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Zhang Z, Tringides ML, Morgan CE, Miyagi M, Mears JA, Hoppel CL, Yu EW. High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology. Mol Cell Proteomics 2023; 22:100666. [PMID: 37839702 PMCID: PMC10709515 DOI: 10.1016/j.mcpro.2023.100666] [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: 06/15/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023] Open
Abstract
The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level.
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Affiliation(s)
- Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Marios L Tringides
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Charles L Hoppel
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
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2
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Ghazouani L, Feriani A, Mufti A, Tir M, Baaziz I, Mansour HB, Mnafgui K. Toxic effect of alpha cypermethrin, an environmental pollutant, on myocardial tissue in male wistar rats. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:5709-5717. [PMID: 31119542 DOI: 10.1007/s11356-019-05336-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
α-Cypermethrin (CYP) is a pyrethroid insecticide-like environmental pollutant, widely found in the environment. New research links exposure to high levels of CYP to health damage; however, little is known about the effect of CYP on cardiovascular disease. The purpose of the present study was to evaluate, for the first time, biochemical and cardiovascular changes in male rats resulting from subchronic CYP exposure. The animals were divided into three groups: group 1 served as the control, group 2 (CYP1) received 4 mg/kg of CYP by gavage, and group 3 (CYP2) received 8 mg/kg of CYP by gavage, for 8 weeks each. Results showed that both CYP1 and CYP2 markedly increased plasma concentrations of cardiac markers (LDH, CK-MB, and troponin-T). Moreover, compared to the control group, CYP treatment elevated cardiac oxidative stress, as shown by increased MDA level and decreased activity of SOD, CAT, and GSH-Px. In addition, CYP2 caused a significant increase of 42% the concentration of total cholesterol and more than 75% in triglycerides compared to the control group. Furthermore, DNA fragmentation and collagen deposition were both amplified owing to CYP toxicity. This harmful effect was confirmed by a histological study using H-E and Sirius Red staining. Overall, our results clearly proved the cardiotoxicity caused by α-cypermethrin.
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Affiliation(s)
- Lakhdar Ghazouani
- Research Unit of Macromolecular Biochemistry and Genetics, Faculty of Sciences of Gafsa, 2112, Gafsa, Tunisia.
| | - Anouar Feriani
- Research Unit of Macromolecular Biochemistry and Genetics, Faculty of Sciences of Gafsa, 2112, Gafsa, Tunisia
| | - Afoua Mufti
- Research Unit of Macromolecular Biochemistry and Genetics, Faculty of Sciences of Gafsa, 2112, Gafsa, Tunisia
| | - Meriam Tir
- UR de Physiologie et Environnement Aquatique, Faculté des Sciences de Tunis, Université Tunis EL Manar, 2092, Tunis, Tunisia
| | - Intissar Baaziz
- Research Unit of Macromolecular Biochemistry and Genetics, Faculty of Sciences of Gafsa, 2112, Gafsa, Tunisia
| | - Hedi Ben Mansour
- Research Unit of Analysis and Process Applied to Environmental (APAE) UR17ES32 Higher Institute of Applied Sciences and Technology Mahdia, "ISSAT", University of Monastir, Monastir, Tunisia
| | - Kais Mnafgui
- Laboratory of Animal Physiology, Faculty of Sciences of Sfax, University of Sfax, P.O. Box 95, 3052, Sfax, Tunisia
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della Valle E, Marracino P, Pakhomova O, Liberti M, Apollonio F. Nanosecond pulsed electric signals can affect electrostatic environment of proteins below the threshold of conformational effects: The case study of SOD1 with a molecular simulation study. PLoS One 2019; 14:e0221685. [PMID: 31454403 PMCID: PMC6711501 DOI: 10.1371/journal.pone.0221685] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/13/2019] [Indexed: 12/19/2022] Open
Abstract
Electric fields can be a powerful tool to interact with enzymes or proteins, with an intriguing perspective to allow protein manipulation. Recently, researchers have focused the interest on intracellular enzyme modifications triggered by the application of nanosecond pulsed electric fields. These findings were also supported by theoretical predictions from molecular dynamics simulations focussing on significant variations in protein secondary structures. In this work, a theoretical study utilizing molecular dynamics simulations is proposed to explore effects of electric fields of high intensity and very short nanosecond duration applied to the superoxide dismutase (Cu/Zn-SOD or SOD-1), an important enzyme involved in the cellular antioxidant defence mechanism. The effects of 100-nanosecond pulsed electric fields, with intensities ranging from 108 to 7x108 V/m, on a single SOD1 enzyme are presented. We demonstrated that the lowest intensity of 108 V/m, although not inducing structural changes, can produce electrostatic modifications on the reaction centre of the enzyme, as apparent from the dipolar response and the electric field distribution of the protein active site. Electric pulses above 5x108 V/m produced a fast transition between the folded and a partially denatured state, as inferred by the secondary structures analysis. Finally, for the highest field intensity used (7x108 V/m), a not reversible transition toward an unfolded state was observed.
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Affiliation(s)
- Elena della Valle
- BioElectronic Vision Lab, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Olga Pakhomova
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, Virginia, United States of America
| | - Micaela Liberti
- Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome, Rome, Italy
| | - Francesca Apollonio
- Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome, Rome, Italy
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4
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Mi C, Teng Y, Wang X, Yu H, Huang Z, Zong W, Zou L. Molecular interaction of triclosan with superoxide dismutase (SOD) reveals a potentially toxic mechanism of the antimicrobial agent. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 153:78-83. [PMID: 29407741 DOI: 10.1016/j.ecoenv.2018.01.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 05/24/2023]
Abstract
In this article, the interaction mechanism between the superoxide dismutase (SOD) and the triclosan (TCS), a kind of antimicrobial agent which is of widely application with potential effects both on environment and human health, was explored through a series of spectroscopic methods, animal experiment and the molecular docking simulation. The negative free energy change ∆G, enthalpy change (∆H = 162.21 kJmol-1) and entropy change (∆S = 615 Jmol-1K-1) demonstrated that TCS could combine with SOD spontaneously through hydrophobic interaction to form a complex. The binding constants of Ka293 and Ka313 were 1.706 × 103 and 1.2 × 105 Lmol-1, respectively. Furthermore, the interaction could also influence the skeleton structure and secondary contents of SOD. The molecular docking analysis revealed the TCS located between two subunits of SOD, and there was a hydrogen bond between TCS and the residue Asn51 of SOD, which influenced the structure of protein and resulted in a decrease of enzyme activity. This work could help understand the interaction mechanism between SOD and TCS. Moreover, it could also be used to consult for toxicity assessment of TCS at molecular level.
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Affiliation(s)
- Chenyu Mi
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi 214122, PR China
| | - Yue Teng
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi 214122, PR China
| | - Xiaofang Wang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi 214122, PR China
| | - Hongyan Yu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi 214122, PR China
| | - Zhenxing Huang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi 214122, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou 215009, PR China
| | - Wansong Zong
- College of Population, Resources and Environment, Shandong Normal University, 88# Wenhua Road, Jinan 250014, PR China
| | - Luyi Zou
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi 214122, PR China.
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Thermostable Fe/Mn superoxide dismutase from Bacillus licheniformis SPB-13 from thermal springs of Himalayan region: Purification, characterization and antioxidative potential. Int J Biol Macromol 2018; 115:1026-1032. [PMID: 29727639 DOI: 10.1016/j.ijbiomac.2018.04.155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/21/2018] [Accepted: 04/28/2018] [Indexed: 11/21/2022]
Abstract
Superoxide dismutase (SOD; EC 1.15.1.1) is an enzyme that scavenges free radicals and increases the longevity. In this study, a thermostable superoxide dismutase (SOD) from Bacillus licheniformis SPB-13, from Himalayan region was purified to homogeneity using ion exchange chromatography (DEAE-Sepharose). The SDS and native PAGE analysis showed that SOD is composed of two subunits of 32 kDa each and total molecular mass of the enzyme was estimated as 68 kDa. The specific activity of enzyme was 3965.51 U/mg and was purified to 16.17 folds. The SOD showed maximum activity with 60 mM Tris-HCl buffer at pH 8.0 for 2 min of incubation. Enzyme along with FeCl3 as metal ion remained active till 70 °C. After reaction variables optimization, enzyme activity increased from 3965.51 to 4015.72 U/mg. Kinetic analysis of SOD showed km of 1.4 mM of NADH and Vmax of 10000 U/mg of protein. Turnover number (kcat) and catalytic efficiency (kcat/Km) were found to be 11,333 s-1 and 7092.2 s-1·mM-1 NADH. The activation energy (Ea) was calculated as 2.67 kJ·mol-1. After typing, it was found to be a member of Fe/Mn SOD family with IC50 value of 25 μg/ml, prevented the cell death at a concentration of 30 μg/ml and it increased the cell viability by 30%.
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Guan T, Song J, Wang Y, Guo L, Yuan L, Zhao Y, Gao Y, Lin L, Wang Y, Wei J. Expression and characterization of recombinant bifunctional enzymes with glutathione peroxidase and superoxide dismutase activities. Free Radic Biol Med 2017; 110:188-195. [PMID: 28603086 DOI: 10.1016/j.freeradbiomed.2017.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/26/2017] [Accepted: 06/06/2017] [Indexed: 01/29/2023]
Abstract
To balance the production and decomposition of reactive oxygen species, living organisms have generated antioxidant enzymes and non-enzymatic antioxidant defense systems. Glutathione peroxidase (GPx) and superoxide dismutase (SOD) are two important antioxidant enzymes. Apart from their catalytic functions, they protect each other, resulting in more efficient removal of reactive oxygen species, protection of cells against injury, and maintenance of the normal metabolism of reactive oxygen species. SOD catalyzes the dismutation of the superoxide anion (O2•-) to oxygen (O2) and hydrogen peroxide (H2O2). H2O2 is then detoxified to water by GPx. In this study, human GPx1Ser and the Alvinella pompejana SOD (ApSOD) gene were used to design and generate several recombinant proteins with both GPx and SOD activities by combining traditional fusion protein technology, a cysteine auxotrophic expression system, and a single protein production (SPP) system. Among the fusion proteins, Se-hGPx1Ser-L-ApSOD exhibited the highest SOD and GPx activities. Additional research was conducted to better understand the properties of Se-hGPx1Ser-L-ApSOD. The synergism of Se-hGPx1Ser-L-ApSOD was evaluated by using an in vitro model. This research may facilitate future studies on the cooperation and catalytic mechanisms of GPx and SOD. We believe that the bifunctional enzyme has potential applications as a potent antioxidant.
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Affiliation(s)
- Tuchen Guan
- College of Pharmaceutical Science, Jilin University, Changchun 130021, PR China
| | - Jian Song
- College of Electronic Science and Engineering, Jilin University, Changchun 130000, PR China
| | - Yanan Wang
- College of Pharmaceutical Science, Jilin University, Changchun 130021, PR China
| | - Liying Guo
- College of Pharmaceutical Science, Jilin University, Changchun 130021, PR China
| | - Lin Yuan
- College of Pharmaceutical Science, Jilin University, Changchun 130021, PR China
| | - Yingding Zhao
- Eighth High School of Changchun, Changchun 130021, PR China
| | - Yuan Gao
- College of Pharmaceutical Science, Jilin University, Changchun 130021, PR China
| | - Liangru Lin
- College of Pharmaceutical Science, Jilin University, Changchun 130021, PR China
| | - Yali Wang
- College of Pharmaceutical Science, Jilin University, Changchun 130021, PR China
| | - Jingyan Wei
- College of Pharmaceutical Science, Jilin University, Changchun 130021, PR China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130000, PR China.
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7
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Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase. J Struct Biol 2017; 199:68-75. [PMID: 28461152 DOI: 10.1016/j.jsb.2017.04.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/10/2017] [Accepted: 04/27/2017] [Indexed: 01/22/2023]
Abstract
Superoxide dismutases (SODs) are enzymes that play a key role in protecting cells from toxic oxygen metabolites by disproportionation of two molecules of superoxide into molecular oxygen and hydrogen peroxide via cyclic reduction and oxidation at the active site metal. The azide anion is a potent competitive inhibitor that binds directly to the metal and is used as a substrate analog to superoxide in studies of SOD. The crystal structure of human MnSOD-azide complex was solved and shows the putative binding position of superoxide, providing a model for binding to the active site. Azide is bound end-on at the sixth coordinate position of the manganese ion. Tetrameric electrostatic surfaces were calculated incorporating accurate partial charges for the active site in three states, including a state with superoxide coordinated to the metal using the position of azide as a model. These show facilitation of the anionic ligand to the active site pit via a 'valley' of positively-charged surface patches. Surrounding ridges of negative charge help guide the superoxide anion. Within the active site pit, Arg173 and Glu162 further guide and align superoxide for efficient catalysis. Superoxide coordination at the sixth position causes the electrostatic surface of the active site pit to become nearly neutral. A model for electrostatic-mediated diffusion, and efficient binding of superoxide for catalysis is presented.
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8
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Azadmanesh J, Trickel SR, Weiss KL, Coates L, Borgstahl GEO. Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals. Acta Crystallogr F Struct Biol Commun 2017; 73:235-240. [PMID: 28368283 PMCID: PMC5379174 DOI: 10.1107/s2053230x17003508] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/04/2017] [Indexed: 11/10/2022] Open
Abstract
Superoxide dismutases (SODs) are enzymes that protect against oxidative stress by dismutation of superoxide into oxygen and hydrogen peroxide through cyclic reduction and oxidation of the active-site metal. The complete enzymatic mechanisms of SODs are unknown since data on the positions of hydrogen are limited. Here, methods are presented for large crystal growth and neutron data collection of human manganese SOD (MnSOD) using perdeuteration and the MaNDi beamline at Oak Ridge National Laboratory. The crystal from which the human MnSOD data set was obtained is the crystal with the largest unit-cell edge (240 Å) from which data have been collected via neutron diffraction to sufficient resolution (2.30 Å) where hydrogen positions can be observed.
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Affiliation(s)
- Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Scott R. Trickel
- Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
| | - Kevin L. Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA
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Xu B, Gao Y, Zhan S, Xiong F, Qiu W, Qian X, Wang T, Wang N, Zhang D, Yang Q, Wang R, Bao X, Dou W, Tian R, Meng S, Gai WP, Huang Y, Yan XX, Ge W, Ma C. Quantitative protein profiling of hippocampus during human aging. Neurobiol Aging 2015; 39:46-56. [PMID: 26923401 DOI: 10.1016/j.neurobiolaging.2015.11.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/23/2015] [Accepted: 11/28/2015] [Indexed: 11/17/2022]
Abstract
The hippocampus appears commonly affected by aging and various neurologic disorders in humans, whereas little is known about age-related change in overall protein expression in this brain structure. Using the 4-plex tandem mass tag labeling, we carried out a quantitative proteomic study of the hippocampus during normal aging using postmortem brains from Chinese subjects. Hippocampal samples from 16 subjects died of non-neurological/psychiatric diseases were divided into 4 age groups: 22-49, 50-69, 70-89, and >90. Among 4582 proteins analyzed, 35 proteins were significantly elevated, whereas 25 proteins were downregulated, along with increasing age. Several upregulated proteins, including transgelin, vimentin, myosin regulatory light polypeptide 9, and calcyphosin, were further verified by quantitative Western blot analysis of hippocampal tissues from additional normal subjects. Bioinformatic analysis showed that the upregulated and downregulated proteins were largely involved in several important protein-protein interaction networks. Proteins in the electron transport chain and synaptic vesicle fusion pathway were consistently downregulated with aging, whereas proteins associated with Alzheimer's disease showed little change. Our study demonstrates substantial protein profile changes in the human hippocampus during aging, which could be of relevance to age-related loss of hippocampal functions.
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Affiliation(s)
- Benhong Xu
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanpan Gao
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Shaohua Zhan
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Feng Xiong
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Wenying Qiu
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaojing Qian
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Tao Wang
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Naili Wang
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Di Zhang
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Qian Yang
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Renzhi Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinjie Bao
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wanchen Dou
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Rui Tian
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Shu Meng
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei-Ping Gai
- Department of Surgery and Centre for Neuroscience, Flinders University School of Medicine, Bedford Park, SA, Australia
| | - Yue Huang
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Xiao-Xin Yan
- Department of Anatomy and Neurobiology, Central South University School of Basic Medical Science, Changsha, Hunan, China
| | - Wei Ge
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
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10
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Pratt AJ, DiDonato M, Shin DS, Cabelli DE, Bruns CK, Belzer CA, Gorringe AR, Langford PR, Tabatabai LB, Kroll JS, Tainer JA, Getzoff ED. Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus. J Bacteriol 2015; 197:3834-47. [PMID: 26459556 PMCID: PMC4652047 DOI: 10.1128/jb.00343-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/29/2015] [Indexed: 12/17/2022] Open
Abstract
UNLABELLED Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen and general pathogenicity factors and are therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomic details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and of SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly, and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes, and suggest general targets for antibacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors of or vaccines against these harmful pathogens. IMPORTANCE By protecting microbes against reactive oxygen insults, SODs aid survival of many bacteria within their hosts. Despite the ubiquity and conservation of these key enzymes, notable species-specific differences relevant to pathogenesis remain undefined. To probe mechanisms that govern the functioning of Neisseria meningitidis and Brucella abortus SODs, we used X-ray structures, enzymology, modeling, and murine infection experiments. We identified virulence determinants common to the two homologs, assembly differences, and a unique metal reservoir within meningococcal SOD that stabilizes the enzyme and may provide a safeguard against copper toxicity. The insights reported here provide a rationale and a basis for SOD-specific drug design and an extension of immunogen design to target two important pathogens that continue to pose global health threats.
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Affiliation(s)
- Ashley J Pratt
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael DiDonato
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - David S Shin
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Diane E Cabelli
- Chemistry Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Cami K Bruns
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Carol A Belzer
- National Animal Disease Center, Ruminant Diseases and Immunology, Ames, Iowa, USA
| | | | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, England, United Kingdom
| | - Louisa B Tabatabai
- National Animal Disease Center, Ruminant Diseases and Immunology, Ames, Iowa, USA
| | - J Simon Kroll
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, England, United Kingdom
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
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11
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Cao Z, Liu R, Dong Z, Yang X, Chen Y. The effect of sarafloxacin on Cu/ZnSOD structure and activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:601-606. [PMID: 25448960 DOI: 10.1016/j.saa.2014.09.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 08/30/2014] [Accepted: 09/18/2014] [Indexed: 06/04/2023]
Abstract
The effect of sarafloxacin to Cu/ZnSOD was evaluated via investigating the change in Cu/ZnSOD structure and the structure basis activity upon sarafloxacin binding. Multi-spectroscopic methods, isothermal titration microcalorimetry (ITC) and molecular docking method were adopted in this study. Sarafloxacin binds to Cu/ZnSOD mainly through hydrophobic and hydrogen bond forces and tends to be saturated as the molar ratio of sarafloxacin to Cu/ZnSOD reaches 4. The binding changed the microenvironment around Tyr and the secondary structure of Cu/ZnSOD but did not affect the activity of Cu/ZnSOD. Molecular docking study revealed that sarafloxacin binds into a hydrophobic area with possibility to form hydrogen bonds with Tyr 108, Asp 25, Pro 100 and Ser 103 of Cu/ZnSOD. The binding area locates on the surface of β-barrel close to the second Greek key loop (GK2) and V-loop but far away from the active site and active site channel of Cu/ZnSOD. These promoted the understanding of the experiment phenomenons. The binding of sarafloxacin does not affect the activity of Cu/ZnSOD should attribute to the binding not to change the microenvironment of Cu/ZnSOD active site and active site channel.
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Affiliation(s)
- Zhaozhen Cao
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province, PR China; School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong Province, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province, PR China.
| | - Ziliang Dong
- China Research Institute of Daily Chemical Industry, Taiyuan 030001, Shanxi Province, PR China
| | - Xinping Yang
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province, PR China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Basic Science, China Pharmaceutical University, Nanjing 210009, PR China
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12
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Li M, Lin YF, Palchik GA, Matsunaga S, Wang D, Chen BPC. The catalytic subunit of DNA-dependent protein kinase is required for cellular resistance to oxidative stress independent of DNA double-strand break repair. Free Radic Biol Med 2014; 76:278-85. [PMID: 25224041 PMCID: PMC4267055 DOI: 10.1016/j.freeradbiomed.2014.08.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 10/24/2022]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and ataxia telangiectasia mutated (ATM) are the two major kinases involved in DNA double-strand break (DSB) repair, and are required for cellular resistance to ionizing radiation. Whereas ATM is the key upstream kinase for DSB signaling, DNA-PKcs is primarily involved in DSB repair through the nonhomologous end-joining (NHEJ) mechanism. In addition to DSB repair, ATM has been shown to be involved in the oxidative stress response and could be activated directly in vitro on hydrogen peroxide (H2O2) treatment. However, the role of DNA-PKcs in cellular response to oxidative stress is not clear. We hypothesize that DNA-PKcs may participate in the regulation of ATM activation in response to oxidative stress, and that this regulatory role is independent of its role in DNA double-strand break repair. Our findings reveal that H2O2 induces hyperactivation of ATM signaling in DNA-PKcs-deficient, but not Ligase 4-deficient cells, suggesting an NHEJ-independent role for DNA-PKcs. Furthermore, DNA-PKcs deficiency leads to the elevation of reactive oxygen species (ROS) production, and to a decrease in cellular survival against H2O2. For the first time, our results reveal that DNA-PKcs plays a noncanonical role in the cellular response to oxidative stress, which is independent from its role in NHEJ. In addition, DNA-PKcs is a critical regulator of the oxidative stress response and contributes to the maintenance of redox homeostasis. Our findings reveal that DNA-PKcs is required for cellular resistance to oxidative stress and suppression of ROS buildup independently of its function in DSB repair.
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Affiliation(s)
- Mengxia Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Cancer Center, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Yu-Fen Lin
- Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Guillermo A Palchik
- Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Shinji Matsunaga
- Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Dong Wang
- Cancer Center, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Benjamin P C Chen
- Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.
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13
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Haikarainen T, Frioux C, Zhnag LQ, Li DC, Papageorgiou AC. Crystal structure and biochemical characterization of a manganese superoxide dismutase from Chaetomium thermophilum. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:422-9. [PMID: 24316252 DOI: 10.1016/j.bbapap.2013.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 11/20/2013] [Accepted: 11/23/2013] [Indexed: 10/25/2022]
Abstract
A manganese superoxide dismutase from the thermophilic fungus Chaetomium thermophilum (CtMnSOD) was expressed in Pichia pastoris and purified to homogeneity. Its optimal temperature was 60°C with approximately 75% of its activity retained after incubation at 70°C for 60min. Recombinant yeast cells carrying C. thermophilum mnsod gene exhibited higher stress resistance to salt and oxidative stress-inducing agents than control yeast cells. In an effort to provide structural insights, CtMnSOD was crystallized and its structure was determined at 2.0Å resolution. The overall architecture of CtMnSOD was found similar to other MnSODs with highest structural similarities obtained against a MnSOD from the thermotolerant fungus Aspergillus fumigatus. In order to explain its thermostability, structural and sequence analysis of CtMnSOD with other MnSODs was carried out. An increased number of charged residues and an increase in the number of intersubunit salt bridges and the Thr:Ser ratio were identified as potential reasons for the thermostability of CtMnSOD.
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Affiliation(s)
- Teemu Haikarainen
- Turku Centre for Biotechnology, University of Turku, BioCity, Turku 20521, Finland; Åbo Akademi University, BioCity, Turku 20521, Finland
| | - Clémence Frioux
- Turku Centre for Biotechnology, University of Turku, BioCity, Turku 20521, Finland; Åbo Akademi University, BioCity, Turku 20521, Finland
| | - Li-Qing Zhnag
- Department of Environmental Biology, Shandong Agricultural University, Taian, Shandong 271018, China; Department of Chemistry and Chemical Engineering, Taishan Medical College, Taian, Shandong 271016, China
| | - Duo-Chuan Li
- Department of Environmental Biology, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Anastassios C Papageorgiou
- Turku Centre for Biotechnology, University of Turku, BioCity, Turku 20521, Finland; Åbo Akademi University, BioCity, Turku 20521, Finland.
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14
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Perry JJP, Tainer JA. Developing advanced X-ray scattering methods combined with crystallography and computation. Methods 2013; 59:363-71. [PMID: 23376408 PMCID: PMC3684416 DOI: 10.1016/j.ymeth.2013.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/15/2013] [Accepted: 01/18/2013] [Indexed: 01/09/2023] Open
Abstract
The extensive use of small angle X-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered as being part of one's repertoire of biophysical analyses, when conducting characterizations of protein and other macromolecular interactions.
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Affiliation(s)
- J. Jefferson P. Perry
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA USA
- School of Biotechnology, Amrita University at Amritapuri, Kollam, Kerala, India
| | - John A. Tainer
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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15
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Pratt AJ, Getzoff ED, Perry JJP. Amyotrophic lateral sclerosis: update and new developments. Degener Neurol Neuromuscul Dis 2012; 2012:1-14. [PMID: 23019386 PMCID: PMC3457793 DOI: 10.2147/dnnd.s19803] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common form of motor neuron disease. It is typically characterized by adult-onset degeneration of the upper and lower motor neurons, and is usually fatal within a few years of onset. A subset of ALS patients has an inherited form of the disease, and a few of the known mutant genes identified in familial cases have also been found in sporadic forms of ALS. Precisely how the diverse ALS-linked gene products dictate the course of the disease, resulting in compromised voluntary muscular ability, is not entirely known. This review addresses the major advances that are being made in our understanding of the molecular mechanisms giving rise to the disease, which may eventually translate into new treatment options.
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Affiliation(s)
- Ashley J Pratt
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,
| | - Elizabeth D Getzoff
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,
| | - J Jefferson P Perry
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,
- The School of Biotechnology, Amrita University, Kollam, Kerala 690525, India,
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16
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Raz-Prag D, Galron R, Segev-Amzaleg N, Solomon AS, Shiloh Y, Barzilai A, Frenkel D. A role for vascular deficiency in retinal pathology in a mouse model of ataxia-telangiectasia. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 179:1533-41. [PMID: 21763675 DOI: 10.1016/j.ajpath.2011.05.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 04/09/2011] [Accepted: 05/09/2011] [Indexed: 02/06/2023]
Abstract
Ataxia-telangiectasia is a multifaceted syndrome caused by null mutations in the ATM gene, which encodes the protein kinase ATM, a key participant in the DNA damage response. Retinal neurons are highly susceptible to DNA damage because they are terminally differentiated and have the highest metabolic activity in the central nervous system. In this study, we characterized the retina in young and aged Atm-deficient mice (Atm(-/-)). At 2 months of age, angiography revealed faint retinal vasculature in Atm(-/-) animals relative to wild-type controls. This finding was accompanied by increased expression of vascular endothelial growth factor protein and mRNA. Fibrinogen, generally absent from wild-type retinal tissue, was evident in Atm(-/-) retinas, whereas mRNA of the tight junction protein occludin was significantly decreased. Immunohistochemistry labeling for occludin in 6-month-old mice showed that this decrease persists in advanced stages of the disease. Concurrently, we noticed vascular leakage in Atm(-/-) retinas. Labeling for glial fibrillary acidic protein demonstrated morphological alterations in glial cells in Atm(-/-) retinas. Electroretinographic examination revealed amplitude aberrations in 2-month-old Atm(-/-) mice, which progressed to significant functional deficits in the older mice. These results suggest that impaired vascularization and astrocyte-endothelial cell interactions in the central nervous system play an important role in the etiology of ataxia-telangiectasia and that vascular abnormalities may underlie or aggravate neurodegeneration.
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Affiliation(s)
- Dorit Raz-Prag
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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17
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Nelson PT, Head E, Schmitt FA, Davis PR, Neltner JH, Jicha GA, Abner EL, Smith CD, Van Eldik LJ, Kryscio RJ, Scheff SW. Alzheimer's disease is not "brain aging": neuropathological, genetic, and epidemiological human studies. Acta Neuropathol 2011; 121:571-87. [PMID: 21516511 PMCID: PMC3179861 DOI: 10.1007/s00401-011-0826-y] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 04/12/2011] [Accepted: 04/13/2011] [Indexed: 01/18/2023]
Abstract
Human studies are reviewed concerning whether "aging"-related mechanisms contribute to Alzheimer's disease (AD) pathogenesis. AD is defined by specific neuropathology: neuritic amyloid plaques and neocortical neurofibrillary tangles. AD pathology is driven by genetic factors related not to aging per se, but instead to the amyloid precursor protein (APP). In contrast to genes involved in APP-related mechanisms, there is no firm connection between genes implicated in human "accelerated aging" diseases (progerias) and AD. The epidemiology of AD in advanced age is highly relevant but deceptively challenging to address given the low autopsy rates in most countries. In extreme old age, brain diseases other than AD approximate AD prevalence while the impact of AD pathology appears to peak by age 95 and decline thereafter. Many distinct brain diseases other than AD afflict older human brains and contribute to cognitive impairment. Additional prevalent pathologies include cerebrovascular disease and hippocampal sclerosis, both high-morbidity brain diseases that appear to peak in incidence later than AD chronologically. Because of these common brain diseases of extreme old age, the epidemiology differs between clinical "dementia" and the subset of dementia cases with AD pathology. Additional aging-associated mechanisms for cognitive decline such as diabetes and synapse loss have been linked to AD and these hypotheses are discussed. Criteria are proposed to define an "aging-linked" disease, and AD fails all of these criteria. In conclusion, it may be most fruitful to focus attention on specific pathways involved in AD rather than attributing it to an inevitable consequence of aging.
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Affiliation(s)
- Peter T Nelson
- Department of Pathology, University of Kentucky, Lexington, KY 40536-0230, USA.
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18
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Abstract
Ataxia-telangiectasia (A-T) is a rare, neurodegenerative, inherited disease arising from mutations in the kinase A-T mutated (ATM), which promotes cell cycle checkpoints and DNA double-strand break repair. Puzzlingly, these ATM activities fail to fully explain A-T neuropathologies, which instead have links to stress induced by reactive oxygen species (ROS). However, a landmark discovery reveals an unexpected intersection of ROS and kinase signaling: ATM can be directly activated by oxidation to form a disulfide-linked dimer in a mechanism distinct from DNA damage activation. When combined with notable structural-based insights into the ATM homolog DNA-PK (DNA-protein kinase) and mTOR (mammalian target of rapamycin), these results suggest conformation and assembly mechanisms to signal oxidative stress through an ATM nodal point. These findings fundamentally affect our understanding of ROS and ATM signaling and of the A-T phenotype, with implications for altering signaling in cancer cells to increase sensitivities to current therapeutic interventions.
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Affiliation(s)
- J Jefferson P Perry
- Skaggs Institute for Chemical Biology, Department of Molecular Biology, La Jolla, CA 92037, USA
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19
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Bennett LE, Jegasothy H, Konczak I, Frank D, Sudharmarajan S, Clingeleffer PR. Total polyphenolics and anti-oxidant properties of selected dried fruits and relationships to drying conditions. J Funct Foods 2011. [DOI: 10.1016/j.jff.2011.03.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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20
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Facile and scalable synthesis of a novel rigid artificial superoxide dismutase based on modified hollow mesoporous silica microspheres. Biosens Bioelectron 2011; 26:1936-41. [DOI: 10.1016/j.bios.2010.06.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 05/26/2010] [Accepted: 06/28/2010] [Indexed: 11/22/2022]
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21
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Rosenfeld RJ, Bonaventura J, Szymczyna BR, MacCoss MJ, Arvai AS, Yates JR, Tainer JA, Getzoff ED. Nitric-oxide synthase forms N-NO-pterin and S-NO-cys: implications for activity, allostery, and regulation. J Biol Chem 2010; 285:31581-9. [PMID: 20659888 DOI: 10.1074/jbc.m109.072496] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Inducible nitric-oxide synthase (iNOS) produces biologically stressful levels of nitric oxide (NO) as a potent mediator of cellular cytotoxicity or signaling. Yet, how this nitrosative stress affects iNOS function in vivo is poorly understood. Here we define two specific non-heme iNOS nitrosation sites discovered by combining UV-visible spectroscopy, chemiluminescence, mass spectrometry, and x-ray crystallography. We detected auto-S-nitrosylation during enzymatic turnover by using chemiluminescence. Selective S-nitrosylation of the ZnS(4) site, which bridges the dimer interface, promoted a dimer-destabilizing order-to-disorder transition. The nitrosated iNOS crystal structure revealed an unexpected N-NO modification on the pterin cofactor. Furthermore, the structurally defined N-NO moiety is solvent-exposed and available to transfer NO to a partner. We investigated glutathione (GSH) as a potential transnitrosation partner because the intracellular GSH concentration is high and NOS can form S-nitrosoglutathione. Our computational results predicted a GSH binding site adjacent to the N-NO-pterin. Moreover, we detected GSH binding to iNOS with saturation transfer difference NMR spectroscopy. Collectively, these observations resolve previous paradoxes regarding this uncommon pterin cofactor in NOS and suggest means for regulating iNOS activity via N-NO-pterin and S-NO-Cys modifications. The iNOS self-nitrosation characterized here appears appropriate to help control NO production in response to cellular conditions.
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Affiliation(s)
- Robin J Rosenfeld
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
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22
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Porta J, Vahedi-Faridi A, Borgstahl GE. Structural Analysis of Peroxide-Soaked MnSOD Crystals Reveals Side-On Binding of Peroxide to Active-Site Manganese. J Mol Biol 2010; 399:377-84. [DOI: 10.1016/j.jmb.2010.04.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/24/2010] [Accepted: 04/18/2010] [Indexed: 10/19/2022]
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23
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Shukla PC, Singh KK, Yanagawa B, Teoh H, Verma S. DNA damage repair and cardiovascular diseases. Can J Cardiol 2010; 26 Suppl A:13A-16A. [DOI: 10.1016/s0828-282x(10)71055-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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24
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Perry J, Shin D, Getzoff E, Tainer J. The structural biochemistry of the superoxide dismutases. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:245-62. [PMID: 19914407 PMCID: PMC3098211 DOI: 10.1016/j.bbapap.2009.11.004] [Citation(s) in RCA: 322] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 01/11/2023]
Abstract
The discovery of superoxide dismutases (SODs), which convert superoxide radicals to molecular oxygen and hydrogen peroxide, has been termed the most important discovery of modern biology never to win a Nobel Prize. Here, we review the reasons this discovery has been underappreciated, as well as discuss the robust results supporting its premier biological importance and utility for current research. We highlight our understanding of SOD function gained through structural biology analyses, which reveal important hydrogen-bonding schemes and metal-binding motifs. These structural features create remarkable enzymes that promote catalysis at faster than diffusion-limited rates by using electrostatic guidance. These architectures additionally alter the redox potential of the active site metal center to a range suitable for the superoxide disproportionation reaction and protect against inhibition of catalysis by molecules such as phosphate. SOD structures may also control their enzymatic activity through product inhibition; manipulation of these product inhibition levels has the potential to generate therapeutic forms of SOD. Markedly, structural destabilization of the SOD architecture can lead to disease, as mutations in Cu,ZnSOD may result in familial amyotrophic lateral sclerosis, a relatively common, rapidly progressing and fatal neurodegenerative disorder. We describe our current understanding of how these Cu,ZnSOD mutations may lead to aggregation/fibril formation, as a detailed understanding of these mechanisms provides new avenues for the development of therapeutics against this so far untreatable neurodegenerative pathology.
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Affiliation(s)
- J.J.P. Perry
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The School of Biotechnology, Amrita University, Kollam, Kerala 690525, India
| | - D.S. Shin
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - E.D. Getzoff
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J.A. Tainer
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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25
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Abstract
OBJECTIVE The potential relation between metabolic activity within the central nervous system and retention of cognitive functioning capacity was assessed. METHODS A detailed literature review was conducted and summarized. RESULTS A large body of scientific evidence describes the interactions among cognitive activity, oxidative stress, neurodegeneration, neuroprotection, cognitive aging, and retention of cognitive functioning ability. CONCLUSION Maintenance of redox balance within the central nervous system can forestall cognitive decline and promote cognitive longevity.
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27
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Weidenheim KM, Dickson DW, Rapin I. Neuropathology of Cockayne syndrome: Evidence for impaired development, premature aging, and neurodegeneration. Mech Ageing Dev 2009; 130:619-36. [PMID: 19647012 DOI: 10.1016/j.mad.2009.07.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 07/16/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
Abstract
Global growth and development failure, premature, accelerated, pathologic aging, and neurodegeneration characterize Cockayne syndrome (CS) and the cerebro-oculo-facial-skeletal and xeroderma pigmentosum/CS syndromes which overlap CS partially in their genetic, somatic, and neuropathologic features. Mutations of CSA or CSB genes jeopardize transcription-coupled repair of damaged nuclear and mitochondrial DNA and resumption of replication and transcription. Resultant defective proteins or gene silencing eventuate in profound dwarfism and micrencephaly, cachexia, vasculopathy, and neurodegeneration. Cellular effects are highly selective. Purkinje cells may die by apoptosis and have grossly dystrophic dendrites. Neuronal death and axonal spheroids indexing neuronal pathology predominate in, but are not limited to, the cerebellum. Progressive loss of retinal, cochlear, and vestibular sensory receptors foster degeneration of ganglion cells and transneuronal brain degeneration. Some proliferating astrocytes are multinucleated and bizarre. Primary damage of oligodendrocytes and Schwann cells may - or may not - explain severe patchy myelin loss ("tigroid leukodystrophy") and segmental demyelinating peripheral neuropathy. Age-related changes are minor in the brain, although precocious severe athero- and arteriolosclerosis are responsible for occasional strokes. Vasculopathology may contribute to myelin loss and to dystrophic mineralization of neurons and vessels, especially in basal ganglia and cerebellum. Understanding the genetics, biochemical, and cellular pathophysiology of these disorders remains fragmentary.
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Affiliation(s)
- Karen M Weidenheim
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
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28
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Bermejo P, Martín-Aragón S, Benedí J, Susín C, Felici E, Gil P, Manuel Ribera J, Villar ÁM. Peripheral levels of glutathione and protein oxidation as markers in the development of Alzheimer's disease from Mild Cognitive Impairment. Free Radic Res 2009; 42:162-70. [DOI: 10.1080/10715760701861373] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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29
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Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. Biochemistry 2009; 48:3417-24. [PMID: 19265433 PMCID: PMC2756076 DOI: 10.1021/bi8023288] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Superoxide dismutase (SOD) enzymes are critical in controlling levels of reactive oxygen species (ROS) that are linked to aging, cancer, and neurodegenerative disease. Superoxide (O(2)(*-)) produced during respiration is removed by the product of the SOD2 gene, the homotetrameric manganese superoxide dismutase (MnSOD). Here, we examine the structural and catalytic roles of the highly conserved active-site residue Tyr34, based upon structure-function studies of MnSOD enzymes with mutations at this site. Substitution of Tyr34 with five different amino acids retained the active-site protein structure and assembly but caused a substantial decrease in the catalytic rate constant for the reduction of superoxide. The rate constant for formation of the product inhibition complex also decreases but to a much lesser extent, resulting in a net increase in the level of product inhibited form of the mutant enzymes. Comparisons of crystal structures and catalytic rates also suggest that one mutation, Y34V, interrupts the hydrogen-bonded network, which is associated with a rapid dissociation of the product-inhibited complex. Notably, with three of the Tyr34 mutants, we also observe an intermediate in catalysis, which has not been reported previously. Thus, these mutants establish a means of trapping a catalytic intermediate that promises to help elucidate the mechanism of catalysis.
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Shin DS, DiDonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA. Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis. J Mol Biol 2009; 385:1534-1555. [PMID: 19063897 PMCID: PMC2669833 DOI: 10.1016/j.jmb.2008.11.03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 11/07/2008] [Accepted: 11/11/2008] [Indexed: 05/31/2023]
Abstract
Prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. Alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees C, with spikes up to 84 degrees C. Here, we used Cu,Zn superoxide dismutase (SOD) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability by supplying better stable mammalian homologs for structural biology and other biophysical characterizations than those from prokaryotic thermophiles. Identification, cloning, characterization, X-ray scattering (small-angle X-ray scattering, SAXS), and crystal structure determinations show that A. pompejana SOD (ApSOD) is superstable, homologous, and informative. SAXS solution analyses identify the human-like ApSOD dimer. The crystal structure shows the active site at 0.99 A resolution plus anchoring interaction motifs in loops and termini accounting for enhanced stability of ApSOD versus human SOD. Such stabilizing features may reduce movements that promote inappropriate intermolecular interactions, such as amyloid-like filaments found in SOD mutants causing the neurodegenerative disease familial amyotrophic lateral sclerosis or Lou Gehrig's disease. ApSOD further provides the structure of a long-sought SOD product complex at 1.35 A resolution, suggesting a unified inner-sphere mechanism for catalysis involving metal ion movement. Notably, this proposed mechanism resolves apparent paradoxes regarding electron transfer. These results extend knowledge of SOD stability and catalysis and suggest that the eukaryote A. pompejana provides macromolecules highly similar to those from humans, but with enhanced stability more suitable for scientific and medical applications.
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Affiliation(s)
- David S. Shin
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael DiDonato
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P. Barondeau
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Greg L. Hura
- Advanced Light Source, Lawrence Berkeley National Laboratory, CA 94720, USA
| | - Chiharu Hitomi
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J. Andrew Berglund
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Elizabeth D. Getzoff
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - S. Craig Cary
- College of Marine Studies, University of Delaware, Lewes, DE 19958, USA
- Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand
| | - John A. Tainer
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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31
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Shin DS, DiDonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA. Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis. J Mol Biol 2009; 385:1534-55. [PMID: 19063897 PMCID: PMC2669833 DOI: 10.1016/j.jmb.2008.11.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 11/07/2008] [Accepted: 11/11/2008] [Indexed: 01/07/2023]
Abstract
Prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. Alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees C, with spikes up to 84 degrees C. Here, we used Cu,Zn superoxide dismutase (SOD) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability by supplying better stable mammalian homologs for structural biology and other biophysical characterizations than those from prokaryotic thermophiles. Identification, cloning, characterization, X-ray scattering (small-angle X-ray scattering, SAXS), and crystal structure determinations show that A. pompejana SOD (ApSOD) is superstable, homologous, and informative. SAXS solution analyses identify the human-like ApSOD dimer. The crystal structure shows the active site at 0.99 A resolution plus anchoring interaction motifs in loops and termini accounting for enhanced stability of ApSOD versus human SOD. Such stabilizing features may reduce movements that promote inappropriate intermolecular interactions, such as amyloid-like filaments found in SOD mutants causing the neurodegenerative disease familial amyotrophic lateral sclerosis or Lou Gehrig's disease. ApSOD further provides the structure of a long-sought SOD product complex at 1.35 A resolution, suggesting a unified inner-sphere mechanism for catalysis involving metal ion movement. Notably, this proposed mechanism resolves apparent paradoxes regarding electron transfer. These results extend knowledge of SOD stability and catalysis and suggest that the eukaryote A. pompejana provides macromolecules highly similar to those from humans, but with enhanced stability more suitable for scientific and medical applications.
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Affiliation(s)
- David S. Shin
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael DiDonato
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P. Barondeau
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Greg L. Hura
- Advanced Light Source, Lawrence Berkeley National Laboratory, CA 94720, USA
| | - Chiharu Hitomi
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J. Andrew Berglund
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Elizabeth D. Getzoff
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - S. Craig Cary
- College of Marine Studies, University of Delaware, Lewes, DE 19958, USA, Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand,Corresponding authors. E-mail addresses: and
| | - John A. Tainer
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,Corresponding authors. E-mail addresses: and
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32
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Edwards RA, Lee MS, Tsutakawa SE, Williams RS, Tainer JA, Glover JNM. The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50. Biochemistry 2008; 47:11446-56. [PMID: 18842000 PMCID: PMC2654182 DOI: 10.1021/bi801115g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 08/20/2008] [Indexed: 12/19/2022]
Abstract
The BARD1 N-terminal RING domain binds BRCA1 while the BARD1 C-terminal ankyrin and tandem BRCT repeat domains bind CstF-50 to modulate mRNA processing and RNAP II stability in response to DNA damage. Here we characterize the BARD1 structural biochemistry responsible for CstF-50 binding. The crystal structure of the BARD1 BRCT domain uncovers a degenerate phosphopeptide binding pocket lacking the key arginine required for phosphopeptide interactions in other BRCT proteins. Small angle X-ray scattering together with limited proteolysis results indicates that ankyrin and BRCT domains are linked by a flexible tether and do not adopt a fixed orientation relative to one another. Protein pull-down experiments utilizing a series of purified BARD1 deletion mutants indicate that interactions between the CstF-50 WD-40 domain and BARD1 involve the ankyrin-BRCT linker but do not require ankyrin or BRCT domains. The structural plasticity imparted by the ANK-BRCT linker helps to explain the regulated assembly of different protein BARD1 complexes with distinct functions in DNA damage signaling including BARD1-dependent induction of apoptosis plus p53 stabilization and interactions. BARD1 architecture and plasticity imparted by the ANK-BRCT linker are suitable to allow the BARD1 C-terminus to act as a hub with multiple binding sites to integrate diverse DNA damage signals directly to RNA polymerase.
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Affiliation(s)
| | | | | | | | | | - J. N. Mark Glover
- Address correspondence to this author. Tel: (780) 492-2136. Fax: (780) 492-0886. E-mail:
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Markovic Z, Trajkovic V. Biomedical potential of the reactive oxygen species generation and quenching by fullerenes (C60). Biomaterials 2008; 29:3561-73. [DOI: 10.1016/j.biomaterials.2008.05.005] [Citation(s) in RCA: 339] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 05/12/2008] [Indexed: 12/22/2022]
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Lee M, Choi JS, Ko KS. Mitochondria targeting delivery of nucleic acids. Expert Opin Drug Deliv 2008; 5:879-87. [DOI: 10.1517/17425247.5.8.879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Rolseth V, Rundén-Pran E, Luna L, McMurray C, Bjørås M, Ottersen OP. Widespread distribution of DNA glycosylases removing oxidative DNA lesions in human and rodent brains. DNA Repair (Amst) 2008; 7:1578-88. [PMID: 18603019 DOI: 10.1016/j.dnarep.2008.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 06/05/2008] [Accepted: 06/06/2008] [Indexed: 12/22/2022]
Abstract
High metabolic activity and low levels of antioxidant enzymes make neurons particularly prone to damage by reactive oxygen species. Thus, repair of oxidative DNA damage is essential for normal brain function. Base excision repair is the major pathway for repair of oxidative DNA damage, and is initiated by DNA glycosylases recognizing and removing the damaged base. In mammalian cells at least five different DNA glycosylases with overlapping substrate specificity, NEIL1, NEIL2, NEIL3, OGG1 and NTH1, remove oxidative DNA base lesions. Here we report mRNA expression and distribution of these five DNA glycosylases in human and rodent brains using in situ hybridization and Northern blotting supported by glycosylase activity assays. NEIL1, NEIL2, OGG1 and NTH1 showed widespread expression at all ages. In situ hybridization studies in mouse brain showed that expression of mNeil1 increased with age. In newborn mouse brain, mNeil3 revealed a discrete expression pattern in brain regions known to harbour stem cell populations, i.e., the subventricular zone, the rostral migratory stream, and the hilar region of the hippocampal formation. Expression of mNeil3 decreased with age, and in old mice brains could be detected only in layer V of neocortex. MNth1 was constitutively expressed during lifespan. In Northern blots, mOgg1 expression showed a transient decrease followed by an increase after 8 weeks of age. Assays for faPy DNA glycosylase activity revealed increased activity level with age in all brain regions analyzed. The widespread but differential expression of the DNA glycosylases recognizing oxidative base lesions suggests distinct and age dependent roles of these enzymes in genome maintenance in brain. The distribution of mNeil3 is particularly intriguing and points to a specific role of this enzyme in stem cell differentiation.
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Affiliation(s)
- Veslemøy Rolseth
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, University of Oslo, Rikshospitalet HF, Oslo, Norway
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Barzilai A, Biton S, Shiloh Y. The role of the DNA damage response in neuronal development, organization and maintenance. DNA Repair (Amst) 2008; 7:1010-27. [DOI: 10.1016/j.dnarep.2008.03.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Bermejo-Bescós P, Piñero-Estrada E, Villar del Fresno AM. Neuroprotection by Spirulina platensis protean extract and phycocyanin against iron-induced toxicity in SH-SY5Y neuroblastoma cells. Toxicol In Vitro 2008; 22:1496-502. [PMID: 18572379 DOI: 10.1016/j.tiv.2008.05.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/08/2008] [Accepted: 05/12/2008] [Indexed: 02/07/2023]
Abstract
We investigated the effect of Spirulina platensis protean extract and the biliprotein phycocyanin isolated from this microalga, on the activities of the antioxidant enzymes SOD, CAT, GPx, and GR, lipid peroxidation inhibitory activity and glutathione levels after the iron induced oxidative stress in SH-SY5Y neuroblastoma cells. Iron is one of the most important agents that produce oxidative stress and decline of neuronal functions. S. platensis protean extract and phycocyanin exert the antioxidant activity by protecting the activity of the cellular antioxidant enzymes total GPx, GPx-Se and GR and by increasing reduced glutathione in cells against oxidative stress induced by iron. These results suggested that S. platensis protean extract is a powerful antioxidant through a mechanism related to antioxidant activity, capable of interfering with radical-mediated cell death. S. platensis may be useful in diseases known to be aggravated by reactive oxygen species and in the development of novel treatments for neurodegenerative disorders as long as iron has been implicated in the neuropathology of several neurodegenerative disorders such as Alzheimer's or Parkinson diseases.
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Affiliation(s)
- Paloma Bermejo-Bescós
- Departamento de Farmacología, Facultad de Farmacia, Universidad Complutense de Madrid, Avenida de la Complutense s/n, Madrid, Spain.
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Biton S, Barzilai A, Shiloh Y. The neurological phenotype of ataxia-telangiectasia: solving a persistent puzzle. DNA Repair (Amst) 2008; 7:1028-38. [PMID: 18456574 DOI: 10.1016/j.dnarep.2008.03.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human genomic instability syndromes affect the nervous system to different degrees of severity, attesting to the vulnerability of the CNS to perturbations of genomic integrity and the DNA damage response (DDR). Ataxia-telangiectasia (A-T) is a typical genomic instability syndrome whose major characteristic is progressive neuronal degeneration but is also associated with immunodeficiency, cancer predisposition and acute sensitivity to ionizing radiation and radiomimetic chemicals. A-T is caused by loss or inactivation of the ATM protein kinase, which mobilizes the complex, multi-branched cellular response to double strand breaks in the DNA by phosphorylating numerous DDR players. The link between ATM's function in the DDR and the neuronal demise in A-T has been questioned in the past. However, recent studies of the ATM-mediated DDR in neurons suggest that the neurological phenotype in A-T is indeed caused by deficiency in this function, similar to other features of the disease. Still, major issues concerning this phenotype remain open, including the presumed differences between the DDR in post-mitotic neurons and proliferating cells, the nature of the damage that accumulates in the DNA of ATM-deficient neurons under normal life conditions, the mode of death of ATM-deficient neurons, and the lack of a major neuronal phenotype in the mouse model of A-T. A-T remains a prototype disease for the study of the DDR's role in CNS development and maintenance.
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Affiliation(s)
- Sharon Biton
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Altieri F, Grillo C, Maceroni M, Chichiarelli S. DNA damage and repair: from molecular mechanisms to health implications. Antioxid Redox Signal 2008; 10:891-937. [PMID: 18205545 DOI: 10.1089/ars.2007.1830] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
DNA is subjected to several modifications, resulting from endogenous and exogenous sources. The cell has developed a network of complementary DNA-repair mechanisms, and in the human genome, >130 genes have been found to be involved. Knowledge about the basic mechanisms for DNA repair has revealed an unexpected complexity, with overlapping specificity within the same pathway, as well as extensive functional interactions between proteins involved in repair pathways. Unrepaired or improperly repaired DNA lesions have serious potential consequences for the cell, leading to genomic instability and deregulation of cellular functions. A number of disorders or syndromes, including several cancer predispositions and accelerated aging, are linked to an inherited defect in one of the DNA-repair pathways. Genomic instability, a characteristic of most human malignancies, can also arise from acquired defects in DNA repair, and the specific pathway affected is predictive of types of mutations, tumor drug sensitivity, and treatment outcome. Although DNA repair has received little attention as a determinant of drug sensitivity, emerging knowledge of mutations and polymorphisms in key human DNA-repair genes may provide a rational basis for improved strategies for therapeutic interventions on a number of tumors and degenerative disorders.
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Affiliation(s)
- Fabio Altieri
- Department of Biochemical Sciences, A. Rossi Fanelli, University La Sapienza, Rome, Italy.
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40
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X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 2008; 40:191-285. [PMID: 18078545 DOI: 10.1017/s0033583507004635] [Citation(s) in RCA: 845] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein-nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.
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Armstrong JS. Mitochondrial medicine: pharmacological targeting of mitochondria in disease. Br J Pharmacol 2007; 151:1154-65. [PMID: 17519949 PMCID: PMC2189819 DOI: 10.1038/sj.bjp.0707288] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mitochondria play a central role in cell life and death and are known to be important in a wide range of diseases including the cancer, diabetes, cardiovascular disease, and the age-related neurodegenerative diseases. The unique structural and functional characteristics of mitochondria enable the selective targeting of drugs designed to modulate the function of this organelle for therapeutic gain. This review discusses mitochondrial drug targeting strategies and a variety of novel mitochondrial drug targets including the electron transport chain, mitochondrial permeability transition, Bcl-2 family proteins and mitochondrial DNA. Mitochondrial drug-targeting strategies will open up avenues for manipulating mitochondrial functions and allow for selective protection or eradication of cells for therapeutic gain in a variety of diseases.
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Affiliation(s)
- J S Armstrong
- Department of Biochemistry, Faculty of Medicine, National University of SingaporeSingapore
- Author for correspondence:
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42
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Tubbs JL, Pegg AE, Tainer JA. DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy. DNA Repair (Amst) 2007; 6:1100-15. [PMID: 17485252 PMCID: PMC1993358 DOI: 10.1016/j.dnarep.2007.03.011] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
O(6)-Alkylguanine-DNA alkyltransferase (AGT) is a crucial target both for the prevention of cancer and for chemotherapy, since it repairs mutagenic lesions in DNA, and it limits the effectiveness of alkylating chemotherapies. AGT catalyzes the unique, single-step, direct damage reversal repair of O(6)-alkylguanines by selectively transferring the O(6)-alkyl adduct to an internal cysteine residue. Recent crystal structures of human AGT alone and in complex with substrate DNA reveal a two-domain alpha/beta fold and a bound zinc ion. AGT uses its helix-turn-helix motif to bind substrate DNA via the minor groove. The alkylated guanine is then flipped out from the base stack into the AGT active site for repair by covalent transfer of the alkyl adduct to Cys145. An asparagine hinge (Asn137) couples the helix-turn-helix DNA binding and active site motifs. An arginine finger (Arg128) stabilizes the extrahelical DNA conformation. With this newly improved structural understanding of AGT and its interactions with biologically relevant substrates, we can now begin to unravel the role it plays in preserving genetic integrity and discover how it promotes resistance to anticancer therapies.
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Affiliation(s)
- Julie L. Tubbs
- The Scripps Research Institute, The Skaggs Institute for Chemical Biology and Department of Molecular Biology, 10550 North Torrey Pines Road, MB4, La Jolla, CA 92037
| | - Anthony E. Pegg
- Department of Cellular and Molecular Physiology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - John A. Tainer
- The Scripps Research Institute, The Skaggs Institute for Chemical Biology and Department of Molecular Biology, 10550 North Torrey Pines Road, MB4, La Jolla, CA 92037
- Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- *To whom correspondence should be addressed: Tel: +1-858-784-8119; fax: +1-858-784-2289;
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