond in pHis is heat and acid-sensitive, making it more challenging to study than the canonical phosphoamino acids pSer, pThr, and pTyr. As advancements in the development of tools to study pHis have been made, the roles of pHis in cells are slowly being revealed. To date, a handful of enzymes responsible for controlling this modification have been identified, including the histidine kinases NME1 and NME2, as well as the phosphohistidine phosphatases PHPT1, LHPP, and PGAM5. These tools have also identified the substrates of these enzymes, granting new insights into previously unknown regulatory mechanisms. Here, we discuss the cellular function of pHis and how it is regulated on known pHis-containing proteins, as well as cellular mechanisms that regulate the activity of the pHis kinases and phosphatases themselves. We further discuss the role of the pHis kinases and phosphatases as potential tumor promoters or suppressors. Finally, we give an overview of various tools and methods currently used to study pHis biology. Given their breadth of functions, unraveling the role of pHis in mammalian systems promises radical new insights into existing and unexplored areas of cell biology.
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Affiliation(s)
- Jia Ning
- Correspondence: (J.N.); (B.S.M.)
| | | | | | | | | | - Brandon S. McCullough
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (M.S.); (J.R.); (R.K.); (T.H.)
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2
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Tossounian MA, Hristov SD, Semelak JA, Yu BYK, Baczynska M, Zhao Y, Estrin DA, Trujillo M, Filonenko V, Gouge J, Gout I. A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1. Int J Mol Sci 2023; 24:9359. [PMID: 37298313 PMCID: PMC10253429 DOI: 10.3390/ijms24119359] [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: 04/09/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Coenzyme A (CoA) is a key cellular metabolite which participates in diverse metabolic pathways, regulation of gene expression and the antioxidant defense mechanism. Human NME1 (hNME1), which is a moonlighting protein, was identified as a major CoA-binding protein. Biochemical studies showed that hNME1 is regulated by CoA through both covalent and non-covalent binding, which leads to a decrease in the hNME1 nucleoside diphosphate kinase (NDPK) activity. In this study, we expanded the knowledge on previous findings by focusing on the non-covalent mode of CoA binding to the hNME1. With X-ray crystallography, we solved the CoA bound structure of hNME1 (hNME1-CoA) and determined the stabilization interactions CoA forms within the nucleotide-binding site of hNME1. A hydrophobic patch stabilizing the CoA adenine ring, while salt bridges and hydrogen bonds stabilizing the phosphate groups of CoA were observed. With molecular dynamics studies, we extended our structural analysis by characterizing the hNME1-CoA structure and elucidating possible orientations of the pantetheine tail, which is absent in the X-ray structure due to its flexibility. Crystallographic studies suggested the involvement of arginine 58 and threonine 94 in mediating specific interactions with CoA. Site-directed mutagenesis and CoA-based affinity purifications showed that arginine 58 mutation to glutamate (R58E) and threonine 94 mutation to aspartate (T94D) prevent hNME1 from binding to CoA. Overall, our results reveal a unique mode by which hNME1 binds CoA, which differs significantly from that of ADP binding: the α- and β-phosphates of CoA are oriented away from the nucleotide-binding site, while 3'-phosphate faces catalytic histidine 118 (H118). The interactions formed by the CoA adenine ring and phosphate groups contribute to the specific mode of CoA binding to hNME1.
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Affiliation(s)
- Maria-Armineh Tossounian
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (S.D.H.); (B.Y.K.Y.); (M.B.); (Y.Z.); (I.G.)
| | - Stefan Denchev Hristov
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (S.D.H.); (B.Y.K.Y.); (M.B.); (Y.Z.); (I.G.)
| | - Jonathan Alexis Semelak
- Departmento de Química Inorgánica Analítica y Química Física, Instituto de Química Física de los Materiales, Medioambiente y Energía (INQUIMAE) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, Pab. 2 C1428EHA, Buenos Aires 1865, Argentina; (J.A.S.); (D.A.E.)
| | - Bess Yi Kun Yu
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (S.D.H.); (B.Y.K.Y.); (M.B.); (Y.Z.); (I.G.)
| | - Maria Baczynska
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (S.D.H.); (B.Y.K.Y.); (M.B.); (Y.Z.); (I.G.)
| | - Yuhan Zhao
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (S.D.H.); (B.Y.K.Y.); (M.B.); (Y.Z.); (I.G.)
| | - Dario Ariel Estrin
- Departmento de Química Inorgánica Analítica y Química Física, Instituto de Química Física de los Materiales, Medioambiente y Energía (INQUIMAE) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, Pab. 2 C1428EHA, Buenos Aires 1865, Argentina; (J.A.S.); (D.A.E.)
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay;
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Valeriy Filonenko
- Department of Cell Signaling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine;
| | - Jerome Gouge
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (S.D.H.); (B.Y.K.Y.); (M.B.); (Y.Z.); (I.G.)
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (S.D.H.); (B.Y.K.Y.); (M.B.); (Y.Z.); (I.G.)
- Department of Cell Signaling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine;
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Stepwise oxidations play key roles in the structural and functional regulations of DJ-1. Biochem J 2021; 478:3505-3525. [PMID: 34515295 DOI: 10.1042/bcj20210245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
DJ-1 is known to play neuroprotective roles by eliminating reactive oxygen species (ROS) as an antioxidant protein. However, the molecular mechanism of DJ-1 function has not been well elucidated. This study explored the structural and functional changes of DJ-1 in response to oxidative stress. Human DJ-1 has three cysteine residues (Cys46, Cys53 and Cys106). We found that, in addition to Cys106, Cys46 is the most reactive cysteine residue in DJ-1, which was identified employing an NPSB-B chemical probe (Ctag) that selectively reacts with redox-sensitive cysteine sulfhydryl. Peroxidatic Cys46 readily formed an intra-disulfide bond with adjacent resolving Cys53, which was identified with nanoUPLC-ESI-q-TOF tandem mass spectrometry (MS/MS) employing DBond algorithm under the non-reducing condition. Mutants (C46A and C53A), not forming Cys46-Cys53 disulfide cross-linking, increased oxidation of Cys106 to sulfinic and sulfonic acids. Furthermore, we found that DJ-1 C46A mutant has distorted unstable structure identified by biochemical assay and employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS) analysis. All three Cys mutants lost antioxidant activities in SN4741 cell, a dopaminergic neuronal cell, unlike WT DJ-1. These findings suggest that all three Cys residues including Cys46-Cys53 disulfide cross-linking are required for maintaining the structural integrity, the regulation process and cellular function as an antioxidant protein. These studies broaden the understanding of regulatory mechanisms of DJ-1 that operate under oxidative conditions.
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Yu BYK, Tossounian MA, Hristov SD, Lawrence R, Arora P, Tsuchiya Y, Peak-Chew SY, Filonenko V, Oxenford S, Angell R, Gouge J, Skehel M, Gout I. Regulation of metastasis suppressor NME1 by a key metabolic cofactor coenzyme A. Redox Biol 2021; 44:101978. [PMID: 33903070 PMCID: PMC8212152 DOI: 10.1016/j.redox.2021.101978] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/28/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023] Open
Abstract
The metastasis suppressor protein NME1 is an evolutionarily conserved and multifunctional enzyme that plays an important role in suppressing the invasion and metastasis of tumour cells. The nucleoside diphosphate kinase (NDPK) activity of NME1 is well recognized in balancing the intracellular pools of nucleotide diphosphates and triphosphates to regulate cytoskeletal rearrangement and cell motility, endocytosis, intracellular trafficking, and metastasis. In addition, NME1 was found to function as a protein-histidine kinase, 3′-5′ exonuclease and geranyl/farnesyl pyrophosphate kinase. These diverse cellular functions are regulated at the level of expression, post-translational modifications, and regulatory interactions. The NDPK activity of NME1 has been shown to be inhibited in vitro and in vivo under oxidative stress, and the inhibitory effect mediated via redox-sensitive cysteine residues. In this study, affinity purification followed by mass spectrometric analysis revealed NME1 to be a major coenzyme A (CoA) binding protein in cultured cells and rat tissues. NME1 is also found covalently modified by CoA (CoAlation) at Cys109 in the CoAlome analysis of HEK293/Pank1β cells treated with the disulfide-stress inducer, diamide. Further analysis showed that recombinant NME1 is efficiently CoAlated in vitro and in cellular response to oxidising agents and metabolic stress. In vitro CoAlation of recombinant wild type NME1, but not the C109A mutant, results in the inhibition of its NDPK activity. Moreover, CoA also functions as a competitive inhibitor of the NME1 NDPK activity by binding non-covalently to the nucleotide binding site. Taken together, our data reveal metastasis suppressor protein NME1 as a novel binding partner of the key metabolic regulator CoA, which inhibits its nucleoside diphosphate kinase activity via non-covalent and covalent interactions. NME1 is a major CoA-binding protein. CoA can bind NME1 through covalent and non-covalent interactions. NME1 CoAlation is induced by oxidative and metabolic stress in mammalian cells. CoA inhibits the NDPK activity of NME1 in vitro.
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Affiliation(s)
- Bess Yi Kun Yu
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Maria-Armineh Tossounian
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Stefan Denchev Hristov
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Ryan Lawrence
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Pallavi Arora
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Yugo Tsuchiya
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Sew Yeu Peak-Chew
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Valeriy Filonenko
- Department of Cell Signaling, Institute of Molecular Biology and Genetics, Kyiv, 143, Ukraine
| | - Sally Oxenford
- School of Pharmacy, University College London, London, WC1N 1AX, United Kingdom
| | - Richard Angell
- School of Pharmacy, University College London, London, WC1N 1AX, United Kingdom
| | - Jerome Gouge
- Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, United Kingdom
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom; Department of Cell Signaling, Institute of Molecular Biology and Genetics, Kyiv, 143, Ukraine.
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5
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Activation of Nm23-H1 to suppress breast cancer metastasis via redox regulation. Exp Mol Med 2021; 53:346-357. [PMID: 33753879 PMCID: PMC8080780 DOI: 10.1038/s12276-021-00575-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/21/2020] [Accepted: 01/12/2021] [Indexed: 02/05/2023] Open
Abstract
Non-metastatic protein 23 H1 (Nm23-H1), a housekeeping enzyme, is a nucleoside diphosphate kinase-A (NDPK-A). It was the first identified metastasis suppressor protein. Nm23-H1 prolongs disease-free survival and is associated with a good prognosis in breast cancer patients. However, the molecular mechanisms underlying the role of Nm23-H1 in biological processes are still not well understood. This is a review of recent studies focusing on controlling NDPK activity based on the redox regulation of Nm23-H1, structural, and functional changes associated with the oxidation of cysteine residues, and the relationship between NDPK activity and cancer metastasis. Further understanding of the redox regulation of the NDPK function will likely provide a new perspective for developing new strategies for the activation of NDPK-A in suppressing cancer metastasis.
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Yu L, Wang X, Zhang W, Khan E, Lin C, Guo C. The multiple regulation of metastasis suppressor NM23-H1 in cancer. Life Sci 2021; 268:118995. [PMID: 33421524 DOI: 10.1016/j.lfs.2020.118995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 10/22/2022]
Abstract
Metastasis is one of the leading causes of mortality in cancer patients. As the firstly identified metastasis suppressor, NM23-H1 has been endowed with expectation as a potent target in metastatic cancer therapy during the past decades. However, many challenges impede its clinical use. Accumulating evidence shows that NM23-H1 has a dichotomous role in tumor metastasis as a suppressor and promoter. It has potentially attributed to its versatile biochemical characteristics such as nucleoside diphosphate kinase (NDPK) activity, histidine kinase activity (HPK), exonuclease activity, and protein scaffold, which further augment the complexity and uncertainty of its physiological function. Simultaneously, tumor cells have evolved multiple ways to regulate the expression and function of NM23-H1 during tumorigenesis and metastasis. This review summarized and discussed the regulatory mechanisms of NM23-H1 in cancer including transcriptional activation, subcellular location, enzymatic activity, and protein degradation, which significantly modulate its anti-metastatic function.
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Affiliation(s)
- Liting Yu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Xindong Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Wanheng Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China; School of Engineering, China Pharmaceutical University, Nanjing, PR China
| | - Eshan Khan
- Department of Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Chenyu Lin
- Department of Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Changying Guo
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China.
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7
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Adam K, Ning J, Reina J, Hunter T. NME/NM23/NDPK and Histidine Phosphorylation. Int J Mol Sci 2020; 21:E5848. [PMID: 32823988 PMCID: PMC7461546 DOI: 10.3390/ijms21165848] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022] Open
Abstract
The NME (Non-metastatic) family members, also known as NDPKs (nucleoside diphosphate kinases), were originally identified and studied for their nucleoside diphosphate kinase activities. This family of kinases is extremely well conserved through evolution, being found in prokaryotes and eukaryotes, but also diverges enough to create a range of complexity, with homologous members having distinct functions in cells. In addition to nucleoside diphosphate kinase activity, some family members are reported to possess protein-histidine kinase activity, which, because of the lability of phosphohistidine, has been difficult to study due to the experimental challenges and lack of molecular tools. However, over the past few years, new methods to investigate this unstable modification and histidine kinase activity have been reported and scientific interest in this area is growing rapidly. This review presents a global overview of our current knowledge of the NME family and histidine phosphorylation, highlighting the underappreciated protein-histidine kinase activity of NME family members, specifically in human cells. In parallel, information about the structural and functional aspects of the NME family, and the knowns and unknowns of histidine kinase involvement in cell signaling are summarized.
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Affiliation(s)
| | | | | | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (K.A.); (J.N.); (J.R.)
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8
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Li Y, Liu W, Saini V, Wong YH. Mutations at the dimer interface and surface residues of Nm23-H1 metastasis suppressor affect its expression and function. Mol Cell Biochem 2020; 474:95-112. [PMID: 32705629 DOI: 10.1007/s11010-020-03836-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/11/2020] [Indexed: 11/25/2022]
Abstract
The Nm23 metastasis suppressor family is involved in a variety of physiological and pathological processes including cell proliferation, differentiation, tumorigenesis, and metastasis. Given that Nm23 proteins may function as hexamers composed of different members of the family, especially Nm23-H1 and H2 isoforms, it is pertinent to assess the importance of interface and surface residues in defining the functional characteristics of Nm23 proteins. Using molecular modeling to identify clusters of residues that may affect dimer formation and isoform specificity, mutants of Nm23-H1 were constructed and assayed for their ability to modulate cell migration. Mutations of dimer interface residues Gly22 and Lys39 affected the expression level of Nm23-H1, without altering the transcript level. The reduced protein expression was not due to increased protein degradation or altered subcellular distribution. Substitution of the surface residues of Nm23-H1 with Nm23-H2-specific Ser131 and/or Lys124/135 affected the electrophoretic mobility of the protein. Moreover, in cell migration assays, several mutants with altered surface residues exhibited impaired ability to suppress the mobility of MDA-MB-231 cells. Collectively, the study suggests that disrupting the dimer interface may affect the expression of Nm23-H1, while the residues at α-helix and β-sheet on the surface of Nm23-H1 may contribute to its metastasis suppressive function.
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Affiliation(s)
- Yuanjun Li
- Division of Life Science and the Biotechnology Research Institute, Hong Kong University of Science and Technology, Hong Kong, China.,Eye Center of Xiangya Hospital, Hunan Key Laboratory of Opthalmology, Xiangya Hospital, Central South University, Changsha, China
| | - Wen Liu
- Division of Life Science and the Biotechnology Research Institute, Hong Kong University of Science and Technology, Hong Kong, China
| | - Vasu Saini
- Division of Life Science and the Biotechnology Research Institute, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yung H Wong
- Division of Life Science and the Biotechnology Research Institute, Hong Kong University of Science and Technology, Hong Kong, China. .,State Key Laboratory of Molecular Neuroscience and the Molecular Neuroscience Center, Hong Kong University of Science and Technology, Hong Kong, China.
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9
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Na S, Lee JJ, Joo JWJ, Lee KJ, Paek E. deMix: Decoding Deuterated Distributions from Heterogeneous Protein States via HDX-MS. Sci Rep 2019; 9:3176. [PMID: 30816214 PMCID: PMC6395696 DOI: 10.1038/s41598-019-39512-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/28/2019] [Indexed: 01/15/2023] Open
Abstract
Characterization of protein structural changes in response to protein modifications, ligand or chemical binding, or protein-protein interactions is essential for understanding protein function and its regulation. Amide hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) is one of the most favorable tools for characterizing the protein dynamics and changes of protein conformation. However, currently the analysis of HDX-MS data is not up to its full power as it still requires manual validation by mass spectrometry experts. Especially, with the advent of high throughput technologies, the data size grows everyday and an automated tool is essential for the analysis. Here, we introduce a fully automated software, referred to as ‘deMix’, for the HDX-MS data analysis. deMix deals directly with the deuterated isotopic distributions, but not considering their centroid masses and is designed to be robust over random noises. In addition, unlike the existing approaches that can only determine a single state from an isotopic distribution, deMix can also detect a bimodal deuterated distribution, arising from EX1 behavior or heterogeneous peptides in conformational isomer proteins. Furthermore, deMix comes with visualization software to facilitate validation and representation of the analysis results.
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Affiliation(s)
- Seungjin Na
- Dept. of Computer Science, Hanyang University, Seoul, 04763, South Korea
| | - Jae-Jin Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, South Korea
| | - Jong Wha J Joo
- Dept. of Computer Science and Engineering, Dongguk University-Seoul, Seoul, 04620, South Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, South Korea
| | - Eunok Paek
- Dept. of Computer Science, Hanyang University, Seoul, 04763, South Korea.
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Kielkopf CS, Ghosh M, Anand GS, Brown SHJ. HDX-MS reveals orthosteric and allosteric changes in apolipoprotein-D structural dynamics upon binding of progesterone. Protein Sci 2018; 28:365-374. [PMID: 30353968 DOI: 10.1002/pro.3534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Abstract
Apolipoprotein-D is a glycosylated tetrameric lipocalin that binds and transports small hydrophobic molecules such as progesterone and arachidonic acid. Like other lipocalins, apolipoprotein-D adopts an eight-stranded β-barrel fold stabilized by two intramolecular disulphide bonds, with an adjacent α-helix. Crystallography studies of recombinant apolipoprotein-D demonstrated no major conformational changes upon progesterone binding. Amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) reports structural changes of proteins in solution by monitoring exchange of amide hydrogens in the protein backbone with deuterium. HDX-MS detects changes in conformation and structural dynamics in response to protein function such as ligand binding that may go undetected in X-ray crystallography, making HDX-MS an invaluable orthogonal technique. Here, we report an HDX-MS protocol for apolipoprotein-D that solved challenges of high protein rigidity and low pepsin cleavage using rigorous quenching conditions and longer deuteration times, yielding 85% sequence coverage and 50% deuterium exchange. The relative fractional deuterium exchange of ligand-free apolipoprotein-D revealed apolipoprotein-D to be a highly structured protein. Progesterone binding was detected by significant reduction in deuterium exchange in eight peptides. Stabilization of apolipoprotein-D dynamics can be interpreted as a combined orthosteric effect in the ligand binding pocket and allosteric effect at the N-terminus and C-terminus. Together, our experiments provide insight into apolipoprotein-D structural dynamics and map the effects of progesterone binding that are relayed to distal parts of the protein. The observed stabilization of apolipoprotein-D dynamics upon progesterone binding demonstrates a common behaviour in the lipocalin family and may have implications for interactions of apolipoprotein-D with receptors or lipoprotein particles. Statement: We reveal for the first time how apolipoprotein-D, which is protective in Alzheimer's disease, becomes more ordered when bound to a molecule of steroid hormone. These results significantly extend the understanding of apolipoprotein-D structure from X-ray crystallography studies by incorporating information on how protein motion changes over time. To achieve these results an improved protocol was developed, suitable for proteins similar to apolipoprotein-D, to elucidate how proteins change flexibility when binding to small molecules.
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Affiliation(s)
- Claudia S Kielkopf
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia.,Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia.,School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Madhubrata Ghosh
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Simon H J Brown
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia.,Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia.,School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
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11
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Zhu X, Poghosyan E, Rezabkova L, Mehall B, Sakakibara H, Hirono M, Kamiya R, Ishikawa T, Yang P. The roles of a flagellar HSP40 ensuring rhythmic beating. Mol Biol Cell 2018; 30:228-241. [PMID: 30427757 PMCID: PMC6589562 DOI: 10.1091/mbc.e18-01-0047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
HSP40s are regarded as cochaperones, perpetually shuttling client polypeptides to HSP70s for refolding. However, many HSP40s that are central for disparate processes diverge from this paradigm. To elucidate the noncanonical mechanisms, we investigated HSP40 in the radial spoke (RS) complex in flagella. Disruption of the gene by the MRC1 transposon in Chlamydomonas resulted in jerky flagella. Traditional electron microscopy, cryo-electron tomography, and sub-tomogram analysis revealed RSs of various altered morphologies that, unexpectedly, differed between the two RS species. This indicates that HSP40 locks the RS into a functionally rigid conformation, facilitating its interactions with the adjacent central pair apparatus for transducing locally varied mechanical feedback, which permits rhythmic beating. Missing HSP40, like missing RSs, could be restored in a tip-to-base direction when HSP40 mutants fused with a HSP40 donor cell. However, without concomitant de novo RS assembly, the repair was exceedingly slow, suggesting HSP40/RS-coupled intraflagellar trafficking and assembly. Biochemical analysis and modeling uncovered spoke HSP40’s cochaperone traits. On the basis of our data, we propose that HSP40 accompanies its client RS precursor when traveling to the flagellar tip. Upon arrival, both refold in concert to assemble into the mature configuration. HSP40’s roles in chaperoning and structural maintenance shed new light on its versatility and flagellar biology.
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Affiliation(s)
- Xiaoyan Zhu
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Emiliya Poghosyan
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Bridget Mehall
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Hitoshi Sakakibara
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Hyogo 651-2492, Japan
| | - Masafumi Hirono
- Department of Frontier Bioscience, Hosei University, Tokyo 184-8584, Japan
| | - Ritsu Kamiya
- Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
| | - Takashi Ishikawa
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
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12
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Lee JJ, Kim HS, Lee JS, Park J, Shin SC, Song S, Lee E, Choi JE, Suh JW, Lee H, Kim EE, Seo EK, Shin DH, Lee HY, Lee HY, Lee KJ. Small molecule activator of Nm23/NDPK as an inhibitor of metastasis. Sci Rep 2018; 8:10909. [PMID: 30026594 PMCID: PMC6053448 DOI: 10.1038/s41598-018-29101-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/27/2018] [Indexed: 12/02/2022] Open
Abstract
Nm23-H1/NDPK-A is a tumor metastasis suppressor having NDP kinase (NDPK) activity. Nm23-H1 is positively associated with prolonged disease-free survival and good prognosis of cancer patients. Approaches to increasing the cellular levels of Nm23-H1 therefore have significance in the therapy of metastatic cancers. We found a small molecule, (±)-trans-3-(3,4-dimethoxyphenyl)-4-[(E)-3,4-dimethoxystyryl]cyclohex-1-ene, that activates Nm23, hereafter called NMac1. NMac1 directly binds to Nm23-H1 and increases its NDPK activity. Employing various NMac1 derivatives and hydrogen/deuterium mass spectrometry (HDX-MS), we identified the pharmacophore and mode of action of NMac1. We found that NMac1 binds to the C-terminal of Nm23-H1 and induces the NDPK activation through its allosteric conformational changes. NMac1-treated MDA-MB-231 breast cancer cells showed dramatic changes in morphology and actin-cytoskeletal organization following inhibition of Rac1 activation. NMac1 also suppressed invasion and migration in vitro, and metastasis in vivo, in a breast cancer mouse model. NMac1 as an activator of NDPK has potential as an anti-metastatic agent.
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Affiliation(s)
- Jae-Jin Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea
| | - Hwang Suk Kim
- Department of Chemistry, Korea Advanced Institute of Science & Technology, Daejeon, 34141, Korea
| | - Ji-Sun Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jimin Park
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea
| | - Sang Chul Shin
- Biomedical Research Institute, Korea Institute of Science & Technology, Seoul, 02792, Korea
| | - Soonwha Song
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea
| | - Eunsun Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea
| | - Jung-Eun Choi
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea
| | - Ji-Wan Suh
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea
| | - Hongsoo Lee
- Department of Chemistry, Korea Advanced Institute of Science & Technology, Daejeon, 34141, Korea
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science & Technology, Seoul, 02792, Korea
| | - Eun Kyoung Seo
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea
| | - Dong Hae Shin
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea
| | - Ho-Young Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hee-Yoon Lee
- Department of Chemistry, Korea Advanced Institute of Science & Technology, Daejeon, 34141, Korea.
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea.
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13
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Lee JJ, Yang SY, Park J, Ferrell JE, Shin DH, Lee KJ. Calcium Ion Induced Structural Changes Promote Dimerization of Secretagogin, Which Is Required for Its Insulin Secretory Function. Sci Rep 2017; 7:6976. [PMID: 28765527 PMCID: PMC5539292 DOI: 10.1038/s41598-017-07072-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022] Open
Abstract
Secretagogin (SCGN), a hexa EF-hand calcium binding protein, plays key roles in insulin secretion in pancreatic β-cells. It is not yet understood how the binding of Ca2+ to human SCGN (hSCGN) promotes secretion. Here we have addressed this question, using mass spectrometry combined with a disulfide searching algorithm DBond. We found that the binding of Ca2+ to hSCGN promotes the dimerization of hSCGN via the formation of a Cys193-Cys193 disulfide bond. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics studies revealed that Ca2+ binding to the EF-hands of hSCGN induces significant structural changes that affect the solvent exposure of N-terminal region, and hence the redox sensitivity of the Cys193 residue. These redox sensitivity changes were confirmed using biotinylated methyl-3-nitro-4-(piperidin-1-ylsulfonyl) benzoate (NPSB-B), a chemical probe that specifically labels reactive cysteine sulfhydryls. Furthermore, we found that wild type hSCGN overexpression promotes insulin secretion in pancreatic β cells, while C193S-hSCGN inhibits it. These findings suggest that insulin secretion in pancreatic cells is regulated by Ca2+ and ROS signaling through Ca2+-induced structural changes promoting dimerization of hSCGN.
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Affiliation(s)
- Jae-Jin Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea
| | - Seo-Yun Yang
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea
| | - Jimin Park
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
| | - Dong-Hae Shin
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea.
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14
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Dautant A, Meyer P, Georgescauld F. Hydrogen/Deuterium Exchange Mass Spectrometry Reveals Mechanistic Details of Activation of Nucleoside Diphosphate Kinases by Oligomerization. Biochemistry 2017; 56:2886-2896. [DOI: 10.1021/acs.biochem.7b00282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alain Dautant
- Université
de Bordeaux, CNRS, Institut de Biochimie et Génétique
Cellulaires, UMR 5095, Bordeaux, France
| | - Philippe Meyer
- Sorbonne Universités,
UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire
et Cellulaire des Eucaryotes, UMR 8226, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Florian Georgescauld
- Sorbonne Universités,
UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire
et Cellulaire des Eucaryotes, UMR 8226, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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15
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Degradation of Redox-Sensitive Proteins including Peroxiredoxins and DJ-1 is Promoted by Oxidation-induced Conformational Changes and Ubiquitination. Sci Rep 2016; 6:34432. [PMID: 27703196 PMCID: PMC5050490 DOI: 10.1038/srep34432] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/14/2016] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) are key molecules regulating various cellular processes. However, what the cellular targets of ROS are and how their functions are regulated is unclear. This study explored the cellular proteomic changes in response to oxidative stress using H2O2 in dose- and recovery time-dependent ways. We found discernible changes in 76 proteins appearing as 103 spots on 2D-PAGE. Of these, Prxs, DJ-1, UCH-L3 and Rla0 are readily oxidized in response to mild H2O2 stress, and then degraded and active proteins are newly synthesized during recovery. In studies designed to understand the degradation process, multiple cellular modifications of redox-sensitive proteins were identified by peptide sequencing with nanoUPLC-ESI-q-TOF tandem mass spectrometry and the oxidative structural changes of Prx2 explored employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that hydrogen/deuterium exchange rate increased in C-terminal region of oxidized Prx2, suggesting the exposure of this region to solvent under oxidation. We also found that Lys191 residue in this exposed C-terminal region of oxidized Prx2 is polyubiquitinated and the ubiquitinated Prx2 is readily degraded in proteasome and autophagy. These findings suggest that oxidation-induced ubiquitination and degradation can be a quality control mechanism of oxidized redox-sensitive proteins including Prxs and DJ-1.
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16
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You DJ, Park CR, Mander S, Ahn C, Seong JY, Hwang JI. Characterization of Functional Domains in NME1L Regulation of NF-κB Signaling. Mol Cells 2016; 39:403-9. [PMID: 27094059 PMCID: PMC4870188 DOI: 10.14348/molcells.2016.2320] [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: 11/25/2015] [Revised: 02/24/2016] [Accepted: 02/29/2016] [Indexed: 11/27/2022] Open
Abstract
NME1 is a well-known metastasis suppressor which has been reported to be downregulated in some highly aggressive cancer cells. Although most studies have focused on NME1, the NME1 gene also encodes the protein (NME1L) containing N-terminal 25 extra amino acids by alternative splicing. According to previous studies, NME1L has potent anti-metastatic activity, in comparison with NME1, by interacting with IKKβ and regulating its activity. In the present study, we tried to define the role of the N-terminal 25 amino acids of NME1L in NF-κB activation signaling. Unfortunately, the sequence itself did not interact with IKKβ, suggesting that it may be not enough to constitute the functional structure. Further construction of NME1L fragments and biochemical analysis revealed that N-terminal 84 residues constitute minimal structure for homodimerization, IKKβ interaction and regulation of NF-κB signaling. The inhibitory effect of the fragment on cancer cell migration and NF-κB-stimulated gene expression was equivalent to that of whole NME1L. The data suggest that the N-terminal 84 residues may be a core region for the anti-metastatic activity of NME1L. Based on this result, further structural analysis of the binding between NME1L and IKKβ may help in understanding the anti-metastatic activity of NME1L and provide direction to NME1L and IKKβ-related anti-cancer drug design.
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Affiliation(s)
- Dong-Joo You
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
| | - Cho Rong Park
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
| | - Sunam Mander
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
| | - Curie Ahn
- Transplantation Research Institute, Cancer Research Institute, Seoul National University, Seoul 110-799,
Korea
| | - Jae Young Seong
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
| | - Jong-Ik Hwang
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
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17
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Lee JJ, Park YS, Lee KJ. Hydrogen-deuterium exchange mass spectrometry for determining protein structural changes in drug discovery. Arch Pharm Res 2015; 38:1737-45. [PMID: 25743629 DOI: 10.1007/s12272-015-0584-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 02/25/2015] [Indexed: 12/11/2022]
Abstract
Protein structures are dynamically changed in response to post-translational modifications, ligand or chemical binding, or protein-protein interactions. Understanding the structural changes that occur in proteins in response to potential candidate drugs is important for predicting the modes of action of drugs and their functions and regulations. Recent advances in hydrogen/deuterium exchange mass spectrometry (HDX-MS) have the potential to offer a tool for obtaining such understanding similarly to other biophysical techniques, such as X-ray crystallography and high resolution NMR. We present here, a review of basic concept and methodology of HDX-MS, how it is being applied for identifying the sites and structural changes in proteins following their interactions with other proteins and small molecules, and the potential of this tool to help in drug discovery.
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Affiliation(s)
- Jae-Jin Lee
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Yeon Seung Park
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul, 120-750, Republic of Korea.
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18
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Kim HJ, Ha S, Lee HY, Lee KJ. ROSics: chemistry and proteomics of cysteine modifications in redox biology. MASS SPECTROMETRY REVIEWS 2015; 34:184-208. [PMID: 24916017 PMCID: PMC4340047 DOI: 10.1002/mas.21430] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 04/30/2013] [Accepted: 11/20/2013] [Indexed: 05/29/2023]
Abstract
Post-translational modifications (PTMs) occurring in proteins determine their functions and regulations. Proteomic tools are available to identify PTMs and have proved invaluable to expanding the inventory of these tools of nature that hold the keys to biological processes. Cysteine (Cys), the least abundant (1-2%) of amino acid residues, are unique in that they play key roles in maintaining stability of protein structure, participating in active sites of enzymes, regulating protein function and binding to metals, among others. Cys residues are major targets of reactive oxygen species (ROS), which are important mediators and modulators of various biological processes. It is therefore necessary to identify the Cys-containing ROS target proteins, as well as the sites and species of their PTMs. Cutting edge proteomic tools which have helped identify the PTMs at reactive Cys residues, have also revealed that Cys residues are modified in numerous ways. These modifications include formation of disulfide, thiosulfinate and thiosulfonate, oxidation to sulfenic, sulfinic, sulfonic acids and thiosulfonic acid, transformation to dehydroalanine (DHA) and serine, palmitoylation and farnesylation, formation of chemical adducts with glutathione, 4-hydroxynonenal and 15-deoxy PGJ2, and various other chemicals. We present here, a review of relevant ROS biology, possible chemical reactions of Cys residues and details of the proteomic strategies employed for rapid, efficient and sensitive identification of diverse and novel PTMs involving reactive Cys residues of redox-sensitive proteins. We propose a new name, "ROSics," for the science which describes the principles of mode of action of ROS at molecular levels.
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Affiliation(s)
- Hee-Jung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans UniversitySeoul, 120-750, Korea
| | - Sura Ha
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST)Daejeon, 305-701, Korea
| | - Hee Yoon Lee
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST)Daejeon, 305-701, Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans UniversitySeoul, 120-750, Korea
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19
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Baez NOD, Reisz JA, Furdui CM. Mass spectrometry in studies of protein thiol chemistry and signaling: opportunities and caveats. Free Radic Biol Med 2015; 80:191-211. [PMID: 25261734 PMCID: PMC4355329 DOI: 10.1016/j.freeradbiomed.2014.09.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/08/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) has become a powerful and widely utilized tool in the investigation of protein thiol chemistry, biochemistry, and biology. Very early biochemical studies of metabolic enzymes have brought to light the broad spectrum of reactivity profiles that distinguish cysteine thiols with functions in catalysis and protein stability from other cysteine residues in proteins. The development of MS methods for the analysis of proteins using electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) coupled with the emergence of high-resolution mass analyzers has been instrumental in advancing studies of thiol modifications, both in single proteins and within the cellular context. This article reviews MS instrumentation and methods of analysis employed in investigations of thiols and their reactivity toward a range of small biomolecules. A selected number of studies are detailed to highlight the advantages brought about by the MS technologies along with the caveats associated with these analyses.
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Affiliation(s)
- Nelmi O Devarie Baez
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Julie A Reisz
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
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20
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Affiliation(s)
- Gregory
F. Pirrone
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - Roxana E. Iacob
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - John R. Engen
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
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21
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Lee JJ, Ha S, Kim HJ, Ha HJ, Lee HY, Lee KJ. Sulfhydryl-specific probe for monitoring protein redox sensitivity. ACS Chem Biol 2014; 9:2883-94. [PMID: 25354229 DOI: 10.1021/cb500839j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Reactive oxygen species (ROS) regulate various biological processes by modifying reactive cysteine residues in the proteins participating in the relevant signaling pathways. Identification of ROS target proteins requires specific reagents that identify ROS-sensitive cysteine sulfhydryls that differ from the known alkylating agents, iodoacetamide and N-ethylmaleimide, which react nonspecifically with oxidized cysteines including sulfenic and sulfinic acid. We designed and synthesized a novel reagent, methyl-3-nitro-4-(piperidin-1-ylsulfonyl)benzoate (NPSB-1), that selectively and specifically reacts with the sulfhydryl of cysteines in model compounds. We validated the specificity of this reagent by allowing it to react with recombinant proteins followed by peptide sequencing with nanoUPLC-ESI-q-TOF tandem mass spectrometry (MS/MS), and mutant studies employed it to identify cellular proteins containing redox-sensitive cysteine residues. We also obtained proteins from cells treated with various concentrations of hydrogen peroxide, labeled them with biotinylated NPSB-1 (NPSB-B), pulled them down with streptavidin beads, and identified them with MS/MS. We grouped these proteins into four families: (1) those having reactive cysteine residues easily oxidized by hydrogen peroxide, (2) those with cysteines reactive only under mild oxidative stress, (3) those with cysteines reactive only after exposure to oxidative stress, and (4) those with cysteines that are reactive regardless of oxidative stress. These results confirm that NPSBs can serve as novel chemical probes for specifically capturing reactive cysteine residues and as powerful tools for measuring their oxidative sensitivity and can help to understand the function of cysteine modifications in ROS-mediated signaling pathways.
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Affiliation(s)
- Jae-Jin Lee
- Graduate
School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea 120-750
| | - Sura Ha
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST), Daejeon, Korea 305-701
| | - Hee-Jung Kim
- Graduate
School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea 120-750
| | - Hyun Joo Ha
- Graduate
School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea 120-750
| | - Hee-Yoon Lee
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST), Daejeon, Korea 305-701
| | - Kong-Joo Lee
- Graduate
School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea 120-750
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22
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Kim HJ, Kim HJ, Jeong JE, Baek JY, Jeong J, Kim S, Kim YM, Kim Y, Nam JH, Huh SH, Seo J, Jin BK, Lee KJ. N-terminal truncated UCH-L1 prevents Parkinson's disease associated damage. PLoS One 2014; 9:e99654. [PMID: 24959670 PMCID: PMC4069018 DOI: 10.1371/journal.pone.0099654] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/16/2014] [Indexed: 11/20/2022] Open
Abstract
Ubiquitin C-terminal hydrolase-L1 (UCH-L1) has been proposed as one of the Parkinson's disease (PD) related genes, but the possible molecular connection between UCH-L1 and PD is not well understood. In this study, we discovered an N-terminal 11 amino acid truncated variant UCH-L1 that we called NT-UCH-L1, in mouse brain tissue as well as in NCI-H157 lung cancer and SH-SY5Y neuroblastoma cell lines. In vivo experiments and hydrogen-deuterium exchange (HDX) with tandem mass spectrometry (MS) studies showed that NT-UCH-L1 is readily aggregated and degraded, and has more flexible structure than UCH-L1. Post-translational modifications including monoubiquitination and disulfide crosslinking regulate the stability and cellular localization of NT-UCH-L1, as confirmed by mutational and proteomic studies. Stable expression of NT-UCH-L1 decreases cellular ROS levels and protects cells from H2O2, rotenone and CCCP-induced cell death. NT-UCH-L1-expressing transgenic mice are less susceptible to degeneration of nigrostriatal dopaminergic neurons seen in the MPTP mouse model of PD, in comparison to control animals. These results suggest that NT-UCH-L1 may have the potential to prevent neural damage in diseases like PD.
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Affiliation(s)
- Hee-Jung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Hyun Jung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Jae-Eun Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Jeong Yeob Baek
- Department of Biochemistry and Molecular Biology, Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Jaeho Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Sun Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Young-Mee Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Youhwa Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Jin Han Nam
- Department of Biochemistry and Molecular Biology, Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Sue Hee Huh
- Department of Biochemistry and Molecular Biology, Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Jawon Seo
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Byung Kwan Jin
- Department of Biochemistry and Molecular Biology, Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Korea
- * E-mail: (KJL); (BKJ)
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
- * E-mail: (KJL); (BKJ)
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23
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A preliminary X-ray study of murine Tnfaip8/Oxi-α. Int J Mol Sci 2014; 15:4523-30. [PMID: 24637935 PMCID: PMC3975411 DOI: 10.3390/ijms15034523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 11/17/2022] Open
Abstract
Tnfaip8/oxidative stress regulated gene-α (Oxi-α) is a novel protein expressed specifically in brain dopaminergic neurons and its over-expression has been reported to protect dopaminergic cells against OS-induced cell death. In this study, murine C165S mutant Tnfaip8/Oxi-α has been crystallized and X-ray data have been collected to 1.8 Å using synchrotron radiation. The crystal belonged to the primitive orthorhombic space group P21212, with unit-cell parameters a = 66.9, b = 72.3, c = 93.5 Å. A full structural determination is under way in order to provide insights into the structure-function relationships of this protein.
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