Allosteric Activation of PI3Kα Results in Dynamic Access to Catalytically Competent Conformations
Tài liệu tham khảo
Abraham, 2015, GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX, 1–2, 19, 10.1016/j.softx.2015.06.001
Bakan, 2011, Computational generation inhibitor-bound conformers of p38 MAP kinase and comparison with experiments, Pac. Symp. Biocomput., 181
Bakan, 2011, ProDy: protein dynamics inferred from theory and experiments, Bioinformatics, 27, 1575, 10.1093/bioinformatics/btr168
Burke, 2012, Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110 (PIK3CA), Proc. Natl. Acad. Sci. U S A, 109, 15259, 10.1073/pnas.1205508109
Campitelli, 2018, Hinge-shift mechanism modulates allosteric regulations in human Pin1, J. Phys. Chem. B, 122, 5623, 10.1021/acs.jpcb.7b11971
Capdevila, 2017, Entropy redistribution controls allostery in a metalloregulatory protein, Proc. Natl. Acad. Sci. U S A, 114, 4424, 10.1073/pnas.1620665114
Carpenter, 1993, Phosphoinositide 3-kinase is activated by phosphopeptides that bind to the SH2 domains of the 85-kDa subunit, J. Biol. Chem., 268, 9478, 10.1016/S0021-9258(18)98375-4
Carson, 2008, Effects of oncogenic p110α subunit mutations on the lipid kinase activity of phosphoinositide 3-kinase, Biochem. J., 409, 519, 10.1042/BJ20070681
Cooper, 1984, Allostery without conformational change: a plausible model, Eur. Biophys. J., 11, 103, 10.1007/BF00276625
Delano, 2002
Dhand, 1994, PI 3-kinase: structural and functional analysis of intersubunit interactions, EMBO J., 13, 511, 10.1002/j.1460-2075.1994.tb06289.x
Eargle
Echeverria, 2015, Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α, FEBS J., 282, 3528, 10.1111/febs.13365
Engelman, 2006, The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism, Nat. Rev. Genet., 7, 606, 10.1038/nrg1879
Floyd, 1962, Algorithm 97: shortest path, Commun. ACM, 5, 345, 10.1145/367766.368168
Fuentes, 2004, Ligand-dependent dynamics and intramolecular signaling in a PDZ domain, J. Mol. Biol., 335, 1105, 10.1016/j.jmb.2003.11.010
Grant, 2006, Bio3d: an R package for the comparative analysis of protein structures, Bioinformatics, 22, 2695, 10.1093/bioinformatics/btl461
Hess, 1997, LINCS: a linear constraint solver for molecular simulations, J. Comput. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Hon, 2012, Regulation of lipid binding underlies the activation mechanism of class IA PI3-kinases, Oncogene, 31, 3655, 10.1038/onc.2011.532
Huang, 2007, The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations, Science, 318, 1744, 10.1126/science.1150799
Huang, 2008, Insights into the oncogenic effects of PIK3CA mutations from the structure of p110α/p85α, Cell Cycle, 7, 1151, 10.4161/cc.7.9.5817
Huang, 2017, CHARMM36m: an improved force field for folded and intrinsically disordered proteins, Nat. Methods, 14, 71, 10.1038/nmeth.4067
Humphrey, 1996, VMD: Visual molecular dynamics, J. Mol. Graph., 14, 33, 10.1016/0263-7855(96)00018-5
Hunter, 2007, Matplotlib: a 2D graphics environment, Comput. Sci. Eng., 9, 90, 10.1109/MCSE.2007.55
Leontiadou, 2018, Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations, Sci. Rep., 8, 15544, 10.1038/s41598-018-27044-6
Maheshwari, 2017, Kinetic and structural analyses reveal residues in phosphoinositide 3-kinase α that are critical for catalysis and substrate recognition, J. Biol. Chem., 292, 13541, 10.1074/jbc.M116.772426
Malay, 2011, Crystal structure of unliganded TRAP: implications for dynamic allostery, Biochem. J., 434, 427, 10.1042/BJ20101813
Mandelker, 2009, A frequent kinase domain mutation that changes the interaction between PI3K and the membrane, Proc. Natl. Acad. Sci. U S A, 106, 16996, 10.1073/pnas.0908444106
McGibbon, 2015, MDTraj: a modern open library for the analysis of molecular dynamics trajectories, Biophys. J., 109, 1528, 10.1016/j.bpj.2015.08.015
Miled, 2007, Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit, Science, 317, 239, 10.1126/science.1135394
Miller, 2014, Structural basis of nSH2 regulation and lipid binding in PI3Kα, Oncotarget, 5, 5198, 10.18632/oncotarget.2263
Nguyen, 2018, NGLview—interactive molecular graphics for Jupyter notebooks, Bioinformatics, 34, 1241, 10.1093/bioinformatics/btx789
Nolte, 1996, Crystal structure of the PI 3-kinase p85 amino-terminal SH2 domain and its phosphopeptide complexes, Nat. Struct. Biol., 3, 364, 10.1038/nsb0496-364
O'Boyle, 2011, Open Babel: an open chemical toolbox, J. Cheminform., 3, 33, 10.1186/1758-2946-3-33
Philp, 2001, The phosphatidylinositol 3′-kinase p85α gene is an oncogene in human ovarian and colon tumors, Cancer Res., 61, 7426
Pirola, 2001, Activation loop sequences confer substrate specificity to phosphoinositide 3-kinase α (PI3Kα): functions of lipid kinase-deficient PI3Kα in signaling, J. Biol. Chem., 276, 21544, 10.1074/jbc.M011330200
Popovych, 2006, Dynamically driven protein allostery, Nat. Struct. Mol. Biol., 13, 831, 10.1038/nsmb1132
2018
Šali, 1993, Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol., 234, 779, 10.1006/jmbi.1993.1626
Sarkar, 2008
Schüttelkopf, 2004, PRODRG: a tool for high-throughput crystallography of protein-ligand complexes, Acta Crystallogr. D Biol. Crystallogr., 60, 1355, 10.1107/S0907444904011679
Tsai, 2008, Allostery: absence of a change in shape does not imply that allostery is not at play, J. Mol. Biol., 378, 1, 10.1016/j.jmb.2008.02.034
Tse, 2015, Molecular dynamics simulations and structural network analysis of c-Abl and c-Src kinase core proteins: capturing allosteric mechanisms and communication pathways from residue centrality, J. Chem. Inf. Model., 55, 1645, 10.1021/acs.jcim.5b00240
Vadas, 2011, Structural basis for activation and inhibition of class I phosphoinositide 3-kinases, Sci. Signal., 4, re2, 10.1126/scisignal.2002165
Vanommeslaeghe, 2009, CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields, J. Comput. Chem., 31, 671
Vogt, 2007, Cancer-specific mutations in phosphatidylinositol 3-kinase, Trends Biochem. Sci., 32, 342, 10.1016/j.tibs.2007.05.005
Walker, 1999, Structural insights into phosphoinositide 3-kinase catalysis and signalling, Nature, 402, 313, 10.1038/46319
Walker, 2000, Structural determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin, and staurosporine, Mol. Cell, 6, 909, 10.1016/S1097-2765(05)00089-4
Weinkam, 2012, Structure-based model of allostery predicts coupling between distant sites, Proc. Natl. Acad. Sci. U S A, 109, 4875, 10.1073/pnas.1116274109
Wu, 2009, Regulation of Class IA PI 3-kinases: C2 domain-iSH2 domain contacts inhibit p85/p110 and are disrupted in oncogenic p85 mutants, Proc. Natl. Acad. Sci. U S A, 106, 20258, 10.1073/pnas.0902369106
Yu, 1998, Regulation of the p85/p110 phosphatidylinositol 3′-kinase: stabilization and inhibition of the p110α catalytic subunit by the p85 regulatory subunit, Mol. Cell. Biol., 18, 1379, 10.1128/MCB.18.3.1379
Yu, 1998, Regulation of the p85/p110α phosphatidylinositol 3′-kinase: distinct roles for the N-terminal and C-terminal SH2 domains, J. Biol. Chem., 273, 30199, 10.1074/jbc.273.46.30199
Zhang, 2019, The mechanism of PI3Kα activation at the atomic level, Chem. Sci., 10, 3671, 10.1039/C8SC04498H