Engineering allostery

Trends in Genetics

Volumn 30, Issue 12, 2014, Pages 521-528

  Raman, Srivatsan ^a,b   Taylor, Noah ^a,b   Genuth, Naomi ^a,b   Fields, Stanley ^c   Church, George M ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; LIGAND; MUTANT PROTEIN; RNA POLYMERASE; TRANSCRIPTION FACTOR; BACTERIAL DNA; BACTERIAL PROTEIN; PROTEIN BINDING;

ALLOSTERISM; BIOTECHNOLOGICAL PROCEDURES; DNA BINDING; DNA SYNTHESIS; ESCHERICHIA COLI; LIGAND BINDING; MOLECULAR DYNAMICS; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PROTEIN DOMAIN; REVIEW; SYNTHETIC BIOLOGY; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; MUTATION; PROTEIN TERTIARY STRUCTURE;

ALLOSTERIC REGULATION; BACTERIAL PROTEINS; BINDING SITES; DNA, BACTERIAL; MODELS, MOLECULAR; MUTATION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION FACTORS;

EID: 84916207914     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2014.09.004     Document Type: Review

References (54)

1. Lu T.K., et al. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27:1139-1150.
2. Dietrich J.A., et al. Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth. Biol. 2013, 2:47-58.
3. Rodriguez G.J., et al. Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:7787-7792.
4. Hilser V.J., et al. Structural and energetic basis of allostery. Annu. Rev. Biophys. 2012, 41:585-609.
5. Bai F., et al. Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch. Science 2010, 327:685-689.
6. Hilser V.J. An ensemble view of allostery. Science 2010, 327:653-654.
7. Goodey N.M., Benkovic S.J. Allosteric regulation and catalysis emerge via a common route. Nat. Chem. Biol. 2008, 4:474-482.
8. Amaro R.E., et al. A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. Biochemistry 2007, 46:2156-2173.
9. Gandhi P.S., et al. Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:1832-1837.
10. Ricketson D., et al. A conformational switch in the ligand-binding domain regulates the dependence of the glucocorticoid receptor on Hsp90. J. Mol. Biol. 2007, 368:729-741.
11. Masterson L.R., et al. Allosteric cooperativity in protein kinase A. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:506-511.
12. Lewis M. The lac repressor. C. R. Biol. 2005, 328:521-548.
13. Bell C.E., Lewis M. A closer view of the conformation of the Lac repressor bound to operator. Nat. Struct. Biol. 2000, 7:209-214.
14. Kleina L.G., Miller J.H. Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J. Mol. Biol. 1990, 212:295-318.
15. Markiewicz P., et al. Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as 'spacers' which do not require a specific sequence. J. Mol. Biol. 1994, 240:421-433.
16. Suckow J., et al. Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure. J. Mol. Biol. 1996, 261:509-523.
17. Xu J., Matthews K.S. Flexibility in the inducer binding region is crucial for allostery in the Escherichia coli lactose repressor. Biochemistry 2009, 48:4988-4998.
18. Swint-Kruse L., et al. Perturbation from a distance: mutations that alter LacI function through long-range effects. Biochemistry 2003, 42:14004-14016.
19. Müller-Hartmann H., Müller-Hill B. The side-chain of the amino acid residue in position 110 of the Lac repressor influences its allosteric equilibrium. J. Mol. Biol. 1996, 257:473-478.
20. de Juan D., et al. Emerging methods in protein co-evolution. Nat. Rev. Genet. 2013, 14:249-261.
21. Parente D.J., Swint-Kruse L. Multiple co-evolutionary networks are supported by the common tertiary scaffold of the LacI/GalR proteins. PLoS ONE 2013, 8:e84398.
22. Süel G.M., et al. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 2002, 10:59-69.
23. Shulman A.I., et al. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 2004, 116:417-429.
24. Fowler D.M., Fields S. Deep mutational scanning: a new style of protein science. Nat. Methods 2014, 11:801-807.
25. Fujino Y., et al. Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning. Biochem. Biophys. Res. Commun. 2012, 428:395-400.
26. Whitehead T.A., et al. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat. Biotechnol. 2012, 30:543-548.
27. Ernst A., et al. Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol. Biosyst. 2010, 6:1782.
28. Araya C.L., et al. A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:16858-16863.
29. Tinberg C.E., et al. Computational design of ligand-binding proteins with high affinity and selectivity. Nature 2013, 501:212-216.
30. Starita L.M., et al. Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:E1263-E1272.
31. Fowler D.M., et al. High-resolution mapping of protein sequence-function relationships. Nat. Methods 2010, 7:741-746.
32. Findlay G.M., et al. Saturation editing of genomic regions by multiplex homology-directed repair. Nature 2014, 513:120-123.
33. Cheng A.A., et al. Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:12462-12467.
34. Kosuri S., et al. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat. Biotechnol. 2010, 28:1295-1299.
35. McLaughlin R.N., et al. The spatial architecture of protein function and adaptation. Nature 2013, 490:138-142.
36. DeVito J.A. Recombineering with tolC as a selectable/counter-selectable marker: remodeling the rRNA operons of Escherichia coli. Nucleic Acids Res. 2008, 36:e4.
37. Isaacs F.J., et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011, 333:348-353.
38. Daily M.D., et al. Contact rearrangements form coupled networks from local motions in allosteric proteins. Proteins 2008, 71:455-466.
39. Fukami-Kobayashi K., et al. Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol. Biol. Evol. 2003, 20:267-277.
40. Gronemeyer H., et al. Principles for modulation of the nuclear receptor superfamily. Nat. Rev. Drug Discov. 2004, 3:950-964.
41. Wurtz J.M., et al. A canonical structure for the ligand-binding domain of nuclear receptors. Nat. Struct. Biol. 1996, 3:87-94.
42. Galperin M.Y. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J. Bacteriol. 2006, 188:4169-4182.
43. Capra E.J., et al. Systematic dissection and trajectory-scanning mutagenesis of the molecular interface that ensures specificity of two-component signaling pathways. PLoS Genet. 2010, 6:e1001220.
44. Ferguson S.S., et al. Role of beta-arrestin in mediating agonist-promoted G protein-coupled receptor internalization. Science 1996, 271:363-366.
45. Schlessinger J. Cell signaling by receptor tyrosine kinases. Cell 2000, 103:211-225.
46. Stynen B., et al. Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol. Mol. Biol. Rev. 2012, 76:331-382.
47. Petschnigg J., et al. The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells. Nat. Methods 2014, 11:585-592.
48. Kittanakom S., et al. CHIP-MYTH: a novel interactive proteomics method for the assessment of agonist-dependent interactions of the human β2-adrenergic receptor. Biochem. Biophys. Res. Commun. 2014, 445:746-756.
49. Yan Y-X., et al. Cell-based high-throughput screening assay system for monitoring G protein-coupled receptor activation using beta-galactosidase enzyme complementation technology. J. Biomol. Screen. 2002, 7:451-459.
50. González-Vera J.A. Probing the kinome in real time with fluorescent peptides. Chem. Soc. Rev. 2012, 41:1652-1664.
51. Morris M.C. Fluorescent biosensors - probing protein kinase function in cancer and drug discovery. Biochim. Biophys. Acta 2013, 1834:1387-1395.
52. Chen C-A., et al. Biosensors of protein kinase action: from in vitro assays to living cells. Biochim. Biophys. Acta 2004, 1697:39-51.
53. Guntas G., et al. Directed evolution of protein switches and their application to the creation of ligand-binding proteins. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:11224-11229.
54. Baird G.S., et al. Circular permutation and receptor insertion within green fluorescent proteins. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:11241-11246.