Disorder driven allosteric control of protein activity

Berezovsky, 2013, Thermodynamics of allostery paves a way to allosteric drugs, Biochim. Biophys. Acta, 1834, 830, 10.1016/j.bbapap.2013.01.024 Berezovsky, 1997, Representation of amino acid sequences in terms of interaction energy in protein globules, FEBS Lett., 418, 43, 10.1016/S0014-5793(97)01346-X Berlow, 2018, Expanding the paradigm: intrinsically disordered proteins and allosteric regulation, J. Mol. Biol., 430, 2309, 10.1016/j.jmb.2018.04.003 Bosco, 2009, Rac1 GTPase: a "Rac" of all trades, Cell. Mol. Life Sci., 66, 370, 10.1007/s00018-008-8552-x Cooper, 1984, Allostery without conformational change. A plausible model, Eur. Biophys. J., 11, 103, 10.1007/BF00276625 Dagliyan, 2016, Engineering extrinsic disorder to control protein activity in living cells, Science, 354, 1441, 10.1126/science.aah3404 Dunker, 2008, Function and structure of inherently disordered proteins, Curr. Opin. Struct. Biol., 18, 756, 10.1016/j.sbi.2008.10.002 Dunker, 2013, What's in a name? Why these proteins are intrinsically disordered: why these proteins are intrinsically disordered, Intrinsically Disord. Proteins, 1, 10.4161/idp.24157 Eisenstein, 1999, Dimerization of the Escherichia coli biotin repressor: corepressor function in protein assembly, Biochemistry, 38, 13077, 10.1021/bi991241q Berezovsky, 2005, Physics and evolution of thermophilic adaptation, Proc. Natl. Acad. Sci. U. S. A, 102, 12742, 10.1073/pnas.0503890102 Ferreon, 2013, Modulation of allostery by protein intrinsic disorder, Nature, 498, 390, 10.1038/nature12294 Garcia-Pino, 2010, Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity, Cell, 142, 101, 10.1016/j.cell.2010.05.039 Gsponer, 2009, The rules of disorder or why disorder rules, Prog. Biophys. Mol. Biol., 99, 94, 10.1016/j.pbiomolbio.2009.03.001 Guarnera, 2016, Allosteric sites: remote control in regulation of protein activity, Curr. Opin. Struct. Biol., 37, 1, 10.1016/j.sbi.2015.10.004 Guarnera, 2016, Structure-based statistical mechanical model accounts for the causality and energetics of allosteric communication, PLoS Comput. Biol., 12, 10.1371/journal.pcbi.1004678 Guarnera, 2019, On the perturbation nature of allostery: sites, mutations, and signal modulation, Curr. Opin. Struct. Biol., 56, 18, 10.1016/j.sbi.2018.10.008 Guarnera, 2019, Toward comprehensive allosteric control over protein activity, Structure, 27, 866, 10.1016/j.str.2019.01.014 Guarnera, 2017, AlloSigMA: allosteric signaling and mutation analysis server, Bioinformatics, 33, 3996, 10.1093/bioinformatics/btx430 Gunasekaran, 2004, Is allostery an intrinsic property of all dynamic proteins?, Proteins, 57, 433, 10.1002/prot.20232 Hilser, 2007, Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins, Proc. Natl. Acad. Sci. U. S. A., 104, 8311, 10.1073/pnas.0700329104 Hinsen, 2000, Harmonicity in slow protein dynamics, Chem. Phys., 261, 25, 10.1016/S0301-0104(00)00222-6 Huang, 2020, Allostery of multidomain proteins with disordered linkers, Curr. Opin. Struct. Biol., 62, 175, 10.1016/j.sbi.2020.01.017 Jacobitz, 2017, Sortase transpeptidases: structural biology and catalytic mechanism, Adv. Protein Chem. Struct. Biol., 109, 223, 10.1016/bs.apcsb.2017.04.008 Karginov, 2010, Engineered allosteric activation of kinases in living cells, Nat. Biotechnol., 28, 743, 10.1038/nbt.1639 Li, 2017, Genetically tunable frustration controls allostery in an intrinsically disordered transcription factor, Elife, 6, 10.7554/eLife.30688 Ma, 2011, Dynamic allostery: linkers are not merely flexible, Structure, 19, 907, 10.1016/j.str.2011.06.002 Mitternacht, 2011, A geometry-based generic predictor for catalytic and allosteric sites, Protein Eng. Des. Sel., 24, 405, 10.1093/protein/gzq115 Mitternacht, 2011, Binding leverage as a molecular basis for allosteric regulation, PLoS Comput. Biol., 7, 10.1371/journal.pcbi.1002148 Mitternacht, 2011, Coherent conformational degrees of freedom as a structural basis for allosteric communication, PLoS Comput. Biol., 7, 10.1371/journal.pcbi.1002301 Monod, 1963, Allosteric proteins and cellular control systems, J. Mol. Biol., 6, 306, 10.1016/S0022-2836(63)80091-1 Motlagh, 2014, The ensemble nature of allostery, Nature, 508, 331, 10.1038/nature13001 Naik, 2006, Staphylococcus aureus Sortase A transpeptidase. Calcium promotes sorting signal binding by altering the mobility and structure of an active site loop, J. Biol. Chem., 281, 1817, 10.1074/jbc.M506123200 Pang, 2015, Disorder-to-Order transition of an active-site loop mediates the allosteric activation of sortase A, Biophys. J., 109, 1706, 10.1016/j.bpj.2015.08.039 Papaleo, 2016, The role of protein loops and linkers in conformational dynamics and allostery, Chem. Rev., 116, 6391, 10.1021/acs.chemrev.5b00623 Saavedra, 2018, Dynamic allostery can drive cold adaptation in enzymes, Nature, 558, 324, 10.1038/s41586-018-0183-2 Sevcsik, 2011, Allostery in a disordered protein: oxidative modifications to alpha-synuclein act distally to regulate membrane binding, J. Am. Chem. Soc., 133, 7152, 10.1021/ja2009554 Tan, 2019, Berezovsky IN: AlloMAPS: allosteric mutation analysis and polymorphism of signaling database, Nucleic Acids Res., 47, D265, 10.1093/nar/gky1028 Tan, 2020, AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations, Nucleic Acids Res., 48, W116, 10.1093/nar/gkaa338 Tee, 2018, Reversing allosteric communication: from detecting allosteric sites to inducing and tuning targeted allosteric response, PLoS Comput. Biol., 14, 10.1371/journal.pcbi.1006228 Tee, 2019, On the allosteric effect of nsSNPs and the emerging importance of allosteric polymorphism, J. Mol. Biol., 431, 3933, 10.1016/j.jmb.2019.07.012 Tokuriki, 2009, Do viral proteins possess unique biophysical features?, Trends Biochem. Sci., 34, 53, 10.1016/j.tibs.2008.10.009 Tsai, 2014, A unified view of "how allostery works, PLoS Comput. Biol., 10, 10.1371/journal.pcbi.1003394 Uversky, 2002, Natively unfolded proteins: a point where biology waits for physics, Protein Sci., 11, 739, 10.1110/ps.4210102 van der Lee, 2014, Classification of intrinsically disordered regions and proteins, Chem. Rev., 114, 6589, 10.1021/cr400525m Wang, 2017, Long distance modulation of disorder-to-order transitions in protein allostery, Biochemistry, 56, 4478, 10.1021/acs.biochem.7b00496 Wright, 1999, Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm, J. Mol. Biol., 293, 321, 10.1006/jmbi.1999.3110 Zong, 2004, Crystal structures of Staphylococcus aureus sortase A and its substrate complex, J. Biol. Chem., 279, 31383, 10.1074/jbc.M401374200