Computational Method of Molecular Dynamics Simulation Identifies Insulin Receptor Binding Site 2 as the Primary Site for Insulin Binding
DOI:
https://doi.org/10.55940/medphar202488Keywords:
Molecular dynamics, Insulin, Insulin receptor, Protein structure, insulin receptor site-2, conformational flexibilityAbstract
ABSTRACTBackground: Insulin receptor (IR) is a homo-dimeric, extensively glycosylated, disulfide-linked, transmembrane tyrosine kinase receptor. IR has two distinctive insulin binding sites, suggesting a process of sequential insulin interactions characterized by negative cooperativity. The crystal structure of the dimeric IR ectodomain [PDB: 4ZXB] provides structural bases for this theory.
Objective: Identifies Insulin Receptor Binding Site 2 as the Primary Site for Insulin Binding
Methods: Molecular dynamics (MD) simulation is performed to study the initial association of insulin with its receptor, leading to full interaction. MD simulation serves as a bridge between theory and experiments, enabling simulations not feasible in the lab. The study utilized the crystal structures of the insulin receptor (PDB: 4ZXB) and insulin molecule (PDB: 1MSO). GROMACS, a tool developed by Groningen University, is used for the molecular dynamics application. Prior to simulation, the receptor was prepared by restoring missing residues and removing those used for crystallization. GROMACS, compatible with several other tools, supported the MD simulations.
Results: During 230 ns of all-atom, explicit-water MD simulations (0.75 million atoms), insulin and ECD-IR exhibited significant asymmetric interdomain and intersubunit conformational fluctuations without altering quaternary structures. Variations in insulin orientation and location, alongside subtle changes in residual contact of ECD-IR, coincided with these fluctuations. The insulin-IR site 2 interaction also induced interdomain conformational changes between the monomers at the subdomains L1-FnIII-2’ (L1’-FnIII-2), with initial separation studied through RMSD calculations, showing a value of 3.3Å starting at 60 ns of simulation. This protein unfolding suggests a step towards major conformational changes in ECD-IR.
Conclusion: Molecular dynamics simulations provided insights into the sequential binding process and structural dynamics of the insulin-IR complex
References
Federation ID. IDF diabetes atlas 8th edition. International diabetes federation. 2017:905-11.
Pollak M. The insulin receptor/insulin-like growth factor receptor family as a therapeutic target in oncology. Clinical cancer research. 2012; 18(1):40-50. DOI:10.1158/1078-0432.CCR-11-0998
Nathan DM, Buse JB, Davidson MB, Ferrannini E, Holman RR, Sherwin R, Zinman B. Medical management of hyperglycemia in type 2 diabetes: a consensus algorithm for the initiation and adjustment of therapy: a consensus statement of the American Diabetes Association and the European Association for the Study of Diabetes. Diabetes care. 2009; 32(1):193-203. DOI: 10.2337/dc08-9025
Lawrence MC. Understanding insulin and its receptor from their three-dimensional structures. Molecular metabolism. 2021; 52:101255. DOI: 10.1016/j.molmet.2021.101255
Croll TI, Smith BJ, Margetts MB, Whittaker J, Weiss MA, Ward CW, Lawrence MC. Higher-resolution structure of the human insulin receptor ectodomain: multi-modal inclusion of the insert domain. Structure. 2016; 24(3):469-76.
Smith GD, Pangborn WA, Blessing RH. The structure of T6 human insulin at 1.0 Å resolution. Acta Crystallographica Section D: Biological Crystallography. 2003; 59(3):474-82. DOI: 10.1107/S0907444902023685
Lawrence MC. Understanding insulin and its receptor from their three-dimensional structures. Molecular metabolism. 2021; 52:101255. DOI: 10.1016/j.molmet.2021.101255
White MF, Kahn CR. Insulin action at a molecular level–100 years of progress. Molecular metabolism. 2021;52:101304. DOI:10.1016/j.molmet.2021.101304
Gutmann T, Kim KH, Grzybek M, Walz T, Coskun Ü. Visualization of ligand-induced transmembrane signaling in the full-length human insulin receptor. Journal of Cell Biology. 2018; 217(5):1643-9. DOI: 10.1083/jcb.201711047
Maruyama IN. Mechanisms of activation of receptor tyrosine kinases: monomers or dimers. Cells. 2014; 3(2):304-30. DOI: 10.3390/cells3020304
Scapin G, Dandey VP, Zhang Z, Prosise W, Hruza A, Kelly T, Mayhood T, Strickland C, Potter CS, Carragher B. Structure of the insulin receptor–insulin complex by single-particle cryo-EM analysis. Nature. 2018; 556 (7699):122-5. DOI: 10.1038/nature26153
Uchikawa E, Choi E, Shang G, Yu H, Bai XC. Activation mechanism of the insulin receptor revealed by cryo-EM structure of the fully liganded receptor–ligand complex. Elife. 2019; 8:e48630. DOI: 10.7554/eLife.48630
Xu Y, Margetts MB, Venugopal H, Menting JG, Kirk NS, Croll TI, Delaine C, Forbes BE, Lawrence MC. How insulin-like growth factor I binds to a hybrid insulin receptor type 1 insulin-like growth factor receptor. Structure. 2022; 30(8):1098-108. DOI:10.1016/j.str.2022.05.007
Nielsen J, Brandt J, Boesen T, Hummelshøj T, Slaaby R, Schluckebier G, Nissen P. Structural investigations of full-length insulin receptor dynamics and signalling. Journal of molecular biology. 2022; 434(5):167458.
DOI: 10.1016/j.jmb.2022.167458
Batishchev OV, Kuzmina NV, Mozhaev AA, Goryashchenko AS, Mileshina ED, Orsa AN, Bocharov EV, Deyev IE, Petrenko AG. Activity-dependent conformational transitions of the insulin receptor–related receptor. Journal of Biological Chemistry. 2021; 296:100534
DOI: 10.1016/j.jbc.2021.100534
Gutmann T, Schäfer IB, Poojari C, Brankatschk B, Vattulainen I, Strauss M, Coskun Ü. Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain. Journal of Cell Biology. 2019; 219(1):e201907210. DOI: 10.1083/jcb.201907210
Massague J, Pilch PF, Czech MP. Electrophoretic resolution of three major insulin receptor structures with unique subunit stoichiometries. Proceedings of the National Academy of Sciences. 1980; 77(12):7137-41. DOI: 10.1073/pnas.77.12.7137
Sinha S, Tam B, Wang SM. Applications of molecular dynamics simulation in protein study. Membranes. 2022; 12(9):844. DOI: 10.3390/membranes12090844
Mohammadiarani H, Vashisth H. All-atom structural models of the transmembrane domains of insulin and type 1 insulin-like growth factor receptors. Frontiers in Endocrinology. 2016; 7:68. DOI: 10.3389/fendo.2016.00068
De Meyts P, Roth J, Neville Jr DM, Gavin III JR, Lesniak MA. Insulin interactions with its receptors: experimental evidence for negative cooperativity. Biochemical and biophysical research communications. 1973; 55(1):154-61. DOI: 10.1016/S0006-291X(73)80072-5
McKern NM, Lawrence MC, Streltsov VA, Lou MZ, Adams TE, Lovrecz GO, Elleman TC, Richards KM, Bentley JD, Pilling PA, Hoyne PA. Structure of the insulin receptor ectodomain reveals a folded-over conformation. Nature. 2006; 443(7108):218-21.
Astuti AD, Refianti R, Mutiara AB. Molecular dynamics simulation on protein using GROMACS. Int J Comput Sci Inf Security. 2011; 9:16-20.
Gorai B, Vashisth H. Progress in simulation studies of insulin structure and function. Frontiers in endocrinology. 2022; 13:908724. DOI: 10.3389/fendo.2022.908724
Bentley G, Dodson E, Dodson GU, Hodgkin D, Mercola DA. Structure of insulin in 4-zinc insulin. Nature. 1976; 261(5556):166-8. DOI: 10.1038/261166a0
Huang K, Xu B, Hu SQ, Chu YC, Hua QX, Qu Y, Li B, Wang S, Wang RY, Nakagawa SH, Theede AM. How insulin binds: The B-chain α-helix contacts the L1 β-helix of the insulin receptor. Journal of molecular biology. 2004; 341(2):529-50. DOI: 10.1016/j.jmb.2004.05.023
Xu B, Hu SQ, Chu YC, Huang K, Nakagawa SH, Whittaker J, Katsoyannis PG, Weiss MA. Diabetes-associated mutations in insulin: consecutive residues in the B chain contact distinct domains of the insulin receptor. Biochemistry. 2004; 43(26):8356-72. DOI: 10.1021/bi0497796
Hao MH. Theoretical calculation of hydrogen-bonding strength for drug molecules. Journal of chemical theory and computation. 2006; 2(3):863-72. DOI: 10.1021/ct0600262
Baig MH, Sudhakar DR, Kalaiarasan P, Subbarao N, Wadhawa G, Lohani M, Khan MK, Khan AU. Insight into the effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase: A molecular dynamics study. PLoS One. 2014; 9(12):e112456. DOI: 10.1371/journal.pone.0112456
Du X, Li Y, Xia YL, Ai SM, Liang J, Sang P, Ji XL, Liu SQ. Insights into protein–ligand interactions: mechanisms, models, and methods. International journal of molecular sciences. 2016;17(2):144. DOI: 10.3390/ijms17020144
Subramanian K, Fee CJ, Fredericks R, Stubbs RS, Hayes MT. Insulin receptor‐insulin interaction kinetics using multiplex surface plasmon resonance. Journal of Molecular Recognition. 2013 ;26(12):643-52. DOI: 10.1002/jmr.2307
Whittaker L, Hao C, Fu W, Whittaker J. High-affinity insulin binding: insulin interacts with two receptor ligand binding sites. Biochemistry. 2008 ;47(48):12900-9. DOI: 10.1021/bi801693h
De Meyts P. The structural basis of insulin and insulin-like growth factor-I receptor binding and negative co-operativity, and its relevance to mitogenic versus metabolic signalling. Diabetologia. 1994 ;37(Suppl 2):S135-48. DOI: 10.1007/BF00400837
Meyts PD, Van Obberghen E, Roth J, Wollmer A, Brandenburg D. Mapping of the residues responsible for the negative cooperativity of the receptor-binding region of insulin. Nature. 1978; 273(5663):504-9. DOI: 10.1038/273504a0
De Meyts P, Roth J, Neville Jr DM, Gavin III JR, Lesniak MA. Insulin interactions with its receptors: experimental evidence for negative cooperativity. Biochemical and biophysical research communications. 1973 ;55(1):154-61. DOI: 10.1016/S0006-291X(73)80072-5
Sun WX, Zhang KH, Zhou Q, Hu SH, Lin Y, Xu W, Zhao SM, Yuan YY. Tryptophanylation of insulin receptor by WARS attenuates insulin signaling. Cellular and Molecular Life Sciences. 2024; 81(1):25. DOI: 10.1007/s00018-023-05082-2
Sena MM, Gromiha MM, Chatterji M, Khedkar A, Ranganathan A. Mapping Structural Drivers of Insulin and its Analogs at the IGF-1 Receptor Using Molecular Dynamics and Free Energy Calculations. bioRxiv. 2023 :2023-12.
Talbot K, Wang HY, Kazi H, Han LY, Bakshi KP, Stucky A, Fuino RL, Kawaguchi KR, Samoyedny AJ, Wilson RS, Arvanitakis Z. Demonstrated brain insulin resistance in Alzheimer’s disease patients is associated with IGF-1 resistance, IRS-1 dysregulation, and cognitive decline. The Journal of clinical investigation. 2012; 122(4):1316-38. DOI: 10.1172/JCI59903
Samson SL, Vellanki P, Blonde L, Christofides EA, Galindo RJ, Hirsch IB, Isaacs SD, Izuora KE, Wang CC, Twining CL, Umpierrez GE. American Association of Clinical Endocrinology Consensus Statement: comprehensive type 2 diabetes management algorithm–2023 update. Endocrine Practice. 2023; 29(5):305-40. DOI: 10.2337/dc08-9025
Alyas J, Rafiq A, Amir H, Khan SU, Sultana T, Ali A, Hameed A, Ahmad I, Kazmi A, Sajid T, Ahmad A. Human insulin: history, recent advances, and expression systems for mass production. Biomedical Research and Therapy. 2021; 8(9):4540-61. DOI 10.15419/bmrat.v8i9.692.
Dhayalan B, Chatterjee D, Chen YS, Weiss MA. Structural lessons from the mutant proinsulin syndrome. Frontiers in Endocrinology. 2021; 12:754693.
DOI: 10.3389/fendo.2021.754693
Liang Y, Chen Q, Zhou E, Bi J, Wang J, Li Y, Li L. Methyl ferulic acid ameliorates prolonged high insulin-induced insulin release and synthesis in pancreatic β-cells via the miR-378b–PI3K–AKT pathway. Journal of Functional Foods. 2023; 105:105568. DOI: 10.1016/j.jff.2023.105568
Du Z, Su H, Wang W, Ye L, Wei H, Peng Z, Anishchenko I, Baker D, Yang J. The trRosetta server for fast and accurate protein structure prediction. Nature protocols. 2021; 16(12):5634-51. DOI: 10.1038/s41596-021-00628-9
Šali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. Journal of molecular biology. 1993; 234(3):779-815. DOI: 10.1006/jmbi.1993.1626
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera—a visualization system for exploratory research and analysis. Journal of computational chemistry. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084
Downloads
Published
How to Cite
License
Copyright (c) 2025 Saousen Diaf, Ra’ed Khashan, Preston Moore
This work is licensed under a Creative Commons Attribution 4.0 International License.
