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Pugh JN, Stretton C, McDonagh B, Brownridge P, McArdle A, Jackson MJ, Close GL. Exercise stress leads to an acute loss of mitochondrial proteins and disruption of redox control in skeletal muscle of older subjects: An underlying decrease in resilience with aging? Free Radic Biol Med 2021; 177:88-99. [PMID: 34655746 DOI: 10.1016/j.freeradbiomed.2021.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
Reactive oxygen species (ROS) are recognized as important signaling molecules in healthy skeletal muscle. Redox sensitive proteins can respond to intracellular changes in ROS by oxidation of reactive thiol groups on cysteine (Cys) residues. Exercise is known to induce the generation of superoxide and nitric oxide, resulting in the activation of several adaptive signaling pathways; however, it has been suggested that aging attenuates these redox-regulated adaptations to acute exercise. In the present study, we used redox proteomics to study the vastus lateralis muscles of Adult (n = 6 male, 6 female; 18-30 yrs) and Old (n = 6 male, 6 female; 64-79 yrs) adults. Participants completed a bout of high intensity cycling exercise consisting of five sets of 2-min intervals performed at 80% maximal aerobic power output (PPO), with 2 min recovery cycling at 40% PPO between sets. Muscle biopsies were collected prior to exercise, and immediately following the first, second, and fifth high intensity interval. Global proteomic analysis indicated differences in abundance of a number of individual proteins between skeletal muscles of Adult and Old subjects at rest with a significant exacerbation of these differences induced by the acute exercise. In particular, we observed an exercise-induced decrease in abundance of mitochondrial proteins in muscles from older subjects only. Redox proteome analysis revealed cysteines from five cytosolic proteins in older subjects with lower oxidation (i.e. greater reduction) than was seen in muscle from the young adults at rest. Redox homeostasis was well maintained in Adult subjects following exercise, but there was significant increase in oxidation of multiple mitochondrial and cytosolic protein cysteines in Old subjects. We also observed that oxidation of peroxiredoxin 3 occurred following exercise in both Adult and Old groups, supporting the possibility that this is a key effector protein for mitochondrial redox signaling. Thus, we show, for the first time that exercise reveals a lack of resilience in muscle of older human participants, that is apparent as a loss of mitochondrial proteins and oxidation of multiple protein cysteines that are not seen in younger subjects. The precise consequences of this redox disruption are unclear, but this likely play a role in the attenuation of multiple adaptations to exercise that are classically seen with aging. Such changes were only seen following the acute stress of exercise., highlighting the need to consider not only basal differences seen during aging but also the difference following physiological challenge.
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Affiliation(s)
- Jamie N Pugh
- School of Sport and Exercise Sciences, Tom Reilly Building, Byrom Street, Liverpool John Moores University, Liverpool, UK
| | - Clare Stretton
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool and MRC- Arthritis Research UK Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), UK
| | - Brian McDonagh
- Discipline of Physiology, School of Medicine, National University of Ireland Galway, Ireland
| | - Philip Brownridge
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool and MRC- Arthritis Research UK Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), UK
| | - Anne McArdle
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool and MRC- Arthritis Research UK Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), UK
| | - Malcolm J Jackson
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool and MRC- Arthritis Research UK Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), UK
| | - Graeme L Close
- School of Sport and Exercise Sciences, Tom Reilly Building, Byrom Street, Liverpool John Moores University, Liverpool, UK.
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Murakami Y, Omori S, Kinoshita K. NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2016; 17:101-110. [PMID: 27530928 PMCID: PMC5274645 DOI: 10.1007/s10969-016-9206-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 07/25/2016] [Indexed: 11/17/2022]
Abstract
NLDB (Natural Ligand DataBase; URL: http://nldb.hgc.jp) is a database of automatically collected and predicted 3D protein–ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. Structural information about these reactions is important for studying the molecular functions of enzymes, however a large number of the 3D interactions are still unknown. Therefore, in order to complement such missing information, we predicted protein–ligand complex structures, and constructed a database of the 3D interactions in reactions. NLDB provides three different types of data resources; the natural complexes are experimentally determined protein–ligand complex structures in PDB, the analog complexes are predicted based on known protein structures in a complex with a similar ligand, and the ab initio complexes are predicted by docking simulations. In addition, NLDB shows the known polymorphisms found in human genome on protein structures. The database has a flexible search function based on various types of keywords, and an enrichment analysis function based on a set of KEGG compound IDs. NLDB will be a valuable resource for experimental biologists studying protein–ligand interactions in specific reactions, and for theoretical researchers wishing to undertake more precise simulations of interactions.
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Affiliation(s)
- Yoichi Murakami
- Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan.,Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Saito-Asagi 7-6-8, Ibaraki-city, Osaka, 567-0085, Japan
| | - Satoshi Omori
- Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan
| | - Kengo Kinoshita
- Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan. .,Institute of Development, Aging and Cancer, Tohoku University, Seiryo-machi 4-1, Aoba-ku, Sendai, 980-8575, Japan. .,Tohoku Medical Megabank Organization, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8573, Japan.
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Chu WT, Zheng QC, Zhang HX. Insights into the phosphatase and the synthase activities of human bisphosphoglycerate mutase: a quantum mechanics/molecular mechanics simulation. Phys Chem Chem Phys 2014; 16:3946-54. [PMID: 24441588 DOI: 10.1039/c3cp53935k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bisphosphoglycerate mutase (BPGM) is a multi-activity enzyme. Its main function is to synthesize the 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. This enzyme can also catalyze the 2,3-bisphosphoglycerate to the 3-phosphoglycerate. In this study, the reaction mechanisms of both the phosphatase and the synthase activities of human bisphosphoglycerate mutase were theoretically calculated by using the quantum mechanics/molecular mechanics method based on the metadynamics and umbrella sampling simulations. The simulation results not only show the free energy curve of the phosphatase and the synthase reactions, but also reveal the important role of some residues in the active site. Additionally, the energy barriers of the two reactions indicate that the activity of the synthase in human bisphosphoglycerate mutase is much higher than that of the phosphatase. The estimated reaction barriers are consistent with the experimental data. Therefore, our work can give important information to understand the catalytic mechanism of the bisphosphoglycerate mutase family.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.
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Amani S, Nasim F, Khan TA, Fazili NA, Furkan M, Bhat IA, Khan JM, Khan RH, Naeem A. Detergent induces the formation of IgG aggregates: a multi-methodological approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:151-160. [PMID: 24184618 DOI: 10.1016/j.saa.2013.09.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/23/2013] [Accepted: 09/29/2013] [Indexed: 06/02/2023]
Abstract
Role of micellar environment created by Triton X-100 (TX-100) and CHAPSO on protein conformation using IgG as a model system has been studied in this paper. A substantial amount of secondary structure with the reduction in constant tertiary contacts was obtained in both bovine and human IgG in the presence of 0.12 mM TX-100 where as 6 and 8 mM CHAPSO concentration was required for this type of secondary structure. Further addition of either of the detergents result in the induction of α-helix in both the IgGs as evident by helix specific peaks in the amide I region of FTIR and circular dichroism spectra. Tryptophan and 8-anilino-1-naphthalene-sulphonic acid (ANS) fluorescence confirmed changes in protein conformation upon addition of detergents. Maximum ANS binding at 0.12 mM TX-100 in both while 6 and 8 mM CHAPSO in bovine and human IgG respectively, indicate a compact ''molten-globule''-like conformation. An increase addition of these detergents results in the burial of hydrophobic patches of both IgG owing to aggregation. Presence of aggregates at 0.2 and 0.16 mM TX-100 and 8 and 9 mM CHAPSO, for bovine and human IgG respectively, was further confirmed by reduction in ANS fluorescence, dynamic light scattering study, thioflavin T fluorescence and congo red absorbance.
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Affiliation(s)
- Samreen Amani
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nasim
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Taqi Ahmed Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Naveed Ahmad Fazili
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Furkan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Imtiyaz Ahmad Bhat
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh 202002, India
| | - Javed Masood Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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Patterson A, Price NC, Nairn J. Unliganded structure of human bisphosphoglycerate mutase reveals side-chain movements induced by ligand binding. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1415-20. [PMID: 21045285 PMCID: PMC3001638 DOI: 10.1107/s1744309110035475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 09/03/2010] [Indexed: 11/10/2022]
Abstract
Erythrocyte-specific bisphosphoglycerate mutase is a trifunctional enzyme which modulates the levels of 2,3-bisphosphoglycerate (2,3-BPG) in red blood cells by virtue of its synthase and phosphatase activities. Low levels of erythrocyte 2,3-BPG increase the affinity of haemoglobin for oxygen, thus limiting the release of oxygen into tissues. 2,3-BPG levels in stored blood decline rapidly owing to the phosphatase activity of bisphosphoglycerate mutase, which is enhanced by a fall in pH. Here, the 1.94 Å resolution X-ray structure of bisphosphoglycerate mutase is presented, focusing on the dynamic nature of key ligand-binding residues and their interaction with the inhibitor citrate. Residues at the binding pocket are complete. In addition, the movement of key residues in the presence and absence of ligand is described and alternative conformations are explored. The conformation in which the ligand citrate would bind at the substrate-binding pocket is proposed, with discussion and representations of its orientation. The characterization of bisphosphoglycerate mutase-citrate interactions will provide a framework for the design of specific inhibitors of the phosphatase activity of this enzyme, which may limit the decline of 2,3-BPG in stored blood.
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Affiliation(s)
- A. Patterson
- Division of Molecular and Cellular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - N. C. Price
- Division of Molecular and Cellular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - J. Nairn
- School of Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, Scotland
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Flachner B, Varga A, Szabó J, Barna L, Hajdú I, Gyimesi G, Závodszky P, Vas M. Substrate-assisted movement of the catalytic Lys 215 during domain closure: site-directed mutagenesis studies of human 3-phosphoglycerate kinase. Biochemistry 2006; 44:16853-65. [PMID: 16363799 DOI: 10.1021/bi051726g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
3-Phosphoglycerate kinase (PGK) is a two-domain hinge-bending enzyme. It is still unclear how the geometry of the active site is formed during domain closure and how the catalytic residues are brought into the optimal position for the reaction. Comparison of the three-dimensional structures in various open and closed conformations suggests a large (10 A) movement of Lys 215 during domain closure. This change would be required for direct participation of this side chain in both the catalyzed phospho transfer and the special anion-caused activation. To test the multiple roles of Lys 215, two mutants (K215A and K215R) were constructed from human PGK and characterized in enzyme kinetic and substrate binding studies. For comparison, mutants (R38A and R38K) of the known essential residue, Arg 38, were also produced. Drastic decreases (1500- and 500-fold, respectively), as in the case of R38A, were observed in the kcat values of mutants K215A and K215R, approving the essential catalytic role of Lys 215. In contrast, the R38K mutation caused an only 1.5-fold decrease in activity. This emphasizes the importance of a very precise positioning of Lys 215 in the active site, in addition to its positive charge. The side chain of Lys 215 is also responsible for the substrate and anion-dependent activation, since these properties are abolished upon mutation. Among the kinetic constants mainly the Km values of MgATP and 1,3-BPG are increased (approximately 20- and approximately 8-fold, respectively) in the case of the neutral K215A mutant, evidence of the interaction of Lys 215 with the transferring phospho group in the functioning complex. Weakening of MgATP binding (a moderate increase in Kd), but not of MgADP binding, upon mutation indicates an initial weak interaction of Lys 215 with the gamma-phosphate already in the nonfunctioning open conformation. Thus, during domain closure, Lys 215 possibly moves together with the transferring phosphate; meanwhile, this group is being positioned properly for catalysis.
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Affiliation(s)
- Beáta Flachner
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary
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Wang Y, Wei Z, Bian Q, Cheng Z, Wan M, Liu L, Gong W. Crystal Structure of Human Bisphosphoglycerate Mutase. J Biol Chem 2004; 279:39132-8. [PMID: 15258155 DOI: 10.1074/jbc.m405982200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bisphosphoglycerate mutase is a trifunctional enzyme of which the main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. The gene coding for bisphosphoglycerate mutase from the human cDNA library was cloned and expressed in Escherichia coli. The protein crystals were obtained and diffract to 2.5 A and produced the first crystal structure of bisphosphoglycerate mutase. The model was refined to a crystallographic R-factor of 0.200 and R(free) of 0.266 with excellent stereochemistry. The enzyme remains a dimer in the crystal. The overall structure of the enzyme resembles that of the cofactor-dependent phosphoglycerate mutase except the regions of 13-21, 98-117, 127-151, and the C-terminal tail. The conformational changes in the backbone and the side chains of some residues reveal the structural basis for the different activities between phosphoglycerate mutase and bisphosphoglycerate mutase. The bisphosphoglycerate mutase-specific residue Gly-14 may cause the most important conformational changes, which makes the side chain of Glu-13 orient toward the active site. The positions of Glu-13 and Phe-22 prevent 2,3-bisphosphoglycerate from binding in the way proposed previously. In addition, the side chain of Glu-13 would affect the Glu-89 protonation ability responsible for the low mutase activity. Other structural variations, which could be connected with functional differences, are also discussed.
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Affiliation(s)
- Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Metzler DE, Metzler CM, Sauke DJ. Transferring Groups by Displacement Reactions. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50015-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Szilágyi AN, Vas M. Anion activation of 3-phosphoglycerate kinase requires domain closure. Biochemistry 1998; 37:8551-63. [PMID: 9622507 DOI: 10.1021/bi973072k] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
3-Phosphoglycerate kinase is a typical two-domain "hinge-bending" enzyme, which is known to be regulated by multivalent anions. Here a relationship between this regulation and the hinge-bending domain closure is proposed on the basis of enzyme kinetic analysis and molecular modeling. Activation of the pig muscle enzyme at low concentrations and inhibition at high concentrations of various anionic analogues of the substrate 3-phosphoglycerate or of the nonsubstrate metal-free ATP are described by a two-site model assuming separate sites for activation and inhibition, respectively. Kinetic experiments with various pairs of analogues suggest the presence of a common site for activation by all effectors, separate from the catalytic site for 3-phosphoglycerate; and a common site for inhibition, except for metal-free ATP, identical with the catalytic site of 3-phosphoglycerate. An additional inhibiting site for all of the anions investigated, including metal-free ATP, is also proposed. A similar two-site model can describe activation of the enzyme by a large excess of each substrate; here the ligand binds to the catalytic site as a substrate and to the regulatory site as an activator. Activation is exerted not only by the physiological substrate, 3-phophoglycerate, but also by a synthetic weak substrate. The activity in the reaction with 3-phosphoglycerate and MgATP is greatly enhanced by the simultaneous presence of the weak substrate. This finding clearly proves the existence of a regulatory site, separate from the catalytic site. This regulatory site, however, may only exist in the catalytically competent closed conformation of the enzyme, as indicated by molecular modeling. Docking of the regulator anions into the known X-ray structures of the enzyme revealed the appearance of an anion binding site between the two domains, including the invariant residues of Lys-215 (C-domain) and of Arg-65 among other residues of the basic cluster (N-domain), as a consequence of the large-scale substrate-induced conformational change that leads to domain closure.
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Affiliation(s)
- A N Szilágyi
- Biological Research Center, Institute of Enzymology, Hungarian Academy of Sciences, Budapest
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