Funnel-metadynamics and solution NMR to estimate protein-ligand affinities

Journal of the American Chemical Society

Volumn 137, Issue 3, 2015, Pages 1273-1281

  Troussicot, Laura ^a   Guillière, Florence ^a   Limongelli, Vittorio ^b,c   Walker, Olivier ^a   Lancelin, Jean Marc ^a  

^a UNIVERSITÉ LYON 1   (France)

^b UNIVERSITY OF LUGANO   (Switzerland)

^c UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; FREE ENERGY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEINS;

ATOMISTIC RESOLUTION; BINDING FREE ENERGY; CHEMICAL EQUILIBRIUMS; DIFFERENT TIME SCALE; FREE-ENERGY CALCULATIONS; INTRINSIC PROPERTY; METADYNAMICS SIMULATIONS; REALISTIC MODEL SYSTEM;

LIGANDS;

4 METHYLCATECHOL; CATECHOL; PEROXIREDOXIN 5; CATECHOL DERIVATIVE; LIGAND; PEROXIREDOXIN; PRDX5 PROTEIN, HUMAN; SOLUTION AND SOLUBILITY;

AQUEOUS SOLUTION; ARTICLE; BINDING AFFINITY; CALCULATION; CONCENTRATION (PARAMETERS); CRYSTALLOGRAPHY; ENERGY; FUNNEL METADYNAMICS; LIGAND BINDING; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SOLUTION AND SOLUBILITY;

CATECHOLS; HUMANS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; PEROXIREDOXINS; SOLUTIONS;

EID: 84921888749     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja511336z     Document Type: Article

References (45)

1. Kuriyan, J.; Konforti, B.; Wemmer, D. The Molecules of Life: Physical and Chemical Principles; Garland Science: New York, 2012.
2. Changeux, J. P. Protein Sci. 2011, 20, 1119.
3. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. Arch. Biochem. Biophys. 1978, 185, 584.
4. Wüthrich, K. Angew. Chem. 2003, 42, 3340.
5. Serber, Z.; Keatinge-Clay, A. T.; Ledwidge, R.; Kelly, A. E.; Miller, S. M.; Dotsch, V. J. Am. Chem. Soc. 2001, 123, 2446.
6. Ernst, R. R. B, G.; Wokaun, A. Principles of Nuclear Magnetic Resonance in One and Two Dimensions; Clarendon Press: Oxford, 1987; Vol. 14.
7. Goodsell, D. S.; Morris, G. M.; Olson, A. J. J. Mol. Recognit. 1996, 9, 1.
8. Guo, L.; Yan, Z.; Zheng, X.; Hu, L.; Yang, Y.; Wang, J. J. Mol. Model. 2014, 20, 2251.
9. Harvey, M. J.; Giupponi, G.; Fabritiis, G. D. J. Chem. Theory Comput. 2009, 5, 1632.
10. Buch, I.; Giorgino, T.; De Fabritiis, G. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 10184.
11. Williamson, M. P. Prog. Nucl. Magn. Reson. Spectrosc. 2013, 73, 1.
12. Limongelli, V.; Bonomi, M.; Marinelli, L.; Gervasio, F. L.; Cavalli, A.; Novellino, E.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 5411.
13. Barducci, A.; Bonomi, M.; Parrinello, M. WIREs Comput. Mol. Sci. 2011, 1, 826.
14. Limongelli, V.; Bonomi, M.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 6358.
15. Wood, Z. A.; Poole, L. B.; Karplus, P. A. Science 2003, 300, 650.
16. Knoops, B.; Goemaere, J.; Van der Eecken, V.; Declercq, J. P. Antioxid. Redox Signal. 2011, 15, 817.
17. Wood, Z. A.; Schroder, E.; Robin Harris, J.; Poole, L. B. Trends Biochem. Sci. 2003, 28, 32.
18. Smeets, A.; Marchand, C.; Linard, D.; Knoops, B.; Declercq, J. P. Arch. Biochem. Biophys. 2008, 477, 98.
19. Declercq, J. P.; Evrard, C.; Clippe, A.; Stricht, D. V.; Bernard, A.; Knoops, B. J. Mol. Biol. 2001, 311, 751.
20. Hall, A.; Parsonage, D.; Poole, L. B.; Karplus, P. A. J. Mol. Biol. 2010, 402, 194.
21. Aguirre, C.; ten Brink, T.; Guichou, J. F.; Cala, O.; Krimm, I. PloS One 2014, 9, e102300.
22. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562.
23. Barducci, A.; Bussi, G.; Parrinello, M. Phys. Rev. Lett. 2008, 100, 020603.
24. Limongelli, V.; De Tito, S.; Cerofolini, L.; Fragai, M.; Pagano, B.; Trotta, R.; Cosconati, S.; Marinelli, L.; Novellino, E.; Bertini, I.; Randazzo, A.; Luchinat, C.; Parrinello, M. Angew. Chem. 2013, 52, 2269.
25. Limongelli, V.; Marinelli, L.; Cosconati, S.; La Motta, C.; Sartini, S.; Mugnaini, L.; Da Settimo, F.; Novellino, E.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 1467.
26. Grazioso, G.; Limongelli, V.; Branduardi, D.; Novellino, E.; De Micheli, C.; Cavalli, A.; Parrinello, M. J. Am. Chem. Soc. 2012, 134, 453.
27. Di Leva, F. S.; Novellino, E.; Cavalli, A.; Parrinello, M.; Limongelli, V. Nucleic Acids Res. 2014, 42, 5447.
28. Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A.; Parrinello, M. Comput. Phys. Commun. 2009, 180, 1961.
29. Fielding, L. Prog. Nucl. Magn. Reson. Spectrosc. 2007, 51, 219.
30. Markin, C. J.; Spyracopoulos, L. J. Biomol. NMR 2012, 53, 125.
31. Barelier, S.; Linard, D.; Pons, J.; Clippe, A.; Knoops, B.; Lancelin, J. M.; Krimm, I. PloS One 2010, 5, e9744.
32. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
33. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712.
34. Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Proteins 2010, 78, 1950.
35. Jorgensen, W. L.; Madura, J. D. J. Am. Chem. Soc. 1983, 105, 1407.
36. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157.
37. Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. J. Mol. Graphics Modell. 2006, 25, 247.
38. Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. J. Comput. Chem. 1999, 20, 786.
39. Humphrey, W.; Dalke, A.; Fau - Schulten, K.; Schulten, K. J. Mol. Graphics 1996, 14, 33.
40. Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S. e.; Wilkins, M.; Appel, R.; Bairoch, A. In The Proteomics Protocols Handbook; Walker, J., Ed.; Humana Press: New York, 2005; p 571.
41. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Pfeifer, J.; Bax, A. J. Biomol. NMR 1995, 6, 277.
42. Johnson, B. A.; Blevins, R. A. J. Biomol. NMR 1994, 4, 603.
43. Farmer, B. T.; Constantine, K. L.; Goldfarb, V.; Friedrichs, M. S.; Wittekind, M.; Yanchunas, J.; Robertson, J. G.; Mueller, L. Nat. Struct. Mol. Biol. 1996, 3, 995.
44. Schumann, F.; Riepl, H.; Maurer, T.; Gronwald, W.; Neidig, K.-P.; Kalbitzer, H. J. Biomol. NMR 2007, 39, 275.
45. Lange, A.; Ismail, M. B.; Riviere, G.; Hologne, M.; Lacabanne, D.; Guilliere, F.; Lancelin, J. M.; Krimm, I.; Walker, O. FEBS Lett. 2012, 586, 3379.