Improving protocols for protein mapping through proper comparison to crystallography data

Journal of Chemical Information and Modeling

Volumn 53, Issue 2, 2013, Pages 391-402

  Lexa, Katrina W ^a   Carlson, Heather A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; COMPUTATIONAL METHODS; MAPPING; MOLECULAR DYNAMICS; PROTEINS;

ATOMIC COORDINATE; COMPUTATIONAL APPROACH; CRYSTALLOGRAPHIC COORDINATES; CRYSTALLOGRAPHIC DENSITY; CRYSTALLOGRAPHIC STRUCTURE; EFFICIENT STRATEGY; EVALUATION OF COMPUTATIONAL METHODS; TARGET STRUCTURE;

ORGANIC SOLVENTS;

PROTEIN;

ANIMAL; ARTICLE; CHEMISTRY; COMPARATIVE STUDY; DRUG DESIGN; ENZYME ACTIVE SITE; HUMAN; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN DATABASE; X RAY CRYSTALLOGRAPHY;

ANIMALS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; DRUG DESIGN; HUMANS; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS;

EID: 84874413947     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300430v     Document Type: Article

References (42)

1. Allen, K. N.; Bellamacina, C. R.; Ding, X.; Jeffery, C. J.; Mattos, C.; Petsko, G. A.; Ringe, D. An Experimental Approach to Mapping the Binding Surfaces of Crystalline Proteins J. Phys. Chem. B 1996, 100, 2605-2611
2. Mattos, C.; Ringe, D. Locating and characterizing binding sites on proteins Nat. Biotechnol. 1996, 14, 595-599
3. Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Discovering high-affinity ligands for proteins: SAR by NMR Science 1996, 274, 1531-1534
4. Clackson, T.; Wells, J. A. A hot spot of binding energy in a hormone-receptor interface Science 1995, 267, 383-6
5. Bogan, A. A.; Thorn, K. S. Anatomy of hot spots in protein interfaces J. Mol. Biol. 1998, 280, 1-9
6. Murray, C. W.; Rees, D. C. The rise of fragment-based drug discovery Nat. Chem. 2009, 1, 187-192
7. Howard, S.; Berdini, V.; Boulstridge, J. A.; Carr, M. G.; Cross, D. M.; Curry, J.; Devine, L. A.; Early, T. R.; Fazal, L.; Gill, A. L.; Heathcote, M.; Maman, S.; Matthews, J. E.; McMenamin, R. L.; Navarro, E. F.; O'Brien, M. A.; O'Reilly, M.; Rees, D. C.; Reule, M.; Tisi, D.; Williams, G.; Vinkovic, M.; Wyatt, P. G. Fragment-based discovery of the pyrazol-4-yl urea (AT9283), a multitargeted kinase inhibitor with potent aurora kinase activity J. Med. Chem. 2009, 52, 379-388
8. Seco, J.; Luque, F. J.; Barril, X. Binding site detection and druggability index from first principles J. Med. Chem. 2009, 52, 2363-2371
9. Guvench, O.; MacKerell, A. D., Jr. Computational fragment-based binding site identification by ligand competitive saturation PLoS Comput. Biol. 2009, 5, e1000435
10. Raman, E. P.; Yu, W.; Guvench, O.; Mackerell, A. D. Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations J. Chem. Inf. Model. 2011, 51, 877-896
11. Bakan, A.; Nevins, N.; Lakdawala, A. S.; Bahar, I. Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules J. Chem. Theory Comput. 2012, 8, 2435-2447
12. Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 1985, 28, 849-857
13. Miranker, A.; Karplus, M. Functionality maps of binding sites: a multiple copy simultaneous search method Proteins: Struct., Funct., Genet. 1991, 11, 29-34
14. Brenke, R.; Kozakov, D.; Chuang, G. Y.; Beglov, D.; Hall, D.; Landon, M. R.; Mattos, C.; Vajda, S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques Bioinformatics 2009, 25, 621-627
15. Kozakov, D.; Hall, D. R.; Chuang, G. Y.; Cencic, R.; Brenke, R.; Grove, L. E.; Beglov, D.; Pelletier, J.; Whitty, A.; Vajda, S. Structural conservation of druggable hot spots in protein-protein interfaces Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 13528-13533
16. Lexa, K. W.; Carlson, H. A. Full Protein Flexibility Is Essential for Proper Hot-Spot Mapping J. Am. Chem. Soc. 2011, 133, 200-202
17. English, A. C.; Done, S. H.; Caves, L. S.; Groom, C. R.; Hubbard, R. E. Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol Proteins: Struct., Funct., Genet. 1999, 37, 628-640
18. Fitzpatrick, P. A.; Steinmetz, A. C.; Ringe, D.; Klibanov, A. M. Enzyme crystal structure in a neat organic solvent Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8653-8657
19. English, A. C.; Groom, C. R.; Hubbard, R. E. Experimental and computational mapping of the binding surface of a crystalline protein Protein Eng. 2001, 14, 47-59
20. Mattos, C.; Bellamacina, C. R.; Peisach, E.; Pereira, A.; Vitkup, D.; Petsko, G. A.; Ringe, D. Multiple solvent crystal structures: probing binding sites, plasticity and hydration J. Mol. Biol. 2006, 357, 1471-1482
21. Deshpande, A.; Nimsadkar, S.; Mande, S. C. Effect of alcohols on protein hydration: crystallographic analysis of hen egg-white lysozyme in the presence of alcohols Acta Crystallogr. D Biol. Crystallogr. 2005, 61, 1005-1008
22. Ho, W. C.; Luo, C.; Zhao, K.; Chai, X.; Fitzgerald, M. X.; Marmorstein, R. High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds Acta Crystallogr. D Biol. Crystallogr. 2006, 62, 1484-1493
23. Dechene, M.; Wink, G.; Smith, M.; Swartz, P.; Mattos, C. Multiple solvent crystal structures of ribonuclease A: an assessment of the method Proteins: Struct., Funct., Bioinf. 2009, 76, 861-881
24. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
25. Davis, I. W.; Leaver-Fay, A.; Chen, V. B.; Block, J. N.; Kapral, G. J.; Wang, X.; Murray, L. W.; Arendall, W. B., 3rd; Snoeyink, J.; Richardson, J. S.; Richardson, D. C. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 2007, 35, W375-W383
26. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
27. Case, D. A.; Darden, T. A.; Cheatham, I., T.E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 10; University of California, San Francisco: 2008.
28. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Bioinf. 2006, 65, 712-725
29. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
30. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-Integration of Cartesian Equations of Motion of a System with Constraints-Molecular-Dynamics of N-Alkanes J. Comput. Phys. 1977, 23, 327-341
31. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald-an N.Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
32. Andrea, T. A.; Swope, W. C.; Andersen, H. C. The role of long ranged forces in determining the structure and properties of liquid water J. Chem. Phys. 1983, 79, 4576-4584
33. Winn, M. D.; Ballard, C. C.; Cowtan, K. D.; Dodson, E. J.; Emsley, P.; Evans, P. R.; Keegan, R. M.; Krissinel, E. B.; Leslie, A. G.; McCoy, A.; McNicholas, S. J.; Murshudov, G. N.; Pannu, N. S.; Potterton, E. A.; Powell, H. R.; Read, R. J.; Vagin, A.; Wilson, K. S. Overview of the CCP4 suite and current developments Acta Crystallogr. D Biol. Crystallogr. 2011, 67, 235-242
34. Bricogne, G.; Blanc, E.; Brandl, M.; Flensburg, C.; Keller, P.; Paciorek, W.; Roversi, P; Sharff, A.; Smart, O. S.; Vonrhein, C.; T.O., W. Buster 2.11.1; Global Phasing Ltd: Cambridge, United Kingdom, 2011.
35. Kleywegt, G. J.; Harris, M. R.; Zou, J.-y.; Taylor, T. C.; Wahlby, A.; Jones, T. A. The Uppsala Electron-Density Server Acta Crystallogr. D Biol. Crystallogr. 2004, 60, 2240-2249
36. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 2004, 25, 1605-1612
37. Emsley, P.; Lohkamp, B.; Scott, W. G.; Cowtan, K. Features and development of Coot Acta Crystallogr. D Biol. Crystallogr. 2010, 66, 486-501
38. DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific: Palo Alto, CA, 2008.
39. Foster, T. J.; Mackerell, A. D., Jr.; Guvench, O. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery J. Comput. Chem. 2012, 33, 1880-1891
40. Englert, L.; Silber, K.; Steuber, H.; Brass, S.; Over, B.; Gerber, H.-D.; Heine, A.; Diederich, W. E.; Klebe, G. Fragment-Based Lead Discovery: Screening and Optimizing Fragments for Thermolysin Inhibition ChemMedChem 2010, 5, 930-940
41. Wang, S. M.; Yang, C. Y. Computational Analysis of Protein Hotspots ACS Med. Chem. Lett. 2010, 1, 125-129
42. Arnold, U.; Leich, F.; Neumann, P.; Lilie, H.; Ulbrich-Hofmann, R. Crystal structure of RNase A tandem enzymes and their interaction with the cytosolic ribonuclease inhibitor FEBS J. 2011, 278, 331-340