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Tsunoda T, Abuelizz HA, Samadi A, Wong CP, Awakawa T, Brumsted CJ, Abe I, Mahmud T. Catalytic Mechanism of Nonglycosidic C-N Bond Formation by the Pseudoglycosyltransferase Enzyme VldE. ACS Catal 2023; 13:13369-13382. [PMID: 38130475 PMCID: PMC10732325 DOI: 10.1021/acscatal.3c02404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The pseudoglycosyltransferase (PsGT) enzyme VldE is a homologue of the retaining glycosyltransferase (GT) trehalose 6-phosphate synthase (OtsA) that catalyzes a coupling reaction between two pseudo-sugar units, GDP-valienol and validamine 7-phosphate, to give a product with α,α-N-pseudo-glycosidic linkage. Despite its biological importance and unique catalytic function, the molecular bases for its substrate specificity and reaction mechanism are still obscure. Here, we report a comparative mechanistic study of VldE and OtsA using various engineered chimeric proteins and point mutants of the enzymes, X-ray crystallography, docking studies, and kinetic isotope effects. We found that the distinct substrate specificities between VldE and OtsA are most likely due to topological differences within the hot spot amino acid regions of their N-terminal domains. We also found that the Asp158 and His182 residues, which are in the active site, play a significant role in the PsGT function of VldE. They do not seem to be directly involved in the catalysis but may be important for substrate recognition or contribute to the overall architecture of the active site pocket. Moreover, results of the kinetic isotope effect experiments suggest that VldE catalyzes a C-N bond formation between GDP-valienol and validamine 7-phosphate via an SNi-like mechanism. The study provides new insights into the substrate specificity and catalytic mechanism of a member of the growing family of PsGT enzymes, which may be used as a basis for developing new PsGTs from GTs.
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Affiliation(s)
- Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, U.S.A
| | - Hatem A. Abuelizz
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, U.S.A
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Arash Samadi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, U.S.A
| | - Chin Piow Wong
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Corey J. Brumsted
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, U.S.A
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, U.S.A
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2
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Yokoyama T, Kusaka K. Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1. FEBS J 2023; 290:4465-4479. [PMID: 37171222 DOI: 10.1111/febs.16817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/10/2023] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Death-associated protein kinase 1 (DAPK1), a Ca2+/calmodulin-regulated serine/threonine kinase, regulates cell apoptosis and autophagy and has been implicated in the pathogenesis of Alzheimer's disease (AD). Targeting DAPK1 may be a promising approach for treating AD. In our previous study, we found that a natural polyphenol, resveratrol (1), is a moderate DAPK1 inhibitor. In the present study, we investigated the interactions between natural and synthetic derivatives of 1 and DAPK1. Binding assays including intrinsic fluorescence quenching, protein thermal shift and isothermal titration calorimetry indicated that oxyresveratrol (3), a hydroxylated derivative, and pinostilbene (5), a methoxylated derivative, bind to DAPK1 with comparable affinity to 1. The enzymatic assay showed that 3 more effectively inhibits the intrinsic ATPase activity of DAPK1 compared with 1. Crystallographic analysis revealed that the binding modes of the methoxylated derivatives were different from those of 1 and 3, resulting in a unique interaction. Our results suggest that 3 may be helpful in treating AD and provide a clue for the development of promising DAPK1 inhibitors.
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Affiliation(s)
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Japan
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3
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Frenett ML, Weis K, Cole MJ, Vargas JCC, Ramsay A, Huang J, Gentry MS, Vander Kooi CW, Raththagala M. Differential activity of glucan phosphatase starch EXcess4 orthologs from agronomic crops. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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4
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Murphy RD, Chen T, Lin J, He R, Wu L, Pearson CR, Sharma S, Vander Kooi CD, Sinai AP, Zhang ZY, Vander Kooi CW, Gentry MS. The Toxoplasma glucan phosphatase TgLaforin utilizes a distinct functional mechanism that can be exploited by therapeutic inhibitors. J Biol Chem 2022; 298:102089. [PMID: 35640720 PMCID: PMC9254107 DOI: 10.1016/j.jbc.2022.102089] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 01/19/2023] Open
Abstract
Toxoplasma gondii is an intracellular parasite that generates amylopectin granules (AGs), a polysaccharide associated with bradyzoites that define chronic T. gondii infection. AGs are postulated to act as an essential energy storage molecule that enable bradyzoite persistence, transmission, and reactivation. Importantly, reactivation can result in the life-threatening symptoms of toxoplasmosis. T. gondii encodes glucan dikinase and glucan phosphatase enzymes that are homologous to the plant and animal enzymes involved in reversible glucan phosphorylation and which are required for efficient polysaccharide degradation and utilization. However, the structural determinants that regulate reversible glucan phosphorylation in T. gondii are unclear. Herein, we define key functional aspects of the T. gondii glucan phosphatase TgLaforin (TGME49_205290). We demonstrate that TgLaforin possesses an atypical split carbohydrate-binding-module domain. AlphaFold2 modeling combined with hydrogen-deuterium exchange mass spectrometry and differential scanning fluorimetry also demonstrate the unique structural dynamics of TgLaforin with regard to glucan binding. Moreover, we show that TgLaforin forms a dual specificity phosphatase domain-mediated dimer. Finally, the distinct properties of the glucan phosphatase catalytic domain were exploited to identify a small molecule inhibitor of TgLaforin catalytic activity. Together, these studies define a distinct mechanism of TgLaforin activity, opening up a new avenue of T. gondii bradyzoite biology as a therapeutic target.
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Affiliation(s)
- Robert D Murphy
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, USA; Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Tiantian Chen
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Jianping Lin
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA
| | - Rongjun He
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA
| | - Li Wu
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA
| | - Caden R Pearson
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Savita Sharma
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Carl D Vander Kooi
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Anthony P Sinai
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Zhong-Yin Zhang
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA.
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, USA.
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, USA.
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5
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Grimm TM, Herbinger M, Krüger L, Müller S, Mayer TU, Hauck CR. Lockdown, a selective small-molecule inhibitor of the integrin phosphatase PPM1F, blocks cancer cell invasion. Cell Chem Biol 2022; 29:930-946.e9. [PMID: 35443151 DOI: 10.1016/j.chembiol.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 03/04/2022] [Accepted: 03/23/2022] [Indexed: 12/18/2022]
Abstract
Phosphatase PPM1F is a regulator of cell adhesion by fine-tuning integrin activity and actin cytoskeleton structures. Elevated expression of this enzyme in human tumors is associated with high invasiveness, enhanced metastasis, and poor prognosis. Thus, PPM1F is a target for pharmacological intervention, yet inhibitors of this enzyme are lacking. Here, we use high-throughput screening to identify Lockdown, a reversible and non-competitive PPM1F inhibitor. Lockdown is selective for PPM1F, because this compound does not inhibit other protein phosphatases in vitro and does not induce additional phenotypes in PPM1F knockout cells. Importantly, Lockdown-treated glioblastoma cells fully re-capitulate the phenotype of PPM1F-deficient cells as assessed by increased phosphorylation of PPM1F substrates and corruption of integrin-dependent cellular processes. Ester modification yields LockdownPro with increased membrane permeability and prodrug-like properties. LockdownPro suppresses tissue invasion by PPM1F-overexpressing human cancer cells, validating PPM1F as a therapeutic target and providing an access point to control tumor cell dissemination.
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Affiliation(s)
- Tanja M Grimm
- Lehrstuhl Zellbiologie, Department of Biology, University of Konstanz, Maildrop 621, Universitätsstrasse 10, 78467 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Marleen Herbinger
- Lehrstuhl Zellbiologie, Department of Biology, University of Konstanz, Maildrop 621, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Lena Krüger
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Silke Müller
- Lehrstuhl Molekulare Genetik, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany; Screening Center, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Thomas U Mayer
- Lehrstuhl Molekulare Genetik, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany; Screening Center, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany
| | - Christof R Hauck
- Lehrstuhl Zellbiologie, Department of Biology, University of Konstanz, Maildrop 621, Universitätsstrasse 10, 78467 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78467 Konstanz, Germany.
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6
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An empirical pipeline for personalized diagnosis of Lafora disease mutations. iScience 2021; 24:103276. [PMID: 34755096 PMCID: PMC8564118 DOI: 10.1016/j.isci.2021.103276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/14/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022] Open
Abstract
Lafora disease (LD) is a fatal childhood dementia characterized by progressive myoclonic epilepsy manifesting in the teenage years, rapid neurological decline, and death typically within ten years of onset. Mutations in either EPM2A, encoding the glycogen phosphatase laforin, or EPM2B, encoding the E3 ligase malin, cause LD. Whole exome sequencing has revealed many EPM2A variants associated with late-onset or slower disease progression. We established an empirical pipeline for characterizing the functional consequences of laforin missense mutations in vitro using complementary biochemical approaches. Analysis of 26 mutations revealed distinct functional classes associated with different outcomes that were supported by clinical cases. For example, F321C and G279C mutations have attenuated functional defects and are associated with slow progression. This pipeline enabled rapid characterization and classification of newly identified EPM2A mutations, providing clinicians and researchers genetic information to guide treatment of LD patients. Lafora disease (LD) patients present with varying clinical progression LD missense mutations differentially affect laforin function An empirical in vitro pipeline is used to classify laforin missense mutations Patient progression can be predicted based on mutation class
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7
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Le Coq J, López Navajas P, Rodrigo Martin B, Alfonso C, Lietha D. A new layer of phosphoinositide-mediated allosteric regulation uncovered for SHIP2. FASEB J 2021; 35:e21815. [PMID: 34314064 DOI: 10.1096/fj.202100561r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/26/2021] [Accepted: 07/08/2021] [Indexed: 11/11/2022]
Abstract
The Src homology 2 containing inositol 5-phosphatase 2 (SHIP2) is a large multidomain enzyme that catalyzes the dephosphorylation of the phospholipid phosphatidylinositol 3,4,5-triphosphate (PI(3,4,5)P3 ) to form PI(3,4)P2 . PI(3,4,5)P3 is a key lipid second messenger controlling the recruitment of signaling proteins to the plasma membrane, thereby regulating a plethora of cellular events, including proliferation, growth, apoptosis, and cytoskeletal rearrangements. SHIP2, alongside PI3K and PTEN, regulates PI(3,4,5)P3 levels at the plasma membrane and has been heavily implicated in serious diseases such as cancer and type 2 diabetes; however, many aspects of its regulation mechanism remain elusive. We recently reported an activating effect of the SHIP2 C2 domain and here we describe an additional layer of regulation via the pleckstrin homology-related (PHR) domain. We show a phosphoinositide-induced transition to a high activity state of the enzyme that increases phosphatase activity up to 10-15 fold. We further show that PI(3,4)P2 directly interacts with the PHR domain to trigger this allosteric activation. Modeling of the PHR-phosphatase-C2 region of SHIP2 on the membrane suggests no major inter-domain interactions with the PHR domain, but close contacts between the two linkers offer a possible path of allosteric communication. Together, our data show that the PHR domain acts as an allosteric module regulating the catalytic activity of SHIP2 in response to specific phosphoinositide levels in the cell membrane.
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Affiliation(s)
- Johanne Le Coq
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Pilar López Navajas
- Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain
| | - Bárbara Rodrigo Martin
- Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain
| | - Carlos Alfonso
- Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain
| | - Daniel Lietha
- Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain
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8
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Mak CA, Weis K, Henao T, Kuchtova A, Chen T, Sharma S, Meekins DA, Thalmann M, Vander Kooi CW, Raththagala M. Cooperative Kinetics of the Glucan Phosphatase Starch Excess4. Biochemistry 2021; 60:2425-2435. [PMID: 34319705 DOI: 10.1021/acs.biochem.1c00307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glucan phosphatases are members of a functionally diverse family of dual-specificity phosphatase (DSP) enzymes. The plant glucan phosphatase Starch Excess4 (SEX4) binds and dephosphorylates glucans, contributing to processive starch degradation in the chloroplast at night. Little is known about the complex kinetics of SEX4 when acting on its complex physiologically relevant glucan substrate. Therefore, we explored the kinetics of SEX4 against both insoluble starch and soluble amylopectin glucan substrates. SEX4 displays robust activity and a unique sigmoidal kinetic response to amylopectin, characterized by a Hill coefficient of 2.77 ± 0.63, a signature feature of cooperativity. We investigated the basis for this positive kinetic cooperativity and determined that the SEX4 carbohydrate-binding module (CBM) dramatically influences the binding cooperativity and substrate transformation rates. These findings provide insights into a previously unknown but important regulatory role for SEX4 in reversible starch phosphorylation and further advances our understanding of atypical kinetic mechanisms.
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Affiliation(s)
- Claudia A Mak
- Department of Chemistry, Skidmore College, Saratoga Springs, New York 12866, United States
| | - Kenyon Weis
- Department of Chemistry, Skidmore College, Saratoga Springs, New York 12866, United States
| | - Tiffany Henao
- Department of Chemistry, Skidmore College, Saratoga Springs, New York 12866, United States
| | - Andrea Kuchtova
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - Tiantian Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - Savita Sharma
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - David A Meekins
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - Matthias Thalmann
- The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - Madushi Raththagala
- Department of Chemistry, Skidmore College, Saratoga Springs, New York 12866, United States
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9
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Simmons ZR, Sharma S, Wayne J, Li S, Vander Kooi CW, Gentry MS. Generation and characterization of a laforin nanobody inhibitor. Clin Biochem 2021; 93:80-89. [PMID: 33831386 PMCID: PMC8217207 DOI: 10.1016/j.clinbiochem.2021.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Mutations in the gene encoding the glycogen phosphatase laforin result in the fatal childhood dementia Lafora disease (LD). A cellular hallmark of LD is cytoplasmic, hyper-phosphorylated, glycogen-like aggregates called Lafora bodies (LBs) that form in nearly all tissues and drive disease progression. Additional tools are needed to define the cellular function of laforin, understand the pathological role of laforin in LD, and determine the role of glycogen phosphate in glycogen metabolism. In this work, we present the generation and characterization of laforin nanobodies, with one being a laforin inhibitor. DESIGN AND METHODS We identify multiple classes of specific laforin-binding nanobodies and determine their binding epitopes using hydrogen deuterium exchange (HDX) mass spectrometry. Using para-nitrophenyl phosphate (pNPP) and a malachite gold-based assay specific for glucan phosphatase activity, we assess the inhibitory effect of one nanobody on laforin's catalytic activity. RESULTS Six families of laforin nanobodies are characterized and their epitopes mapped. One nanobody is identified and characterized that serves as an inhibitor of laforin's phosphatase activity. CONCLUSIONS The six generated and characterized laforin nanobodies, with one being a laforin inhibitor, are an important set of tools that open new avenues to define unresolved glycogen metabolism questions.
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Affiliation(s)
- Zoe R Simmons
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States
| | - Savita Sharma
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States
| | - Jeremiah Wayne
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States
| | - Sheng Li
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, United States
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, KY 40536, United States
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, KY 40536, United States.
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10
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Yokoyama T, Suzuki R, Mizuguchi M. Crystal structure of death-associated protein kinase 1 in complex with the dietary compound resveratrol. IUCRJ 2021; 8:131-138. [PMID: 33520249 PMCID: PMC7792996 DOI: 10.1107/s2052252520015614] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Death-associated protein kinase 1 (DAPK1) is a large multidomain protein with an N-terminal serine/threonine protein kinase domain. DAPK1 is considered to be a promising molecular target for the treatment of Alzheimer's disease (AD). In the present study, the inhibitory potency of resveratrol (RSV), a dietary polyphenol found in red wine, against the catalytic activity of DAPK1 was investigated. Kinetic and fluorescent probe competitive binding analyses revealed that RSV directly inhibited the catalytic activity of DAPK1 by binding to the ATP-binding site. Crystallographic analysis of DAPK1 in complex with RSV revealed that the A-ring of RSV occupied the nucleobase-binding position. Determination of the binding mode provided a structural basis for the design of more potent DAPK1 inhibitors. In conclusion, the data here clearly show that RSV is an ATP-competitive inhibitor of DAPK1, encouraging speculation that RSV may be useful for the development of AD inhibitors.
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Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0914, Japan
| | - Ryoya Suzuki
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0914, Japan
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11
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Zhu M, Ou D, Khan MH, Zhao S, Zhu Z, Niu L. Structural insights into the formation of oligomeric state by a type I Hsp40 chaperone. Biochimie 2020; 176:45-51. [PMID: 32621942 DOI: 10.1016/j.biochi.2020.06.009] [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: 05/16/2019] [Revised: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 10/23/2022]
Abstract
Molecular chaperones can prevent and repair protein misfolding and aggregation to maintain protein homeostasis in cells. Hsp40 chaperones interact with unfolded client proteins via the dynamic multivalent interaction (DMI) mechanism with their multiple client-binding sites. Here we report that a type I Hsp40 chaperone from Streptococcus pneumonia (spHsp40) forms a concentration-independent polydispersity oligomer state in solution. The crystal structure of spHsp40 determined at 2.75 Å revealed that each monomer has a type I Hsp40 structural fold containing a zinc finger domain and C-terminal domains I and II (CTD I and CTD II). Subsequent quaternary structure analysis using a PISA server generated two dimeric models. The interface mutational analysis suggests the conserved C-terminal dimeric motif as a basis for dimer formation and that the novel dimeric interaction between a client-binding site in CTD I and the zinc finger domain promotes the formation of the spHsp40 oligomeric state. In vitro functional analysis demonstrated that spHsp40 oligomer is fully active and possess the optimal activity in stimulating the ATPase activity of spHsp70. The oligomer state of type I Hsp40 and its formation might be important in understanding Hsp40 function and its interaction with client proteins.
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Affiliation(s)
- Min Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China
| | - Dingmin Ou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China
| | - Muhammad Hidayatullah Khan
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China
| | - Shasha Zhao
- Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610075, China
| | - Zhongliang Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China.
| | - Liwen Niu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China.
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12
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Carrillo JB, Torresi F, Morales LL, Ricordi M, Gomez-Casati DF, Busi MV, Martín M. Identification and characterization of ChlreSEX4, a novel glucan phosphatase from Chlamydomonas reinhardtii green alga. Arch Biochem Biophys 2020; 680:108235. [PMID: 31877265 DOI: 10.1016/j.abb.2019.108235] [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: 10/27/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022]
Abstract
Chlamydomonas reinhardtii is the best known unicellular green alga model which has long been used to investigate all kinds of cellular processes, including starch metabolism. Here we identified and characterized a novel enzyme, ChlreSEX4, orthologous to glucan phosphatase SEX4 from Arabidopsis thaliana, that is capable of binding and dephosphorylating amylopectin in vitro. We also reported that cysteine 224 and tryptophan 305 residues are critical for enzyme catalysis and substrate binding. Furthermore, we verified that ChlreSEX4 gene is expressed in vivo and that glucan phosphatase activity is measurable in Chlamydomonas protein extracts. In view of the results presented, we suggest ChlreSEX4 as a functional phosphoglucan phosphatase from C. reinhardtii. Our data obtained so far contribute to understanding the phosphoglucan phosphatases evolutionary process in the green lineage and their role in starch reversible phosphorylation. In addition, this allows to position Chlamydomonas as a potential tool to obtain starches with different degrees of phosphorylation for industrial or biotechnological purposes.
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Affiliation(s)
- Julieta B Carrillo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Florencia Torresi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Luisina L Morales
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Micaela Ricordi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Maria V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina.
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina.
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13
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Discovery of a new class of MTH1 inhibitor by X-ray crystallographic screening. Eur J Med Chem 2019; 167:153-160. [DOI: 10.1016/j.ejmech.2019.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 11/19/2022]
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14
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The Mycobacterium tuberculosis Pup-proteasome system regulates nitrate metabolism through an essential protein quality control pathway. Proc Natl Acad Sci U S A 2019; 116:3202-3210. [PMID: 30723150 DOI: 10.1073/pnas.1819468116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis encodes a proteasome that carries out regulated degradation of bacterial proteins. It has been proposed that the proteasome contributes to nitrogen metabolism in M. tuberculosis, although this hypothesis had not been tested. Upon assessing M. tuberculosis growth in several nitrogen sources, we found that a mutant strain lacking the Mycobacterium proteasomal activator Mpa was unable to use nitrate as a sole nitrogen source due to a specific failure in the pathway of nitrate reduction to ammonium. We found that the robust activity of the nitrite reductase complex NirBD depended on expression of the groEL/groES chaperonin genes, which are regulated by the repressor HrcA. We identified HrcA as a likely proteasome substrate, and propose that the degradation of HrcA is required for the full expression of chaperonin genes. Furthermore, our data suggest that degradation of HrcA, along with numerous other proteasome substrates, is enhanced during growth in nitrate to facilitate the derepression of the chaperonin genes. Importantly, growth in nitrate is an example of a specific condition that reduces the steady-state levels of numerous proteasome substrates in M. tuberculosis.
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15
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Structure-function studies of the asparaginyl-tRNA synthetase from Fasciola gigantica: understanding the role of catalytic and non-catalytic domains. Biochem J 2018; 475:3377-3391. [DOI: 10.1042/bcj20180700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/29/2018] [Accepted: 10/04/2018] [Indexed: 01/14/2023]
Abstract
The asparaginyl-tRNA synthetase (NRS) catalyzes the attachment of asparagine to its cognate tRNA during translation. NRS first catalyzes the binding of Asn and ATP to form the NRS-asparaginyl adenylate complex, followed by the esterification of Asn to its tRNA. We investigated the role of constituent domains in regulating the structure and activity of Fasciola gigantica NRS (FgNRS). We cloned the full-length FgNRS, along with its various truncated forms, expressed, and purified the corresponding proteins. Size exclusion chromatography indicated a role of the anticodon-binding domain (ABD) of FgNRS in protein dimerization. The N-terminal domain (NTD) was not essential for cognate tRNA binding, and the hinge region between the ABD and the C-terminal domain (CTD) was crucial for regulating the enzymatic activity. Molecular docking and fluorescence quenching experiments elucidated the binding affinities of the substrates to various domains. The molecular dynamics simulation of the modeled protein showed the presence of an unstructured region between the NTD and ABD that exhibited a large number of conformations over time, and further analysis indicated this region to be intrinsically disordered. The present study provides information on the structural and functional regulation, protein-substrate(s) interactions and dynamics, and the role of non-catalytic domains in regulating the activity of FgNRS.
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16
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Garcia-Gimeno MA, Rodilla-Ramirez PN, Viana R, Salas-Puig X, Brewer MK, Gentry MS, Sanz P. A novel EPM2A mutation yields a slow progression form of Lafora disease. Epilepsy Res 2018; 145:169-177. [PMID: 30041081 DOI: 10.1016/j.eplepsyres.2018.07.003] [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: 06/01/2018] [Revised: 07/11/2018] [Accepted: 07/13/2018] [Indexed: 12/19/2022]
Abstract
Lafora disease (LD, OMIM 254780) is a rare disorder characterized by epilepsy and neurodegeneration leading patients to a vegetative state and death, usually within the first decade from the onset of the first symptoms. In the vast majority of cases LD is related to mutations in either the EPM2A gene (encoding the glucan phosphatase laforin) or the EPM2B gene (encoding the E3-ubiquitin ligase malin). In this work, we characterize the mutations present in the EPM2A gene in a patient displaying a slow progression form of the disease. The patient is compound heterozygous with Y112X and N163D mutations in the corresponding alleles. In primary fibroblasts obtained from the patient, we analyzed the expression of the mutated alleles by quantitative real time PCR and found slightly lower levels of expression of the EPM2A gene respect to control cells. However, by Western blotting we were unable to detect endogenous levels of the protein in crude extracts from patient fibroblasts. The Y112X mutation would render a truncated protein lacking the phosphatase domain and likely degraded. Since minute amounts of laforin-N163D might still play a role in cell physiology, we analyzed the biochemical characteristics of the N163D mutation. We found that recombinant laforin N163D protein was as stable as wild type and exhibited near wild type phosphatase activity towards biologically relevant substrates. On the contrary, it showed a severe impairment in the interaction profile with previously identified laforin binding partners. These results lead us to conclude that the slow progression of the disease present in this patient could be either due to the specific biochemical properties of laforin N163D or to the presence of alternative genetic modifying factors separate from pathogenicity.
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Affiliation(s)
| | | | - Rosa Viana
- IBV-CSIC. Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Xavier Salas-Puig
- Epilepsy Unit, Neurology Dept., Hospital Vall Hebron, Barcelona, Spain
| | - M Kathryn Brewer
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, USA; Lafora Epilepsy Cure Initiative, USA
| | - Pascual Sanz
- IBV-CSIC. Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain; CIBERER. Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Lafora Epilepsy Cure Initiative, USA.
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17
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Casey GR, Stains CI. Interrogating Protein Phosphatases with Chemical Activity Probes. Chemistry 2018; 24:7810-7824. [PMID: 29338103 PMCID: PMC5986605 DOI: 10.1002/chem.201705194] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 12/30/2022]
Abstract
Protein phosphatases, while long overlooked, have recently become appreciated as drivers of both normal- and disease-associated signaling events. As a result, the spotlight is now turning torwards this enzyme family and efforts geared towards the development of modern chemical tools for studying these enzymes are well underway. This Minireview focuses on the evolution of chemical activity probes, both optical and covalent, for the study of protein phosphatases. Small-molecule probes, global monitoring of phosphatase activity through the use of covalent modifiers, and targeted fluorescence-based activity probes are discussed. We conclude with an overview of open questions in the field and highlight the potential impact of chemical tools for studying protein phosphatases.
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Affiliation(s)
- Garrett R Casey
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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18
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Carrillo JB, Gomez-Casati DF, Martín M, Busi MV. Identification and analysis of OsttaDSP, a phosphoglucan phosphatase from Ostreococcus tauri. PLoS One 2018; 13:e0191621. [PMID: 29360855 PMCID: PMC5779698 DOI: 10.1371/journal.pone.0191621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/08/2018] [Indexed: 11/18/2022] Open
Abstract
Ostreococcus tauri, the smallest free-living (non-symbiotic) eukaryote yet described, is a unicellular green alga of the Prasinophyceae family. It has a very simple cellular organization and presents a unique starch granule and chloroplast. However, its starch metabolism exhibits a complexity comparable to higher plants, with multiple enzyme forms for each metabolic reaction. Glucan phosphatases, a family of enzymes functionally conserved in animals and plants, are essential for normal starch or glycogen degradation in plants and mammals, respectively. Despite the importance of O. tauri microalgae in evolution, there is no information available concerning the enzymes involved in reversible phosphorylation of starch. Here, we report the molecular cloning and heterologous expression of the gene coding for a dual specific phosphatase from O. tauri (OsttaDSP), homologous to Arabidopsis thaliana LSF2. The recombinant enzyme was purified to electrophoretic homogeneity to characterize its oligomeric and kinetic properties accurately. OsttaDSP is a homodimer of 54.5 kDa that binds and dephosphorylates amylopectin. Also, we also determined that residue C162 is involved in catalysis and possibly also in structural stability of the enzyme. Our results could contribute to better understand the role of glucan phosphatases in the metabolism of starch in green algae.
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Affiliation(s)
- Julieta B. Carrillo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Diego F. Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
- * E-mail: (MM); (MVB)
| | - Maria V. Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
- * E-mail: (MM); (MVB)
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19
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Figueiredo SA, de Moraes DC, Vilela FMP, de Faria AN, Dos Santos MH, Fonseca MJV. A novel research model for evaluating sunscreen protection in the UV-A1. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 178:61-68. [PMID: 29112891 DOI: 10.1016/j.jphotobiol.2017.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/18/2017] [Accepted: 10/26/2017] [Indexed: 12/01/2022]
Abstract
The use of a broad spectrum sunscreen is considered one of the main and most popular measures for preventing the damaging effects of ultraviolet radiation (UVR) on the skin. In this study we have developed a novel in vitro method to assess sunscreens efficacy to protect calcineurin enzyme activity, a skin cell marker. The photoprotective efficacy of sunscreen products was assessed by measuring the UV-A1 radiation-induced depletion of calcineurin (Cn) enzyme activity in primary neonatal human dermal fibroblast (HDFn) cell lysates. After exposure to 24J/cm2 UV-A1 radiation, the sunscreens containing larger amounts of UV-A1 filters (brand B), the astaxanthin (UV-A1 absorber) and the Tinosorb® M (UV-A1 absorber) were capable of preventing loss of Cn activity when compared to the sunscreens formulations of brand A (low concentration of UV-A1 filters), with the Garcinia brasiliensis extract (UV-B absorber) and with the unprotected cell lysate and exposed to irradiation (Irradiated Control - IC). The Cn activity assay is a reproducible, accurate and selective technique for evaluating the effectiveness of sunscreens against the effects of UV-A1 radiation. The developed method showed that calcineurin activity have the potential to act as a biological indicator of UV-A1 radiation-induced damages in skin and the assay might be used to assess the efficacy of sunscreens agents and plant extracts prior to in vivo tests.
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Affiliation(s)
- Sônia Aparecida Figueiredo
- Quality Control and Photochemoprevention Laboratory, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, s/n, Ribeirão Preto, SP 14040-903, Brazil
| | - Dayane Cristina de Moraes
- Quality Control and Photochemoprevention Laboratory, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, s/n, Ribeirão Preto, SP 14040-903, Brazil
| | - Fernanda Maria Pinto Vilela
- Faculty of Pharmacy, Federal University of Juiz de Fora, Rua José Lourenço Kelmer, s/n, Juiz de Fora, Minas Gerais 36036-900, Brazil
| | - Amanda Natalina de Faria
- Department of Biochemistry, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900, Brazil
| | - Marcelo Henrique Dos Santos
- Department of Chemistry, Federal University of Viçosa, Avenida Peter Henry Rolfs, s/n, Viçosa, MG 36570-000, Brazil
| | - Maria José Vieira Fonseca
- Quality Control and Photochemoprevention Laboratory, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, s/n, Ribeirão Preto, SP 14040-903, Brazil.
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20
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Carrillo JB, Gomez-Casati DF, Busi MV, Martín M. Development of fast and simple chromogenic methods for glucan phosphatases in-gel activity assays. Anal Biochem 2017; 517:36-39. [PMID: 27836260 DOI: 10.1016/j.ab.2016.11.005] [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: 10/11/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
Abstract
Glucan phosphatases are essential for normal starch degradation in plants and glycogen metabolism in mammals. Here we develop two chromogenic methods for the detection of glucan phosphatase activity in situ after non denaturing poliacrylamide gel electrophoresis; one method uses pNPP and the second one applies BCIP/NBT. The assays are sensitive, fast, simple, reliable and cost-effective preventing the use of radioactive or fluorogenic compounds. Taking advantage of an efficient separation method combined with the reported assays it is possible to obtain information about oligomeric state of the active enzymes as well as to simultaneously detect glucan substrate binding and phosphatase activity.
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Affiliation(s)
- Julieta B Carrillo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Maria V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina.
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina.
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21
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ATPase activity measurement of DNA replicative helicase from Bacillus stearothermophilus by malachite green method. Anal Biochem 2016; 509:46-49. [PMID: 27372608 DOI: 10.1016/j.ab.2016.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 11/24/2022]
Abstract
The DnaB helicase from Bacillus stearothermophilus (DnaBBst) was a model protein for studying the bacterial DNA replication. In this work, a non-radioactive method for measuring ATPase activity of DnaBBst helicase was described. The working parameters and conditions were optimized. Furthermore, this method was applied to investigate effects of DnaG primase, ssDNA and helicase loader protein (DnaI) on ATPase activity of DnaBBst. Our results showed this method was sensitive and efficient. Moreover, it is suitable for the investigation of functional interaction between DnaB and related factors.
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22
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Romá-Mateo C, Raththagala M, Gentry MS, Sanz P. Assessing the Biological Activity of the Glucan Phosphatase Laforin. Methods Mol Biol 2016; 1447:107-119. [PMID: 27514803 PMCID: PMC5339740 DOI: 10.1007/978-1-4939-3746-2_7] [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] [Indexed: 06/06/2023]
Abstract
Glucan phosphatases are a recently discovered family of enzymes that dephosphorylate either starch or glycogen and are essential for proper starch metabolism in plants and glycogen metabolism in humans. Mutations in the gene encoding the only human glucan phosphatase, laforin, result in the fatal, neurodegenerative, epilepsy known as Lafora disease. Here, we describe phosphatase assays to assess both generic laforin phosphatase activity and laforin's unique glycogen phosphatase activity.
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Affiliation(s)
- Carlos Romá-Mateo
- Department of Physiology, School of Medicine and Dentistry, University of Valencia and FIHCUV-INCLIVA, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Jaime Roig 11, 46010, Valencia, Spain
| | - Madushi Raththagala
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, KY, USA
| | - Mathew S Gentry
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, KY, USA
| | - Pascual Sanz
- Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Jaime Roig 11, 46010, Valencia, Spain.
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23
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Meekins DA, Raththagala M, Auger KD, Turner BD, Santelia D, Kötting O, Gentry MS, Vander Kooi CW. Mechanistic Insights into Glucan Phosphatase Activity against Polyglucan Substrates. J Biol Chem 2015; 290:23361-70. [PMID: 26231210 DOI: 10.1074/jbc.m115.658203] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 01/11/2023] Open
Abstract
Glucan phosphatases are central to the regulation of starch and glycogen metabolism. Plants contain two known glucan phosphatases, Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2), which dephosphorylate starch. Starch is water-insoluble and reversible phosphorylation solubilizes its outer surface allowing processive degradation. Vertebrates contain a single known glucan phosphatase, laforin, that dephosphorylates glycogen. In the absence of laforin, water-soluble glycogen becomes insoluble, leading to the neurodegenerative disorder Lafora Disease. Because of their essential role in starch and glycogen metabolism glucan phosphatases are of significant interest, yet a comparative analysis of their activities against diverse glucan substrates has not been established. We identify active site residues required for specific glucan dephosphorylation, defining a glucan phosphatase signature motif (CζAGΨGR) in the active site loop. We further explore the basis for phosphate position-specific activity of these enzymes and determine that their diverse phosphate position-specific activity is governed by the phosphatase domain. In addition, we find key differences in glucan phosphatase activity toward soluble and insoluble polyglucan substrates, resulting from the participation of ancillary glucan-binding domains. Together, these data provide fundamental insights into the specific activity of glucan phosphatases against diverse polyglucan substrates.
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Affiliation(s)
- David A Meekins
- From the Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536
| | - Madushi Raththagala
- From the Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536
| | - Kyle D Auger
- From the Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536
| | - Benjamin D Turner
- From the Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536
| | - Diana Santelia
- Institute of Plant Biology, University of Zürich, CH-8008, Zürich, Switzerland, and
| | - Oliver Kötting
- Institute of Agricultural Sciences, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland
| | - Matthew S Gentry
- From the Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536,
| | - Craig W Vander Kooi
- From the Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536,
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24
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Structural mechanism of laforin function in glycogen dephosphorylation and lafora disease. Mol Cell 2014; 57:261-72. [PMID: 25544560 DOI: 10.1016/j.molcel.2014.11.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 11/13/2014] [Accepted: 11/18/2014] [Indexed: 01/30/2023]
Abstract
Glycogen is the major mammalian glucose storage cache and is critical for energy homeostasis. Glycogen synthesis in neurons must be tightly controlled due to neuronal sensitivity to perturbations in glycogen metabolism. Lafora disease (LD) is a fatal, congenital, neurodegenerative epilepsy. Mutations in the gene encoding the glycogen phosphatase laforin result in hyperphosphorylated glycogen that forms water-insoluble inclusions called Lafora bodies (LBs). LBs induce neuronal apoptosis and are the causative agent of LD. The mechanism of glycogen dephosphorylation by laforin and dysfunction in LD is unknown. We report the crystal structure of laforin bound to phosphoglucan product, revealing its unique integrated tertiary and quaternary structure. Structure-guided mutagenesis combined with biophysical and biochemical analyses reveal the basis for normal function of laforin in glycogen metabolism. Analyses of LD patient mutations define the mechanism by which subsets of mutations disrupt laforin function. These data provide fundamental insights connecting glycogen metabolism to neurodegenerative disease.
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25
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Brewer MK, Husodo S, Dukhande VV, Johnson MB, Gentry MS. Expression, purification and characterization of soluble red rooster laforin as a fusion protein in Escherichia coli. BMC BIOCHEMISTRY 2014; 15:8. [PMID: 24690255 PMCID: PMC4234410 DOI: 10.1186/1471-2091-15-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 03/27/2014] [Indexed: 01/20/2023]
Abstract
Background The gene that encodes laforin, a dual-specificity phosphatase with a carbohydrate-binding module, is mutated in Lafora disease (LD). LD is an autosomal recessive, fatal progressive myoclonus epilepsy characterized by the intracellular buildup of insoluble, hyperphosphorylated glycogen-like particles, called Lafora bodies. Laforin dephosphorylates glycogen and other glucans in vitro, but the structural basis of its activity remains unknown. Recombinant human laforin when expressed in and purified from E. coli is largely insoluble and prone to aggregation and precipitation. Identification of a laforin ortholog that is more soluble and stable in vitro would circumvent this issue. Results In this study, we cloned multiple laforin orthologs, established a purification scheme for each, and tested their solubility and stability. Gallus gallus (Gg) laforin is more stable in vitro than human laforin, Gg-laforin is largely monomeric, and it possesses carbohydrate binding and phosphatase activity similar to human laforin. Conclusions Gg-laforin is more soluble and stable than human laforin in vitro, and possesses similar activity as a glucan phosphatase. Therefore, it can be used to model human laforin in structure-function studies. We have established a protocol for purifying recombinant Gg-laforin in sufficient quantity for crystallographic and other biophysical analyses, in order to better understand the function of laforin and define the molecular mechanisms of Lafora disease.
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Affiliation(s)
| | | | | | | | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, College of Medicine, University of Kentucky, 741 S, Limestone, Lexington, Kentucky 40536-0509, USA.
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26
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Characterization of mycobacterial UDP-N-acetylglucosamine enolpyruvyle transferase (MurA). Res Microbiol 2014; 165:91-101. [PMID: 24463011 DOI: 10.1016/j.resmic.2014.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/13/2014] [Indexed: 11/23/2022]
Abstract
The mycobacterial peptidoglycan has structure and biosynthetic pathways to similar those of other bacteria. UDP-N-acetylglucosamine enolpyruvyle transferase (MurA) catalyzes the first reaction in the biosynthesis of peptidoglycan. The MurA enzyme has been identified from various bacterial species, but the in-depth biochemical properties of mycobacterial MurA have not been characterized. In this study, both Mycobacterium tuberculosis MurA protein and Mycobacterium smegmatis MurA protein were overexpressed in Escherichia coli and purified by affinity chromatography. MurA activity was detected by HPLC. A colorimetric assay of MurA activity was also developed and the kinetic properties of Mtb MurA and Msm MurA were determined using this colorimetric assay. A conditional murA gene knockout strain was constructed by DNA homologous recombination. The disruption of murA in the genome of M. smegmatis led to loss of viability at a non-permissive temperature. Drastic morphological and structural alterations in the M. smegmatis murA knockout strain were observed by scanning electron microscopy and transmission electron microscopy. These results demonstrated that murA was an essential gene for growth of M. smegmatis. Therefore, MurA is a potential target for developing new anti-tuberculosis drugs.
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27
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Sherwood AR, Johnson MB, Delgado-Escueta AV, Gentry MS. A bioassay for Lafora disease and laforin glucan phosphatase activity. Clin Biochem 2013; 46:1869-76. [PMID: 24012855 DOI: 10.1016/j.clinbiochem.2013.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 08/21/2013] [Accepted: 08/28/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Lafora disease is a rare yet invariably fatal form of progressive neurodegenerative epilepsy resulting from mutations in the phosphatase laforin. Several therapeutic options for Lafora disease patients are currently being explored, and these therapies would benefit from a biochemical means of assessing functional laforin activity following treatment. To date, only clinical outcomes such as decreases in seizure frequency and severity have been used to indicate success of epilepsy treatment. However, these qualitative measures exhibit variability and must be assessed over long periods of time. In this work, we detail a simple and sensitive bioassay that can be used for the detection of functional endogenous laforin from human and mouse tissue. DESIGN AND METHODS We generated antibodies capable of detecting and immunoprecipitating endogenous laforin. Following laforin immunoprecipitation, laforin activity was assessed via phosphatase assays using para-nitrophenylphosphate (pNPP) and a malachite green-based assay specific for glucan phosphatase activity. RESULTS We found that antibody binding to laforin does not impede laforin activity. Furthermore, the malachite green-based glucan phosphatase assay used in conjunction with a rabbit polyclonal laforin antibody was capable of detecting endogenous laforin activity from human and mouse tissues. Importantly, this assay discriminated between laforin activity and other phosphatases. CONCLUSIONS The bioassay that we have developed utilizing laforin antibodies and an assay specific for glucan phosphatase activity could prove valuable in the rapid detection of functional laforin in patients to which novel Lafora disease therapies have been administered.
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Affiliation(s)
- Amanda R Sherwood
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, KY 405036-0001, USA
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Dimerization of the glucan phosphatase laforin requires the participation of cysteine 329. PLoS One 2013; 8:e69523. [PMID: 23922729 PMCID: PMC3724922 DOI: 10.1371/journal.pone.0069523] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/11/2013] [Indexed: 01/08/2023] Open
Abstract
Laforin, encoded by a gene that is mutated in Lafora Disease (LD, OMIM 254780), is a modular protein composed of a carbohydrate-binding module and a dual-specificity phosphatase domain. Laforin is the founding member of the glucan-phosphatase family and regulates the levels of phosphate present in glycogen. Multiple reports have described the capability of laforin to form dimers, although the function of these dimers and their relationship with LD remains unclear. Recent evidence suggests that laforin dimerization depends on redox conditions, suggesting that disulfide bonds are involved in laforin dimerization. Using site-directed mutagenesis we constructed laforin mutants in which individual cysteine residues were replaced by serine and then tested the ability of each protein to dimerize using recombinant protein as well as a mammalian cell culture assay. Laforin-Cys329Ser was the only Cys/Ser mutant unable to form dimers in both assays. We also generated a laforin truncation lacking the last three amino acids, laforin-Cys329X, and this truncation also failed to dimerize. Interestingly, laforin-Cys329Ser and laforin-Cys329X were able to bind glucans, and maintained wild type phosphatase activity against both exogenous and biologically relevant substrates. Furthermore, laforin-Cys329Ser was fully capable of participating in the ubiquitination process driven by a laforin-malin complex. These results suggest that dimerization is not required for laforin phosphatase activity, glucan binding, or for the formation of a functional laforin-malin complex. Cumulatively, these results suggest that cysteine 329 is specifically involved in the dimerization process of laforin. Therefore, the C329S mutant constitutes a valuable tool to analyze the physiological implications of laforin’s oligomerization.
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Meekins DA, Guo HF, Husodo S, Paasch BC, Bridges TM, Santelia D, Kötting O, Vander Kooi CW, Gentry MS. Structure of the Arabidopsis glucan phosphatase like sex four2 reveals a unique mechanism for starch dephosphorylation. THE PLANT CELL 2013; 25:2302-14. [PMID: 23832589 PMCID: PMC3723627 DOI: 10.1105/tpc.113.112706] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/31/2013] [Accepted: 06/12/2013] [Indexed: 05/20/2023]
Abstract
Starch is a water-insoluble, Glc-based biopolymer that is used for energy storage and is synthesized and degraded in a diurnal manner in plant leaves. Reversible phosphorylation is the only known natural starch modification and is required for starch degradation in planta. Critical to starch energy release is the activity of glucan phosphatases; however, the structural basis of dephosphorylation by glucan phosphatases is unknown. Here, we describe the structure of the Arabidopsis thaliana starch glucan phosphatase like sex four2 (LSF2) both with and without phospho-glucan product bound at 2.3Å and 1.65Å, respectively. LSF2 binds maltohexaose-phosphate using an aromatic channel within an extended phosphatase active site and positions maltohexaose in a C3-specific orientation, which we show is critical for the specific glucan phosphatase activity of LSF2 toward native Arabidopsis starch. However, unlike other starch binding enzymes, LSF2 does not possess a carbohydrate binding module domain. Instead we identify two additional glucan binding sites located within the core LSF2 phosphatase domain. This structure is the first of a glucan-bound glucan phosphatase and provides new insights into the molecular basis of this agriculturally and industrially relevant enzyme family as well as the unique mechanism of LSF2 catalysis, substrate specificity, and interaction with starch granules.
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Affiliation(s)
- David A. Meekins
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Hou-Fu Guo
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Satrio Husodo
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Bradley C. Paasch
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Travis M. Bridges
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Diana Santelia
- Institute of Plant Biology, University of Zürich, 8092 Zurich, Switzerland
| | - Oliver Kötting
- Institute for Agricultural Sciences, ETH Zürich, 8092 Zurich, Switzerland
| | - Craig W. Vander Kooi
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
- Address correspondence to
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