References
- Bagler, G., & Sinha, S. (2005). Network properties of protein structures. Physica A: Statistical Mechanics and Its Applications, 346(1–2), 27–33. https://doi.org/https://doi.org/10.1016/j.physa.2004.08.046
- Ballesteros, J. A., & Weinstein, H. (1995). Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. In S. C. Sealfon (Eds.), Methods in neurosciences (Vol. 25, pp. 366–428). Academic Press.
- Bertheleme, N., Singh, S., Dowell, S. J., Hubbard, J., & Byrne, B. (2013). Loss of constitutive activity is correlated with increased thermostability of the human adenosine A2A receptor. British Journal of Pharmacology, 169(5), 988–998. https://doi.org/https://doi.org/10.1111/bph.12165
- Bhattacharya, S., & Vaidehi, N. (2014). Differences in allosteric communication pipelines in the inactive and active states of a GPCR. Biophysical Journal, 107(2), 422–434. https://doi.org/https://doi.org/10.1016/j.bpj.2014.06.015
- Bhattacharya, S., Salomon-Ferrer, R., Lee, S., & Vaidehi, N. (2016). Conserved mechanism of conformational stability and dynamics in G-protein-coupled receptors. Journal of Chemical Theory and Computation, 12(11), 5575–5584. https://doi.org/https://doi.org/10.1021/acs.jctc.6b00618
- Bradley, M. J., Chivers, P. T., & Baker, N. A. (2008). Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. Journal of Molecular Biology, 378(5), 1155–1173. https://doi.org/https://doi.org/10.1016/j.jmb.2008.03.010
- Brinda, K. V., Surolia, A., & Vishveshwara, S. (2005). Insights into the quaternary association of proteins through structure graphs: A case study of lectins. The Biochemical Journal, 391(Pt 1), 1–15. https://doi.org/https://doi.org/10.1042/BJ20050434
- Burstein, E. S., Spalding, T. A., & Brann, M. R. (1998). The second intracellular loop of the m5 muscarinic receptor is the switch which enables G-protein coupling. The Journal of Biological Chemistry, 273(38), 24322–24327. https://doi.org/https://doi.org/10.1074/jbc.273.38.24322
- Carpenter, B., Nehme, R., Warne, T., Leslie, A. G., & Tate, C. G. (2016). Structure of the adenosine A(2A) receptor bound to an engineered G protein. Nature, 536(7614), 104–107. https://doi.org/https://doi.org/10.1038/nature18966
- Chen, J. F., Eltzschig, H. K., & Fredholm, B. B. (2013). Adenosine receptors as drug targets-what are the challenges? Nature Reviews. Drug Discovery, 12(4), 265–286. https://doi.org/https://doi.org/10.1038/nrd3955
- Cheng, R. K. Y., Segala, E., Robertson, N., Deflorian, F., Doré, A. S., Errey, J. C., Fiez-Vandal, C., Marshall, F. H., & Cooke, R. M. J. S. (2017). Structures of human A1 and A2A adenosine receptors with xanthines reveal determinants of selectivity. Structure (London, England : 1993)), 25(8), 1275–1285. e1274. https://doi.org/https://doi.org/10.1016/j.str.2017.06.012
- Chennubhotla, C., Yang, Z., & Bahar, I. (2008). Coupling between global dynamics and signal transduction pathways: A mechanism of allostery for chaperonin GroEL. Molecular Biosystems, 4(4), 287–292. https://doi.org/https://doi.org/10.1039/b717819k
- Clark, S. D., Tran, H. T., Zeng, J., & Reinscheid, R. K. (2010). Importance of extracellular loop one of the neuropeptide S receptor for biogenesis and function. Peptides, 31(1), 130–138. https://doi.org/https://doi.org/10.1016/j.peptides.2009.10.015
- De Filippo, E., Namasivayam, V., Zappe, L., El-Tayeb, A., Schiedel, A. C., & Muller, C. E. (2016). Role of extracellular cysteine residues in the adenosine A2A receptor. Purinergic Signalling, 12(2), 313–329. https://doi.org/https://doi.org/10.1007/s11302-016-9506-7
- Dore, A. S., Robertson, N., Errey, J. C., Ng, I., Hollenstein, K., Tehan, B., Hurrell, E., Bennett, K., Congreve, M., Magnani, F., Tate, C. G., Weir, M., & Marshall, F. H. (2011). Structure of the adenosine A(2A) receptor in complex with ZM241385 and the xanthines XAC and caffeine. Structure (London, England: 1993)), 19(9), 1283–1293. https://doi.org/https://doi.org/10.1016/j.str.2011.06.014
- Eddy, M. T., Lee, M. Y., Gao, Z. G., White, K. L., Didenko, T., Horst, R., Audet, M., Stanczak, P., McClary, K. M., Han, G. W., Jacobson, K. A., Stevens, R. C., & Wuthrich, K. (2018). Allosteric coupling of drug binding and intracellular signaling in the A2A adenosine receptor. Cell, 172(1–2), 68–80 e12. https://doi.org/https://doi.org/10.1016/j.cell.2017.12.004
- Feinberg, E. N., Farimani, A. B., Hernandez, C. X., & Pande, V. S. (2018). Kinetic machine learning unravels ligand-directed conformational change of μ opioid receptor. Biophysical Journal, 114(3), 56a.
- Floyd, R. W. J. C. o t A. (1962). Algorithm 97: Shortest path. Communications of the Acm, 5(6), 345. https://doi.org/https://doi.org/10.1145/367766.368168
- Fuentes, E. J., Gilmore, S. A., Mauldin, R. V., & Lee, A. L. (2006). Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. Journal of Molecular Biology, 364(3), 337–351. https://doi.org/https://doi.org/10.1016/j.jmb.2006.08.076
- Garcia-Nafria, J., Lee, Y., Bai, X., Carpenter, B., & Tate, C. G. (2018). Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein. eLife, 7, e35946. https://doi.org/https://doi.org/10.7554/eLife.35946
- Grassberger, P. (1988). Finite-sample corrections to entropy and dimension estimates. Physics Letters A, 128(6–7), 369–373. https://doi.org/https://doi.org/10.1016/0375-9601(88)90193-4
- Hempel, T., Plattner, N., & Noe, F. (2020). Coupling of conformational switches in calcium sensor unraveled with local Markov models and transfer entropy. Journal of Chemical Theory and Computation, 16(4), 2584–2593. https://doi.org/https://doi.org/10.1021/acs.jctc.0c00043
- Jaakola, V. P., Griffith, M. T., Hanson, M. A., Cherezov, V., Chien, E. Y. T., Lane, J. R., IJzerman, A. P., & Stevens, R. C. (2008). The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science (New York, N.Y.).), 322(5905), 1211–1217. https://doi.org/https://doi.org/10.1126/science.1164772
- Jaakola, V. P., Lane, J. R., Lin, J. Y., Katritch, V., IJzerman, A. P., & Stevens, R. C. (2010). Ligand binding and subtype selectivity of the human A(2A) adenosine receptor: Identification and characterization of essential amino acid residues. The Journal of Biological Chemistry, 285(17), 13032–13044. https://doi.org/https://doi.org/10.1074/jbc.M109.096974
- Jacobson, K. A., & Gao, Z. G. (2006). Adenosine receptors as therapeutic targets. Nature Reviews. Drug Discovery, 5(3), 247–264. https://doi.org/https://doi.org/10.1038/nrd1983
- Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., & Schulten, K. (1999). NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151(1), 283–312. https://doi.org/https://doi.org/10.1006/jcph.1999.6201
- Katritch, V., Cherezov, V., & Stevens, R. C. (2013). Structure-function of the G protein-coupled receptor superfamily. Annual Review of Pharmacology and Toxicology, 53(1), 531–556. https://doi.org/https://doi.org/10.1146/annurev-pharmtox-032112-135923
- Kim, J., Wess, J., van Rhee, A. M., Schoneberg, T., & Jacobson, K. A. (1995). Site-directed mutagenesis identifies residues involved in ligand recognition in the human A2a adenosine receptor. The Journal of Biological Chemistry, 270(23), 13987–13997. https://doi.org/https://doi.org/10.1074/jbc.270.23.13987
- Lane, J. R., Herenbrink, C. K., van Westen, G. J. P., Spoorendonk, J. A., Hoffmann, C., & IJzerman, A. P. (2012). A novel nonribose agonist, LUF5834, engages residues that are distinct from those of adenosine-like ligands to activate the adenosine A(2a) receptor. Molecular Pharmacology, 81(3), 475–487. https://doi.org/https://doi.org/10.1124/mol.111.075937
- Lange, O. F., & Grubmuller, H. (2006). Generalized correlation for biomolecular dynamics. Proteins, 62(4), 1053–1061. https://doi.org/https://doi.org/10.1002/prot.20784
- Lebon, G., Bennett, K., Jazayeri, A., & Tate, C. G. (2011). Thermostabilisation of an agonist-bound conformation of the human adenosine A(2A) receptor. Journal of Molecular Biology, 409(3), 298–310. https://doi.org/https://doi.org/10.1016/j.jmb.2011.03.075
- Lebon, G., Edwards, P. C., Leslie, A. G., & Tate, C. G. (2015). Molecular determinants of CGS21680 binding to the human adenosine A2A receptor. Molecular Pharmacology, 87(6), 907–915. https://doi.org/https://doi.org/10.1124/mol.114.097360
- Lee, S., Bhattacharya, S., Grisshammer, R., Tate, C., & Vaidehi, N. (2014). Dynamic behavior of the active and inactive states of the adenosine A(2A) receptor. The Journal of Physical Chemistry. B, 118(12), 3355–3365. https://doi.org/https://doi.org/10.1021/jp411618h
- Lee, S., Nivedha, A. K., Tate, C. G., & Vaidehi, N. (2019). Dynamic role of the G protein in stabilizing the active state of the adenosine A2A receptor. Structure (London, England : 1993)), 27(4), 703–712. e703. https://doi.org/https://doi.org/10.1016/j.str.2018.12.007
- Li, L., Uversky, V. N., Dunker, A. K., & Meroueh, S. O. (2007). A computational investigation of allostery in the catabolite activator protein. Journal of the American Chemical Society, 129(50), 15668–15676. https://doi.org/https://doi.org/10.1021/ja076046a
- Liu, W., Chun, E., Thompson, A. A., Chubukov, P., Xu, F., Katritch, V., Han, G. W., Roth, C. B., Heitman, L. H., IJzerman, A. P., Cherezov, V., & Stevens, R. C. (2012). Structural basis for allosteric regulation of GPCRs by sodium ions. Science (New York, N.Y.).), 337(6091), 232–236. https://doi.org/https://doi.org/10.1126/science.1219218
- MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., … Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry. B, 102(18), 3586–3616. https://doi.org/https://doi.org/10.1021/jp973084f
- Magnani, F., Shibata, Y., Serrano-Vega, M. J., & Tate, C. G. (2008). Co-evolving stability and conformational homogeneity of the human adenosine A2a receptor. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10744–10749. https://doi.org/https://doi.org/10.1073/pnas.0804396105
- Massink, A., Gutiérrez-de-Terán, H., Lenselink, E. B., Ortiz Zacarías, N. V., Xia, L., Heitman, L. H., Katritch, V., Stevens, R. C., & IJzerman, A. P. (2015). Sodium ion binding pocket mutations and adenosine A2A receptor function. Molecular Pharmacology, 87(2), 305–313. https://doi.org/https://doi.org/10.1124/mol.114.095737
- Massink, A., Louvel, J., Adlere, I., van Veen, C., Huisman, B. J. H., Dijksteel, G. S., Guo, D., Lenselink, E. B., Buckley, B. J., Matthews, H., Ranson, M., Kelso, M., & IJzerman, A. P. (2016). 5'-substituted amiloride derivatives as allosteric modulators binding in the sodium ion pocket of the adenosine A2A receptor. Journal of Medicinal Chemistry, 59(10), 4769–4777. https://doi.org/https://doi.org/10.1021/acs.jmedchem.6b00142
- McClendon, C. L., Friedland, G., Mobley, D. L., Amirkhani, H., & Jacobson, M. P. (2009). Quantifying correlations between allosteric sites in thermodynamic ensembles. Journal of Chemical Theory and Computation, 5(9), 2486–2502. https://doi.org/https://doi.org/10.1021/ct9001812
- Naranjo, A. N., Chevalier, A., Cousins, G. D., Ayettey, E., McCusker, E. C., Wenk, C., & Robinson, A. S. (2015). Conserved disulfide bond is not essential for the adenosine A2A receptor: Extracellular cysteines influence receptor distribution within the cell and ligand-binding recognition. Biochimica et Biophysica Acta, 1848(2), 603–614. https://doi.org/https://doi.org/10.1016/j.bbamem.2014.11.010
- Niesen, M. J., Bhattacharya, S., Grisshammer, R., Tate, C. G., & Vaidehi, N. (2013). Thermostabilization of the β1-adrenergic receptor correlates with increased entropy of the inactive state. The Journal of Physical Chemistry. B, 117(24), 7283–7291. https://doi.org/https://doi.org/10.1021/jp403207c
- Nygaard, R., Frimurer, T. M., Holst, B., Rosenkilde, M. M., & Schwartz, T. W. (2009). Ligand binding and micro-switches in 7TM receptor structures. Trends in Pharmacological Sciences, 30(5), 249–259. https://doi.org/https://doi.org/10.1016/j.tips.2009.02.006
- Peeters, M. C., van Westen, G. J. P., Li, Q., & IJzerman, A. P. (2011). Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation. Trends in Pharmacological Sciences, 32(1), 35–42. https://doi.org/https://doi.org/10.1016/j.tips.2010.10.001
- Rask-Andersen, M., Almen, M. S., & Schioth, H. B. (2011). Trends in the exploitation of novel drug targets. Nature Reviews. Drug Discovery, 10(8), 579–590. https://doi.org/https://doi.org/10.1038/nrd3478
- Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/https://doi.org/10.1016/0021-9991(77)90098-5
- Segala, E., Guo, D., Cheng, R. K. Y., Bortolato, A., Deflorian, F., Doré, A. S., Errey, J. C., Heitman, L. H., Ijzerman, A. P., Marshall, F. H., & Cooke, R. M. (2016). Controlling the dissociation of ligands from the adenosine A2A receptor through modulation of salt bridge strength. Journal of Medicinal Chemistry, 59(13), 6470–6479. https://doi.org/https://doi.org/10.1021/acs.jmedchem.6b00653
- Shulman, A. I., Larson, C., Mangelsdorf, D. J., & Ranganathan, R. (2004). Structural determinants of allosteric ligand activation in RXR heterodimers. Cell, 116(3), 417–429. https://doi.org/https://doi.org/10.1016/S0092-8674(04)00119-9
- Steuer, R., Kurths, J., Daub, C. O., Weise, J., & Selbig, J. (2002). The mutual information: Detecting and evaluating dependencies between variables. Bioinformatics, 18(Suppl 2), S231–S240. https://doi.org/https://doi.org/10.1093/bioinformatics/18.suppl_2.S231
- Sun, X., Agren, H., & Tu, Y. (2014). Functional water molecules in rhodopsin activation. The Journal of Physical Chemistry. B, 118(37), 10863–10873. https://doi.org/https://doi.org/10.1021/jp505180t
- Susac, L., Eddy, M. T., Didenko, T., Stevens, R. C., & Wuthrich, K. (2018). A2A adenosine receptor functional states characterized by 19F-NMR . Proceedings of the National Academy of Sciences of the United States of America, 115(50), 12733–12738. https://doi.org/https://doi.org/10.1073/pnas.1813649115
- Xiao, J., & Salsbury, F. R. (2019). Na(+)-binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling. Physical Chemistry Chemical Physics: PCCP , 21(8), 4320–4330. https://doi.org/https://doi.org/10.1039/C8CP07293K
- Xiao, J., Melvin, R. L., & Salsbury, F. R. Jr. (2019). Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning. Journal of Biomolecular Structure & Dynamics, 37(4), 982–999. https://doi.org/https://doi.org/10.1080/07391102.2018.1445032
- Xie, X. L., Li, C. H., Yang, Y. X., Jin, L., Tan, J. J., Zhang, X. Y., Su, J. G., & Wang, C. X. (2015). Allosteric transitions of ATP-binding cassette transporter MsbA studied by the adaptive anisotropic network model. Proteins, 83(9), 1643–1653. https://doi.org/https://doi.org/10.1002/prot.24850