Atomistic mechanism of leptin and leptin-receptor association

References

• Agarwal, S., Verma, E., Kumar, V., Lall, N., Sau, S., Iyer, A. K., & Kashaw, S. K. (2018). An integrated computational approach of molecular dynamics simulations, receptor binding studies and pharmacophore mapping analysis in search of potent inhibitors against tuberculosis. Journal of Molecular Graphics & Modelling, 83, 17–32. https://doi.org/10.1016/j.jmgm.2018.04.019
   PubMed Web of Science ®Google Scholar
• Aguilar Pineda, J., Albaghdadi, M., Jiang, W., Vera Lopez, K., Davila Del-Carpio, G., Gomez Valdez, B., Lindsay, M. E., Malhotra, R., & Cardenas, C. L. (2020). Structural and functional analysis of female sex hormones against SARS-CoV2 cell entry. SSRN Electronic Journal, 22, 1–18. https://doi.org/10.2139/ssrn.3671734
   Google Scholar
• Ahrén, B., Baldwin, R., & Havel, P. (2000). Pharmacokinetics of human leptin in mice and rhesus monkeys. International Journal of Obesity and Related Metabolic Disorders, 24(12), 1579–1585. https://doi.org/10.1038/sj.ijo.0801447
   PubMed Web of Science ®Google Scholar
• Aier, I., Varadwaj, P. K., & Raj, U. (2016). Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific Reports, 6(1), 34984. https://doi.org/10.1038/srep34984
   PubMed Web of Science ®Google Scholar
• Bahadur, R. P., & Zacharias, M. (2008). The interface of protein-protein complexes: Analysis of contacts and prediction of interactions. Cellular and Molecular Life Sciences, 65(7–8), 1059–1072. https://doi.org/10.1007/s00018-007-7451-x
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. In B. Pullman (Eds.), Intermolecular forces. The Jerusalem symposia on quantum chemistry and biochemistry (Vol. 14, pp. 331–342). Springer. https://doi.org/10.1007/978-94-015-7658-1_21
   Google Scholar
• Caro-Gómez, L. A., Rosas-Trigueros, J. L., Mixcoha, E., Vique-Sánchez, J. L., Gasperin-Sánchez, H., Benítez-Cardoza, C. G., & Zamorano-Carillo, A. (2019). Exploring the conformational space of Bcl-2 protein variants: Dynamic contributions of the flexible loop domain and transmembrane region. Molecules, 24(21), 3896. https://doi.org/10.3390/molecules24213896
   PubMed Web of Science ®Google Scholar
• Carpenter, B., Hemsworth, G. R., Wu, Z., Maamra, M., Strasburger, C. J., Ross, R. J., & Artymiuk, P. J. (2012). Structure of the human obesity receptor leptin-binding domain reveals the mechanism of leptin antagonism by a monoclonal antibody. Structure (London, England: 1993), 20(3), 487–497. https://doi.org/10.1016/j.str.2012.01.019
   PubMed Web of Science ®Google Scholar
• Chimal-Vega, B., Paniagua-Castro, N., Carrillo Vazquez, J., Rosas-Trigueros, J. L., Zamorano-Carrillo, A., & Benítez-Cardoza, C. G. (2015). Exploring the structure and conformational landscape of human leptin. A molecular dynamics approach. Journal of Theoretical Biology, 385, 90–101. https://doi.org/10.1016/j.jtbi.2015.08.014
   PubMed Web of Science ®Google Scholar
• Chimal-Vega, B., Paniagua-Castro, N., Perez-Rebollar, J., Carrillo-Vazquez, J., Zamorano-Carrillo, A., & Benítez-Cardoza, C. (2014). Antiobesity effects of human soluble leptin in mice nourished with a high-fat/high fructose diet. American Journal of Agricultural and Biological Sciences, 9(3), 430–438. https://doi.org/10.3844/ajabssp.2014.430.438
   Google Scholar
• Cui, H., López, M., & Rahmouni, K. (2017). The cellular and molecular bases of leptin and ghrelin resistance in obesity. Nature Reviews. Endocrinology, 13(6), 338–351. https://doi.org/10.1038/nrendo.2016.222
   PubMed Web of Science ®Google Scholar
• Daghestani, M., Purohit, R., Daghestani, M., Daghistani, M., & Warsy, A. (2019). Molecular dynamic (MD) studies on Gln233Arg (rs1137101) polymorphism of leptin receptor gene and associated variations in the anthropometric and metabolic profiles of Saudi women. PLOS One, 14(2), e0211381. https://doi.org/10.1371/journal.pone.0211381
   PubMed Web of Science ®Google Scholar
• Danielsson, J., Noel, J. K., Simien, J. M., Duggan, B. M., Oliveberg, M., Onuchic, J. N., Jennings, P. A., & Haglund, E. (2020). The pierced lasso topology leptin has a bolt on dynamic domain composed by the disordered loops I and III. Journal of Molecular Biology, 432(9), 3050–3063. https://doi.org/10.1016/j.jmb.2020.01.035
   PubMed Web of Science ®Google Scholar
• Dardeno, T. A., Chou, S. H., Moon, H.-S., Chamberland, J. P., Fiorenza, C. G., & Mantzoros, C. S. (2010). Leptin in human physiology and therapeutics. Frontiers in Neuroendocrinology, 31(3), 377–393. https://doi.org/10.1016/j.yfrne.2010.06.002
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. {CCP4} Newsletter on Protein Crystallography, 40, 1–8. http://www.ccp4.ac.uk/newsletters/newsletter40/11_pymol.pdf
   Google Scholar
• Durga Bhavani, S., Suvarnavani, K., & Sinha, S. (2011). Mining of protein contact maps for protein fold prediction. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 1(4), 362–368. https://doi.org/10.1002/widm.35
   Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Gasperin-Sánchez, H., Benítez-Cardoza, C. G., Caro-Gómez, L. A., Rosas-Trigueros, J. L., & Zamorano-Carrillo, A. (2020). Transit of Procaspase-9 towards its activation. New mechanistic insights from molecular dynamics simulations. Journal of Molecular Modeling, 26(2), 1–11. https://doi.org/10.1007/s00894-019-4285-z
   Web of Science ®Google Scholar
• Haglund, E., Nguyen, L., Schafer, N. P., Lammert, H., Jennings, P. A., & Onuchic, J. N. (2018). Uncovering the molecular mechanisms behind disease-associated leptin variants. The Journal of Biological Chemistry, 293(33), 12919–12933. https://doi.org/10.1074/jbc.RA118.003957
   PubMed Web of Science ®Google Scholar
• Halaas, J. L., Gajiwala, K. S., Maffei, M., Cohen, S. L., Chait, B. T., Rabinowitz, D., Lallone, R. L., Burley, S. K., & Friedman, J. M. (1995). Weight-reducing effects of the plasma protein encoded by the obese gene. Science (New York, NY), 269(5223), 543–546. https://doi.org/10.1126/science.7624777
   Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Hiroike, T., Higo, J., Jingami, H., & Toh, H. (2000). Homology modeling of human leptin/leptin receptor complex. Biochemical and Biophysical Research Communications, 275(1), 154–158. https://doi.org/10.1006/bbrc.2000.3275
   PubMed Web of Science ®Google Scholar
• Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review A, General Physics, 31(3), 1695–1697. https://doi.org/10.1103/physreva.31.1695
   PubMedGoogle Scholar
• Imagawa, K., Numata, Y., Katsuura, G., Sakaguchi, I., Morita, A., Kikuoka, S., Matumoto, Y., Tsuji, T., Tamaki, M., Sasakura, K., Teraoka, H., Hosoda, K., Ogawa, Y., & Nakao, K. (1998). Structure-function studies of human leptin. The Journal of Biological Chemistry, 273(52), 35245–35249. https://doi.org/10.1074/jbc.273.52.35245
   PubMed Web of Science ®Google Scholar
• Iserentant, H., Peelman, F., Defeau, D., Vandekerckhove, J., Zabeau, L., & Tavernier, J. (2005). Mapping of the interface between leptin and the leptin receptor CRH2 domain. Journal of Cell Science, 118(Pt 11), 2519–2527. https://doi.org/10.1242/jcs.02386
   PubMed Web of Science ®Google Scholar
• Jiménez-García, B., Pons, C., & Fernández-Recio, J. (2013). pyDockWEB: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics (Oxford, England), 29(13), 1698–1699. https://doi.org/10.1093/bioinformatics/btt262
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., & Tirado-Rives, J. (1988). The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110(6), 1657–1666. https://doi.org/10.1021/ja00214a001
   PubMed Web of Science ®Google Scholar
• Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9(9), 646–652. https://doi.org/10.1038/nsb0902-646
   PubMedGoogle Scholar
• Klepeis, J. L., Lindorff-Larsen, K., Dror, R. O., & Shaw, D. E. (2009). Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology, 19(2), 120–127. https://doi.org/10.1016/j.sbi.2009.03.004
   PubMed Web of Science ®Google Scholar
• Krissinel, E. (2015). Stock-based detection of protein oligomeric states in jsPISA. Nucleic Acids Research, 43(W1), W314–W319. https://doi.org/10.1093/nar/gkv314
   PubMed Web of Science ®Google Scholar
• Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England), 23(21), 2947–2948. https://doi.org/10.1093/bioinformatics/btm404
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Lee, B., & Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology, 55(3), 379–400. https://doi.org/10.1016/0022-2836(71)90324-X
   PubMed Web of Science ®Google Scholar
• Lee, C., & Ham, S. (2011). Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water. Journal of Computational Chemistry, 32(2), 349–355. https://doi.org/10.1002/jcc.21628
   PubMed Web of Science ®Google Scholar
• Lemkul, J. (2019). From proteins to perturbed Hamiltonians: A suite of tutorials for the GROMACS-2018 molecular simulation package [article v1.0]. Living Journal of Computational Molecular Science, 1(1), 5068. https://doi.org/10.33011/livecoms.1.1.5068
   Google Scholar
• Lindahl, E., Abraham, M. J., Berk, H., & Van Der Spoel, D. (2019). GROMACS 2019.4 manual. GROMACS Documentation, 35–200. https://doi.org/10.5281/zenodo.3460415
   Google Scholar
• Mancour, L. V., Daghestani, H. N., Dutta, S., Westfield, G. H., Schilling, J., Oleskie, A. N., Herbstman, J. F., Chou, S. Z., & Skiniotis, G. (2012). Ligand-induced architecture of the leptin receptor signaling complex. Molecular Cell, 48(4), 655–661. https://doi.org/10.1016/j.molcel.2012.09.003
   PubMed Web of Science ®Google Scholar
• Mazen, I., El-Gammal, M., Abdel-Hamid, M., & Amr, K. (2009). A novel homozygous missense mutation of the leptin gene (N103K) in an obese Egyptian patient. Molecular Genetics and Metabolism, 97(4), 305–308. https://doi.org/10.1016/j.ymgme.2009.04.002
   PubMed Web of Science ®Google Scholar
• Moharana, K., Zabeau, L., Peelman, F., Ringler, P., Stahlberg, H., Tavernier, J., & Savvides, S. N. (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure (London, England: 1993), 22(6), 866–877. https://doi.org/10.1016/j.str.2014.04.012
   PubMed Web of Science ®Google Scholar
• Mukherjee, S., & Zhang, Y. (2009). MM-align: A quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Research, 37(11), e83. https://doi.org/10.1093/nar/gkp318
   PubMed Web of Science ®Google Scholar
• Müller, T. D., Sullivan, L. M., Habegger, K., Yi, C.-X., Kabra, D., Grant, E., Ottaway, N., Krishna, R., Holland, J., Hembree, J., Perez-Tilve, D., Pfluger, P. T., DeGuzman, M. J., Siladi, M. E., Kraynov, V. S., Axelrod, D. W., DiMarchi, R., Pinkstaff, J. K., & Tschöp, M. H. (2012). Restoration of leptin responsiveness in diet-induced obese mice using an optimized leptin analog in combination with exendin-4 or FGF21. Journal of Peptide Science, 18(6), 383–393. https://doi.org/10.1002/psc.2408
   PubMed Web of Science ®Google Scholar
• Münzberg, H., & Morrison, C. D. (2015). Structure, production and signaling of leptin. Metabolism: Clinical and Experimental, 64(1), 13–23. https://doi.org/10.1016/j.metabol.2014.09.010
   PubMed Web of Science ®Google Scholar
• Niv-Spector, L., Gonen-Berger, D., Gourdou, I., Biener, E., Gussakovsky, E. E., Benomar, Y., Ramanujan, K. V., Taouis, M., Herman, B., Callebaut, I., Djiane, J., & Gertler, A. (2005). Identification of the hydrophobic strand in the A-B loop of leptin as major binding site III: Implications for large-scale preparation of potent recombinant human and ovine leptin antagonists. The Biochemical Journal, 391(Pt 2), 221–230. https://doi.org/10.1042/BJ20050457
   PubMedGoogle Scholar
• Nosé, S. (1984). A molecular dynamics method for simulations in the canonical ensemble. Molecular Physics, 52(2), 255–268. https://doi.org/10.1080/00268978400101201
   Web of Science ®Google Scholar
• Olivares-Illana, V., Riveros-Rosas, H., Cabrera, N., Tuena de Gómez-Puyou, M., Pérez-Montfort, R., Costas, M., & Gómez-Puyou, A. (2017). A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease. Proteins, 85(7), 1190–1211. https://doi.org/10.1002/prot.25299
   PubMed Web of Science ®Google Scholar
• Park, H.-K., & Ahima, R. S. (2014). Leptin signaling. F1000prime Reports, 6(September), 73. https://doi.org/10.12703/P6-73
   PubMedGoogle Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Peelman, F., Iserentant, H., De Smet, A. S., Vandekerckhove, J., Zabeau, L., & Tavernier, J. (2006). Mapping of binding site III in the leptin receptor and modeling of a hexameric leptin leptin receptor complex. The Journal of Biological Chemistry, 281(22), 15496–15504. https://doi.org/10.1074/jbc.M512622200
   PubMed Web of Science ®Google Scholar
• Peelman, F., Van Beneden, K., Zabeau, L., Iserentant, H., Ulrichts, P., Defeau, D., Verhee, A., Catteeuw, D., Elewaut, D., & Tavernier, J. (2004). Mapping of the leptin binding sites and design of a leptin antagonist. The Journal of Biological Chemistry, 279(39), 41038–41046. https://doi.org/10.1074/jbc.M404962200
   PubMed Web of Science ®Google Scholar
• Prabhakar, P. K., Srivastava, A., Rao, K. K., & Balaji, P. V. (2016). Monomerization alters the dynamics of the lid region in Campylobacter jejuni CstII: An MD simulation study. Journal of Biomolecular Structure & Dynamics, 34(4), 778–791. https://doi.org/10.1080/07391102.2015.1054430
   PubMed Web of Science ®Google Scholar
• Reva, B. A., Finkelstein, A. V., & Skolnick, J. (1998). What is the probability of a chance prediction of a protein structure with an RMSD of 6 Å? Folding and Design, 3(2), 141–147. https://doi.org/10.1016/S1359-0278(98)00019-4
   PubMedGoogle Scholar
• Sandowski, Y., Raver, N., Gussakovsky, E. E., Shochat, S., Dym, O., Livnah, O., Rubinstein, M., Krishna, R., & Gertler, A. (2002). Subcloning, expression, purification, and characterization of recombinant human leptin-binding domain. The Journal of Biological Chemistry, 277(48), 46304–46309. https://doi.org/10.1074/jbc.M207556200
   PubMed Web of Science ®Google Scholar
• Strobel, A., Issad, T., Camoin, L., Ozata, M., & Strosberg, A. D. (1998). A leptin missense mutation associated with hypogonadism and morbid obesity. Nature Genetics, 18(3), 213–215. https://doi.org/10.1038/ng0398-213
   PubMed Web of Science ®Google Scholar
• Sun, Z., Liu, Q., Qu, G., Feng, Y., & Reetz, M. T. (2019). Utility of B-factors in protein science: Interpreting rigidity, flexibility, and internal motion and engineering thermostability [Review-article]. Chemical Reviews, 119(3), 1626–1665. https://doi.org/10.1021/acs.chemrev.8b00290
   PubMed Web of Science ®Google Scholar
• Tartaglia, L. A., Dembski, M., Weng, X., Deng, N., Culpepper, J., Devos, R., Richards, G. J., Campfield, L. A., Clark, F. T., Deeds, J., Muir, C., Sanker, S., Moriarty, A., Moore, K. J., Smutko, J. S., Mays, G. G., Wool, E. A., Monroe, C. A., & Tepper, R. I. (1995). Identification and expression cloning of a leptin receptor, OB-R. Cell, 83(7), 1263–1271. https://doi.org/10.1016/0092-8674(95)90151-5
   PubMed Web of Science ®Google Scholar
• Tovchigrechko, A., & Vakser, I. A. (2006). GRAMM-X public web server for protein-protein docking. Nucleic Acids Research, 34(Web Server), W310–314. https://doi.org/10.1093/nar/gkl206
   PubMedGoogle Scholar
• Tutone, M., Pantano, L., Lauria, A., & Almerico, A. M. (2014). Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target. Journal of Molecular Modeling, 20(5), 2247. https://doi.org/10.1007/s00894-014-2247-z
   PubMed Web of Science ®Google Scholar
• Van Heek, M., Compton, D. S., France, C. F., Tedesco, R. P., Fawzi, A. B., Graziano, M. P., Sybertz, E. J., Strader, C. D., & Davis, H. R. (1997). Diet-induced obese mice develop peripheral, but not central, resistance to leptin. Journal of Clinical Investigation, 99(3), 385–390. https://doi.org/10.1172/JCI119171
   PubMed Web of Science ®Google Scholar
• van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016). The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
   PubMed Web of Science ®Google Scholar
• Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., Jain, S., Lewis, S. M., Arendall, W. B., Snoeyink, J., Adams, P. D., Lovell, S. C., Richardson, J. S., & Richardson, D. C. (2018). MolProbity: More and better reference data for improved all-atom structure validation. Protein Science, 27(1), 293–315. https://doi.org/10.1002/pro.3330
   PubMed Web of Science ®Google Scholar
• Yang, J., & Zhang, Y. (2015). I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Research, 43(W1), W174–W181. https://doi.org/10.1093/nar/gkv342
   PubMed Web of Science ®Google Scholar
• Zabeau, L., Defeau, D., Van Der Heyden, J., Iserentant, H., Vandekerckhove, J., & Tavernier, J. (2004). Functional analysis of leptin receptor activation using a janus kinase/signal transducer and activator of transcription complementation assay. Molecular Endocrinology (Baltimore, MD), 18(1), 150–161. https://doi.org/10.1210/me.2003-0078
   PubMedGoogle Scholar
• Zabeau, L., Peelman, F., & Tavernier, J. (2015). Leptin: From structural insights to the design of antagonists. Life Sciences, 140, 49–56. https://doi.org/10.1016/j.lfs.2015.04.015
   PubMed Web of Science ®Google Scholar
• Zhang, F., Basinski, M. B., Beals, J. M., Briggs, S. L., Churgay, L. M., Clawson, D. K., DiMarchi, R. D., Furman, T. C., Hale, J. E., Hsiung, H. M., Schoner, B. E., Smith, D. P., Zhang, X. Y., Wery, J.-P., & Schevitz, R. W. (1997). Crystal structure of the obese protein leptin-E100. Nature, 387(6629), 206–209. https://doi.org/10.1038/387206a0
   PubMed Web of Science ®Google Scholar