Ligand binding energy and enzyme efficiency from reductions in protein dynamics

Journal of Molecular Biology

Volumn 355, Issue 4, 2006, Pages 760-767

  Williams, Dudley H ^a   Zhou, Min ^a   Stephens, Elaine ^a  

^a Department of Chemistry ^*  (United Kingdom)

Author keywords

Binding energy; Cooperativity; Enzyme catalysis; Non covalent interactions

Indexed keywords

GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; NICOTINAMIDE ADENINE DINUCLEOTIDE;

ARTICLE; BINDING AFFINITY; CATALYSIS; CHEMICAL BOND; ENZYME BINDING; LIGAND BINDING; MASS SPECTROMETRY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FUNCTION; REDUCTION KINETICS;

ORYCTOLAGUS CUNICULUS;

EID: 29144443497     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.11.015     Document Type: Article

References (37)

1. D.E. Koshland Jr Application of a theory of enzyme specificity to protein synthesis Proc. Natl Acad. Sci. USA 44 1958 98 104
2. W.P. Jencks Binding energy, specificity, and enzymic catalysis: the circe effect Advan. Enzymol. Relat. Areas Mol. Biol. 43 1975 219 410
3. F.J. Blanco, G. Rivas, and L. Serrano A short linear peptide that folds into a native stable beta-hairpin in aqueous-solution Nature Struct. Biol. 1 1994 584 590
4. A. Jasanoff, and A.R. Fersht Quantitative-determination of helical propensities from trifluoroethanol titration curves Biochemistry 33 1994 2129 2135
5. J.P.L. Cox, P.A. Evans, L.C. Packman, D.H. Williams, and D.N. Woolfson Dissecting the structure of a partially folded protein: circular dichroism and nuclear magnetic resonance studies of peptides from ubiquitin J. Mol. Biol. 234 1993 483 492
6. P.E. Wright, H.J. Dyson, and R.A. Lerner Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding Biochemistry 27 1988 7167 7175
7. A. Conway, and D.E. Koshland Jr Negative cooperativity in enzyme action. The binding of diphosphopyridine nucleotide to glyceraldehyde 3-phosphate dehydrogenase Biochemistry 7 1968 4011 4022
8. K. Kirschner, E. Gallego, I. Schuster, and D. Goodall Co-operative binding of nicotinamide-adenine dinucleotide to yeast glyceraldehyde-3-phosphate dehydrogenase J. Mol. Biol. 58 1971 29 50
9. A.G.W. Leslie, and A.J. Wonacott Coenzyme binding in crystals of glyceraldehyde-3-phosphate dehydrogenase J. Mol. Biol. 165 1983 375 391
10. J. Schlessinger, and A. Levitzki Molecular basis of negative co-operativity in rabbit muscle glyceraldehyde-3-phosphate dehydrogenase J. Mol. Biol. 82 1974 547 561
11. A.N. Hoofnagle, K.A. Resing, and N.G. Ahn Protein analysis by hydrogen exchange mass spectrometry Annu. Rev. Biophys. Biomol. Struct. 32 2003 1 25
12. V. Katta, and B.T. Chait Hydrogen-deuterium exchange electrospray- ionization mass-spectrometry - a method for probing protein conformational change in solution J. Am. Chem. Soc. 115 1993 6317 6321
13. K. Gekko, and K. Yamagami Compressibility and volume changes of lysozyme due to inhibitor binding Chem. Letters 1998 839 840
14. W.D. Mercer, S.I. Winn, and H.C. Watson Twinning in crystals of human skeletal muscle d-glyceraldehyde-3-phosphate dehydrogenase J. Mol. Biol. 104 1976 277 283
15. J.P. Mackay, U. Gerhard, D.A. Beauregard, R.A. Maplestone, and D.H. Williams Dissection of the contributions towards dimerization of glycopeptide antibiotics J. Am. Chem. Soc. 116 1994 4581 4590
16. J.P. Mackay, U. Gerhard, D.A. Beauregard, M.S. Westwell, M.S. Searle, and D.H. Williams Glycopeptide activity and the possible role of dimerization. A model for biological signaling J. Am. Chem. Soc. 116 1994 4581 4590
17. D.H. Williams, A.J. Maguire, W. Tsuzuki, and M.S. Westwell An analysis of the origins of a cooperative binding energy of dimerization Science 280 1998 711 714
18. D.H. Williams, E. Stephens, D.P. O'Brien, and M. Zhou Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motions within receptors and enzymes Angew. Chem. Int. Ed. 43 2004 6596 6616
19. S.W. Cowan-Jacob, M. Kaufmann, A.N. Anselmo, W. Stark, and M.G. Grütter Structure of rabbit-muscle glyceraldehyde-3-phosphate dehydrogenase Acta Crystallog. sect. D 59 2003 2218 2227
20. D.H. Williams, E. Stephens, and M. Zhou Ligand binding energy and catalytic efficiency from improved packing within receptors and enzymes J. Mol. Biol. 329 2003 389 399
21. + concentration Biochem. Biophys. Res. Commun. 40 1970 481 488
22. P. Levashov, V. Orlov, S. Boschi-Muller, F. Talfournier, R. Asryants, and I. Bulatnikov Thermal unfolding of phosphorylating d-glyceraldehyde-3-phosphate dehydrogenase studied by differential scanning calorimetry Biochim. Biophys. Acta 1433 1999 294 306
23. J.A. Morrison, L.E. Drain, and J.S. Dugdale Phase transition in multimolecular layers of adsorbed nitrogen Can. J. Chem. 30 1952 890 903
24. T. Skarzynski, and A.J. Wonacott Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus J. Mol. Biol. 203 1988 1097 1118
25. M.L. Jones, and G.P. Kurzban Non-cooperativity of biotin binding to tetrameric strepatividin Biochemistry 34 1995 11750 11756
26. F. Wang, R.W. Miles, G.E.N. Kicska, V.L. Schramm, and R.H. Angeletti Immucillin-H binding to purine nucleoside phosphorylase reduces dynamic solvent exchange Protein Sci. 9 2000 1660 1668
27. F. Wang, W. Shi, E. Nieves, R.H. Angeletti, V.L. Schramm, and C. Grubmeyer A transition-state analogue reduces protein dynamics in hypoxanthine-guanine phosphoribosyltransferase Biochemistry 40 2001 8043 8054
28. A. Radzicka, and R. Wolfenden A proficient enzyme Science 267 1995 90 93
29. M.J. Snider, S. Gaunitz, C. Ridgway, S.A. Short, and R. Wolfenden Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor" Biochemistry 39 2000 9746 9753
30. R. Wolfenden, M. Snider, C. Ridgway, and B. Miller The temperature dependence of enzyme rate enhancements J. Am. Chem. Soc. 121 1999 7419 7420
31. T.P.W. McMullen, R.N.A.H. Lewis, and R.N. McElahney Differential scanning calorimetric and Fourier transform infrared spectroscopic studies of the effects of cholesterol on the thermotropic phase behavior and organization of a homologous series of linear saturated phosphatidylserine bilayer membranes Biophys. J. 79 2000 2056 2065
32. M.S. Celej, G.G. Montich, and G.D. Fidelio Protein stability induced by ligand binding correlates with changes in protein flexibility Protein Sci. 12 2003 1496 1506
33. J.J. Englander, C. Del Mar, W. Li, S.W. Englander, J.S. Kim, and D.D. Stranz Protein structure changes studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry Proc. Natl Acad. Sci. USA 100 2003 7062 7075
34. J. Monod, J. Wyman, and J.-P. Changeaux On the nature of allosteric transitions: a plausible model J. Mol. Biol. 12 1965 88 118
35. W. Bloch, R.A. MacQuarrie, and S.A. Bernhard The nucleotide and acyl group content of native rabbit muscle glyceraldehyde-3-phosphate dehydrogenase J. Biol. Chem. 246 1971 780 790
36. B.D. Peczon, and H.O. Spivey Catalytic sites in rabbit muscle glyceraldehyde-3-phosphate dehydrogenase. Their number and their kinetic and spectral properties Biochemistry 11 1972 2209 2217
37. J.B. Fox Jr, and W.B. Dandliker The coenzyme content of rabbit muscle d-glyceraldehyde-3-phosphate dehydrogenase J. Biol. Chem. 221 1956 1005 1017