Nanometer propagation of millisecond motions in V-type allostery

Structure

Volumn 18, Issue 12, 2010, Pages 1596-1607

  Lipchock, James M ^a   Loria, J Patrick ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACRYLAMIDE; GLUTAMINE; IMIDAZOLE; N' [(5' PHOSPHORIBULOSYL)FORMIMINO] 5 AMINOIMIDAZOLE 4 CARBOXAMIDE RIBONUCLEOTIDE; PHOSPHATE; RIBONUCLEOTIDE; SYNTHETASE; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; CATALYSIS; ENZYME ACTIVATION; HYDROLYSIS; MOTION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL;

ALLOSTERIC SITE; AMINOHYDROLASES; BINDING SITES; ENTROPY; IMIDAZOLES; KINETICS; LIGANDS; MAGNETIC RESONANCE IMAGING; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOTION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; RIBONUCLEOTIDES; TIME FACTORS;

EID: 78649766072     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2010.09.020     Document Type: Article

References (56)

1. G.K. Ackers, M.L. Doyle, D. Myers, and M.A. Daugherty Molecular code for cooperativity in hemoglobin Science 255 1991 54 63
2. R.E. Amaro, R.S. Myers, V.J. Davisson, and Z.A. Luthey-Schulten Structural elements in IGP synthase exclude water to optimize ammonia transfer Biophys. J. 89 2005 475 487
3. R.E. Amaro, A. Sethi, R.S. Myers, V.J. Davisson, and Z.A. Luthey-Schulten A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase Biochemistry 46 2007 2156 2173
4. S. Beismann-Driemeyer, and R. Sterner Imidazole glycerol phosphate synthase from Thermotoga maritima - quaternary structure, steady-state kinetics, and reaction mechanism of the bienzyme complex J. Biol. Chem. 276 2001 20387 20396
5. D. Bertrand, and M. Gopalakrishnan Allosteric modulation of nicotinic acetylcholine receptors Biochem. Pharmacol. 74 2007 1155 1163
6. S. Bruschweiler, P. Schanda, K. Kloiber, B. Brutscher, G. Kontaxis, R. Konrat, and M. Tollinger Direct observation of the dynamic process underlying allosteric signal transmission J. Am. Chem. Soc. 131 2009 3063 3068
7. J.F. Carpenter, and S.C. Hand Comparison of pH-dependent allostery and dissociation for phosphofructokinases from Artemia embryos and rabbit muscle: nature of the enzymes acylated with diethylpyrocarbonate Arch. Biochem. Biophys. 248 1986 1 9
8. B.N. Chaudhuri, S.C. Lange, R.S. Myers, S.V. Chittur, V.J. Davisson, and J.L. Smith Crystal structure of imidazole glycerol phosphate synthase: a tunnel through a (beta/alpha)8 barrel joins two active sites Structure 9 2001 987 997
9. B.N. Chaudhuri, S.C. Lange, R.S. Myers, V.J. Davisson, and J.L. Smith Toward understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerolphosphate synthase: crystal structures of a ternary complex and the free enzyme Biochemistry 42 2003 7003 7012
10. S.V. Chittur, T.J. Klem, C.M. Shafer, and V.J. Davisson Mechanism for acivicin inactivation of triad glutamine amidotransferases Biochemistry 40 2001 876 887
11. A. Cooper, and D.T.F. Dryden Allostery without conformational change Eur. Biophys. J. 11 1984 103 109
12. R. Das, M.T. Mazhab-Jafari, S. Chowdhury, S. SilDas, R. Selvaratnam, and G. Melacini Entropy-driven cAMP-dependent allosteric control of inhibitory interactions in exchange proteins directly activated by cAMP J. Biol. Chem. 283 2008 19691 19703
13. V.J. Davisson, I.L. Deras, S.E. Hamilton, and L.L. Moore A plasmid-based approach for the synthesis of a histidine biosynthetic intermediate J. Org. Chem. 59 1994 137 143
14. F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Bax NMRPipe: a multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6 1995 277 293
15. A. Douangamath, M. Walker, S. Beismann-Driemeyer, M.C. Vega-Fernandez, R. Sterner, and M. Wilmanns Structural evidence for ammonia tunneling across the (beta alpha)(8) barrel of the imidazole glycerol phosphate synthase bienzyme complex Structure 10 2002 185 193
16. J.E. Dueber, B.J. Yeh, K. Chak, and W.A. Lim Reprogramming control of an allosteric signaling switch through modular recombination Science 301 2003 1904 1908
17. J.E. Dueber, E.A. Mirsky, and W.A. Lim Engineering synthetic signaling proteins with ultrasensitive input/output control Nat. Biotechnol. 25 2007 660 662
18. A.W. Fenton Allostery: an illustrated definition for the "second secret of life" Trends Biochem. Sci. 33 2008 420 425
19. E.J. Fuentes, C.J. Der, and A.L. Lee Ligand-dependent dynamics and intramolecular signaling in a PDZ domain J. Mol. Biol. 335 2004 1105 1115
20. N.K. Goto, K.H. Gardner, G.A. Mueller, R.C. Willis, and L.E. Kay A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated 15N-, 13C-, 2H-labeled proteins J. Biomol. NMR 13 1999 369 374
21. V.A. Jarymowycz, and M.J. Stone Remote changes in the dynamics of the phosphotyrosine-binding domain of insulin receptor substrate-1 induced by phosphopeptide binding Biochemistry 47 2008 13371 13382
22. D. Kern, and E.R. Zuiderweg The role of dynamics in allosteric regulation Curr. Opin. Struct. Biol. 13 2003 748 757
23. J.L. Kimmel, and G.D. Reinhart Reevaluation of the accepted allosteric mechanism of phosphofructokinase from Bacillus stearothermophilus Proc. Natl. Acad. Sci. USA 97 2000 3844 3849
24. T.J. Klem, and V.J. Davisson Imidazole glycerol phosphate synthase - the glutamine amidotransferase in histidine biosynthesis Biochemistry 32 1993 5177 5186
25. T.J. Klem, Y. Chen, and V.J. Davisson Subunit interactions and glutamine utilization by Escherichia coli imidazole glycerol phosphate synthase J. Bacteriol. 183 2001 989 996
26. D.G. Kneller, and I.D. Kuntz Ucsf Sparky - an Nmr Display, Annotation and Assignment Tool 1993 University of California San Francisco 254
27. S. Koide, S. Yokoyama, H. Matsuzawa, T. Miyazawa, and T. Ohta Conformational equilibrium of an enzyme catalytic site in the allosteric transition Biochemistry 31 1992 5362 5368
28. D.M. Korzhnev, K. Kloiber, and L.E. Kay Multiple-quantum relaxation dispersion NMR spectroscopy probing millisecond time-scale dynamics in proteins: theory and application J. Am. Chem. Soc. 126 2004 7320 7329
29. J.M. Krahn, J.H. Kim, M.R. Burns, R.J. Parry, H. Zalkin, and J.L. Smith Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site Biochemistry 36 1997 11061 11068
30. J. Lipchock, and J.P. Loria Millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima J. Biomol. NMR 45 2009 73 84
31. L. Liu, M.E. Wales, and J.R. Wild Temperature effects on the allosteric responses of native and chimeric aspartate transcarbamoylases J. Mol. Biol. 282 1998 891 901
32. J. Monod, J.P. Changeux, and F. Jacob Allosteric proteins and cellular control systems J. Mol. Biol. 6 1963 306 329
33. F.A. Mulder, N.R. Skrynnikov, B. Hon, F.W. Dahlquist, and L.E. Kay Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme J. Am. Chem. Soc. 123 2001 967 975 (Pubitemid 32151376)
34. R.S. Myers, J.R. Jensen, I.L. Deras, J.L. Smith, and V.J. Davisson Substrate-induced changes in the ammonia channel for imidazole glycerol phosphate synthase Biochemistry 42 2003 7013 7022
35. R. Omi, H. Mizuguchi, M. Goto, I. Miyahara, H. Hayashi, H. Kagamiyama, and K. Hirotsu Structure of imidazole glycerol phosphate synthase from Thermus thermophilus HB8: open-closed conformational change and ammonia tunneling J Biochem 132 2002 759 765
36. J.N. Onuchic, C. Kobayashi, O. Miyashita, P. Jennings, and K.K. Baldridge Exploring biomolecular machines: energy landscape control of biological reactions Philos. Trans. R. Soc. Lond. B Biol. Sci. 361 2006 1439 1443
37. M. Ostermeier Engineering allosteric protein switches by domain insertion Protein Eng. Des. Sel. 18 2005 359 364
38. K. Pervushin, R. Riek, G. Wider, and K. Wuthrich Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution Proc. Natl. Acad. Sci. USA 94 1997 12366 12371
39. C.M. Petit, J. Zhang, P.J. Sapienza, E.J. Fuentes, and A.L. Lee Hidden dynamic allostery in a PDZ domain Proc. Natl. Acad. Sci. USA 106 2009 18249 18254
40. N. Popovych, S. Sun, R.H. Ebright, and C.G. Kalodimos Dynamically driven protein allostery Nat. Struct. Mol. Biol. 13 2006 831 838
41. N. Popovych, S.R. Tzeng, M. Tonelli, R.H. Ebright, and C.G. Kalodimos Structural basis for cAMP-mediated allosteric control of the catabolite activator protein Proc. Natl. Acad. Sci. USA 106 2009 6927 6932
42. R. Raddatz, H. Schaffhauser, and M.J. Marino Allosteric approaches to the targeting of G-protein-coupled receptors for novel drug discovery: a critical assessment Biochem. Pharmacol. 74 2007 383 391
43. G.D. Reinhart Quantitative analysis and interpretation of allosteric behavior Methods Enzymol. 380 2004 187 203
44. R.A. Ross Allosterism and cannabinoid CB(1) receptors: the shape of things to come Trends Pharmacol. Sci. 28 2007 567 572
45. J. Rudolph, and J. Stubbe Investigation of the mechanism of phosphoribosylamine transfer from glutamine phosphoribosylpyrophosphate amidotransferase to glycinamide ribonucleotide synthetase Biochemistry 34 1995 2241 2250
46. A. Schweizer, H. Roschitzki-Voser, P. Amstutz, C. Briand, M. Gulotti-Georgieva, E. Prenosil, H.K. Binz, G. Capitani, A. Baici, A. Pluckthun, and M.G. Grutter Inhibition of caspase-2 by a designed ankyrin repeat protein: specificity, structure, and inhibition mechanism Structure 15 2007 625 636
47. Z. Shi, K.A. Resing, and N.G. Ahn Networks for the allosteric control of protein kinases Curr. Opin. Struct. Biol. 16 2006 686 692
48. N.R. Skrynnikov, F.A. Mulder, B. Hon, F.W. Dahlquist, and L.E. Kay Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme J. Am. Chem. Soc. 123 2001 4556 4566 (Pubitemid 32923384)
49. G. Spraggon, C. Kim, X. Nguyen-Huu, M.C. Yee, C. Yanofsky, and S.E. Mills The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan Proc. Natl. Acad. Sci. USA 98 2001 6021 6026
50. J.B. Thoden, H.M. Holden, G. Wesenberg, F.M. Raushel, and I. Rayment Structure of carbamoyl phosphate synthetase: a journey of 96 A from substrate to product Biochemistry 36 1997 6305 6316
51. J.B. Thoden, S.G. Miran, J.C. Phillips, A.J. Howard, F.M. Raushel, and H.M. Holden Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis Biochemistry 37 1998 8825 8831
52. V. Tugarinov, and L.E. Kay Side chain assignments of Ile delta 1 methyl groups in high molecular weight proteins: an application to a 46 ns tumbling molecule J. Am. Chem. Soc. 125 2003 5701 5706
53. V. Tugarinov, R. Sprangers, and L.E. Kay Probing side-chain dynamics in the proteasome by relaxation violated coherence transfer NMR spectroscopy J. Am. Chem. Soc. 129 2007 1743 1750
54. J. Yan, Y. Liu, S.M. Lukasik, N.A. Speck, and J.H. Bushweller CBFbeta allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium Nat. Struct. Mol. Biol. 11 2004 901 906
55. E.W. Yu, and D.E. Koshland Jr. Propagating conformational changes over long (and short) distances in proteins Proc. Natl. Acad. Sci. USA 98 2001 9517 9520
56. H. Zalkin, and J.L. Smith Enzymes utilizing glutamine as an amide donor Adv. Enzymol. Relat. Areas Mol. Biol. 72 1998 87 144