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Kish M, Subramanian S, Smith V, Lethbridge N, Cole L, Vollmer F, Bond NJ, Phillips JJ. Allosteric Regulation of Glycogen Phosphorylase by Order/Disorder Transition of the 250' and 280s Loops. Biochemistry 2023; 62:1360-1368. [PMID: 36989206 PMCID: PMC10116597 DOI: 10.1021/acs.biochem.2c00671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Allostery is a fundamental mechanism of protein activation, yet the precise dynamic changes that underlie functional regulation of allosteric enzymes, such as glycogen phosphorylase (GlyP), remain poorly understood. Despite being the first allosteric enzyme described, its structural regulation is still a challenging problem: the key regulatory loops of the GlyP active site (250' and 280s) are weakly stable and often missing density or have large b-factors in structural models. This led to the longstanding hypothesis that GlyP regulation is achieved through gating of the active site by (dis)order transitions, as first proposed by Barford and Johnson. However, testing this requires a quantitative measurement of weakly stable local structure which, to date, has been technically challenging in such a large protein. Hydrogen-deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for studying protein dynamics, and millisecond HDX-MS has the ability to measure site-localized stability differences in weakly stable structures, making it particularly valuable for investigating allosteric regulation in GlyP. Here, we used millisecond HDX-MS to measure the local structural perturbations of glycogen phosphorylase b (GlyPb), the phosphorylated active form (GlyPa), and the inhibited glucose-6 phosphate complex (GlyPb:G6P) at near-amino acid resolution. Our results support the Barford and Johnson hypothesis for GlyP regulation by providing insight into the dynamic changes of the key regulatory loops.
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Affiliation(s)
- Monika Kish
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, U.K
| | - Sivaraman Subramanian
- Living Systems Institute, Department of Physics, University of Exeter, Stocker Road, Exeter, EX4 6QD, U.K
| | | | | | - Lindsay Cole
- Applied Photophysics Ltd, Leatherhead, KT227BA, U.K
| | - Frank Vollmer
- Living Systems Institute, Department of Physics, University of Exeter, Stocker Road, Exeter, EX4 6QD, U.K
| | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Milstein Building, Granta Park, Cambridge, CB21 6GH, U.K
| | - Jonathan J Phillips
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, U.K
- Alan Turing Institute, British Library, London, NW1 2DB, U.K
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Huang J, Chu X, Luo Y, Wang Y, Zhang Y, Zhang Y, Li H. Insights into Phosphorylation-Induced Protein Allostery and Conformational Dynamics of Glycogen Phosphorylase via Integrative Structural Mass Spectrometry and In Silico Modeling. ACS Chem Biol 2022; 17:1951-1962. [PMID: 35675581 DOI: 10.1021/acschembio.2c00393] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric regulation plays a fundamental role in innumerable biological processes. Understanding its dynamic mechanism and impact at the molecular level is of great importance in disease diagnosis and drug discovery. Glycogen phosphorylase (GP) is a phosphoprotein responding to allosteric regulation and has significant biological importance to glycogen metabolism. Although the atomic structures of GP have been previously solved, the conformational dynamics of GP related to allostery regulation remain largely elusive due to its macromolecular size (∼196 kDa). Here, we integrated native top-down mass spectrometry (nTD-MS), hydrogen-deuterium exchange MS (HDX-MS), protection factor (PF) analysis, molecular dynamics (MD) simulations, and allostery signaling analysis to examine the structural basis and dynamics for the allosteric regulation of GP by phosphorylation. nTD-MS reveals differences in structural stability as well as oligomeric state between the unphosphorylated (GPb) and phosphorylated (GPa) forms. HDX-MS, PF analysis, and MD simulations further pinpoint the structural differences between GPb and GPa involving the binding interfaces (the N-terminal and tower-tower helices), catalytic site, and PLP-binding region. More importantly, it also allowed us to complete the missing link of the long-range communication process from the N-terminal tail to the catalytic site caused by phosphorylation. This integrative MS and in silico-based platform is highly complementary to biophysical approaches and yields valuable insights into protein structures and dynamic regulation.
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Affiliation(s)
- Jing Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou Higher Education Mega Center, No. 132 Wai Huan Dong Lu, Guangzhou 510006, China
| | - Xiakun Chu
- Advanced Materials Thrust, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong 511400, China
| | - Yuxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou Higher Education Mega Center, No. 132 Wai Huan Dong Lu, Guangzhou 510006, China
| | - Yong Wang
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, College of Life Sciences, Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Haining 314400, China
| | - Ying Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou Higher Education Mega Center, No. 132 Wai Huan Dong Lu, Guangzhou 510006, China
| | - Yu Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou Higher Education Mega Center, No. 132 Wai Huan Dong Lu, Guangzhou 510006, China.,Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
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Zhai L, Wan X, Wu R, Yu X, Li H, Zhong R, Zhu D, Zhang Y. Linc-RAM promotes muscle cell differentiation via regulating glycogen phosphorylase activity. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:8. [PMID: 35254536 PMCID: PMC8901937 DOI: 10.1186/s13619-022-00109-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) are important regulators of diverse biological processes, especially skeletal muscle cell differentiation. Most of the lncRNAs identified to date are localized in the nucleus and play regulatory roles in gene expression. The cytoplasmic lncRNAs are less well understood. We previously identified a long intergenic non-coding RNA (linc-RNA) activator of myogenesis (Linc-RAM) that directly binds MyoD in the nucleus to enhance muscle cell differentiation. Here, we report that a substantial fraction of Linc-RAM is localized in the cytoplasm of muscle cells. To explore the molecular functions of cytoplasmic Linc-RAM, we sought to identify Linc-RAM-binding proteins. We report here that Linc-RAM physically interacts with glycogen phosphorylase (PYGM) in the cytoplasm. Knockdown of PYGM significantly attenuates the function of Linc-RAM in promoting muscle cell differentiation. Loss-of-function and gain-of function assays demonstrated that PYGM enhances muscle cell differentiation in an enzymatic activity-dependent manner. Finally, we show that the interaction between Linc-RAM and PYGM positively regulates the enzymatic activity of PYGM in muscle cells. Collectively, our findings unveil a molecular mechanism through which cytoplasmic Linc-RAM contributes to muscle cell differentiation by regulating PYGM activity. Our findings establish that there is crosstalk between lncRNAs and cellular metabolism during myogenic cell differentiation.
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Affiliation(s)
- Lili Zhai
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.,Present address: NCPC New Drug Research and Development Co., Ltd., State Key Laboratory of Antibody Research & Development, Shijiazhuang, 052165, China
| | - Xin Wan
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Rimao Wu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.,The Max-Planck Center for Tissue Stem Cell Research and Regenerative Medicine, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Xiaohua Yu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Hu Li
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.,The Max-Planck Center for Tissue Stem Cell Research and Regenerative Medicine, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Ran Zhong
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Dahai Zhu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China. .,The Max-Planck Center for Tissue Stem Cell Research and Regenerative Medicine, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
| | - Yong Zhang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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Gaboriaud-Kolar N, Skaltsounis AL. Glycogen phosphorylase inhibitors: a patent review (2008 - 2012). Expert Opin Ther Pat 2013; 23:1017-32. [PMID: 23627914 DOI: 10.1517/13543776.2013.794790] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Glycogen phosphorylase (GP) is the enzyme responsible for the synthesis of glucose-1-phosphate, the source of energy for muscles and the rest of the body. The binding of different ligands in catalytic or allosteric sites assures activation and deactivation of the enzyme. A description of the regulation mechanism and the implications in glycogen metabolism are given. AREAS COVERED Deregulation of GP has been observed in diseases such as diabetes mellitus or cancers. Therefore, it appears as an attractive therapeutic target for the treatment of such pathologies. Numbers of inhibitors have been published in academic literature or patented in the last two decades. This review presents the main patent claims published between 2008 and 2012. EXPERT OPINION Good inhibitors with interesting IC50 and in vivo results are presented. However, such therapeutic strategy raises questions and some answers are proposed to bring new insights in the field.
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Agasimundin YS, Mumper MW, Hosmane RS. Inhibitors of glycogen phosphorylase b: synthesis, biochemical screening, and molecular modeling studies of novel analogues of hydantocidin. Bioorg Med Chem 1998; 6:911-23. [PMID: 9730227 DOI: 10.1016/s0968-0896(98)00055-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The synthesis and biochemical screening of four novel spironucleosides 1-4 against rabbit liver glycogen phosphorylase b (Gpb), along with molecular modeling studies on compound 2 and its 4-hydroxy analogue VII, have been presented. Gpb is a key enzyme of glycogen metabolism, and is known to be involved in the control of diabetes mellitus. The general strategy for synthesis involved base-catalyzed condensation of diethyl 2,4-dioxoimidazolidine-5-phosphonate (5) with either 2-deoxy-D-ribose or D-ribose, followed by sequential reactions involving ring-closure with phenylselenenyl chloride and reduction with tri-n-butyltin hydride catalyzed by azobisisobutyronitrile. Compounds 2 and 4 were found to be weak competitive inhibitors of Gpb, whereas 1 and 3 were inactive.
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Affiliation(s)
- Y S Agasimundin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County 21250, USA
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Abstract
A transducer is a device that receives energy from one system and transmits it, often in a different form, to another. Glycogen phosphorylase receives information from the cell or organism in the form of metabolic signals. The energy associated with the binding of these ligand signals is integrated and transmitted at an atomic level, allowing precise adjustment of the enzymatic activity. Understanding this elegant allosteric control has required several different approaches, but the structural requirements of allostery are being defined.
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Affiliation(s)
- M F Browner
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448
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