Computational alanine scanning mutagenesis: MM-PBSA vs TI

Journal of Chemical Theory and Computation

Volumn 9, Issue 3, 2013, Pages 1311-1319

  Martins, Sílvia A ^a   Perez, Marta A S ^a   Moreira, Irina S ^a   Sousa, Sérgio F ^a   Ramos, M J ^a   Fernandes, P A ^a  

^a UNIVERSITY OF PORTO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84874848450     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct4000372     Document Type: Article

References (53)

1. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Hot spots-A review of the protein-protein interface determinant amino-acid residues Proteins 2007, 68, 803-812
2. Bogan, A. A.; Thorn, K. S. Anatomy of hot spots in protein interfaces J. Mol. Biol. 1998, 280, 1-9
3. Higueruelo, A. P.; Schreyer, A.; Bickerton, G. R. J.; Pitt, W. R.; Groom, C. R.; Blundell, T. L. Atomic interactions and profile of small molecules disrupting protein-protein interfaces: The TIMBAL Database Chem. Biol. Drug Des. 2009, 74, 457-467
4. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Computational alanine scanning mutagenesis-An improved methodological approach J. Comput. Chem. 2007, 28, 644-654
5. Tuncbag, N.; Gursoy, A.; Keskin, O. Identification of computational hot spots in protein interfaces: Combining solvent accessibility and inter-residue potentials improves the accuracy Bioinformatics 2009, 25, 1513-1520
6. Xia, J. F.; Zhao, X. M.; Song, J. N.; Huang, D. S. APIS: Accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility BMC Bioinf. 2010, 11, 174
7. Darnell, S. J.; LeGault, L.; Mitchell, J. C. KFC Server: Interactive forecasting of protein interaction hot spots Nucleic Acids Res. 2008, 36, W265-W269
8. Darnell, S. J.; Page, D.; Mitchell, J. C. An automated decision-tree approach to predicting protein interaction hot spots Proteins 2007, 68, 813-823
9. Cho, K.-i.; Kim, D.; Lee, D. A feature-based approach to modeling protein-protein interaction hot spots Nucleic Acids Res. 2009, 37, 2672-2687
10. Liu, Q. A.; Li, J. Y. Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective. BMC Bioinf. 11, 244.
11. Cho, K. I.; Kim, D.; Lee, D. A feature-based approach to modeling protein-protein interaction hot spots Nucleic Acids Res. 2009, 37, 2672-2687
12. Guharoy, M.; Chakrabarti, P. Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes J. Comput.-Aided Mol. Des. 2009, 23, 645-654
13. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models Acc. Chem. Res. 2000, 33, 889-897
14. Massova, I.; Kollman, P. A. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies J. Am. Chem. Soc. 1999, 121, 8133-8143
15. Huo, S.; Massova, I.; Kollman, P. A. Computational alanine scanning of the 1:1 human growth hormone-receptor complex J. Comput. Chem. 2002, 23, 15-27
16. Wiesmann, C.; Fuh, G.; Christinger, H. W.; Eigenbrot, C.; Wells, J. A.; de Vos, A. M. Crystal structure at 1.7 Å resolution of VEGF in complex with domain 2 of the Flt-1 receptor Cell 1997, 91, 695-704
17. Buckle, A. M.; Schreiber, G.; Fersht, A. R. Protein-protein recognition-Crystal structural-analysis of a Barnase Barstar complex at 2.0 Å resolution Biochemistry 1994, 33, 8878-8889
18. Mosyak, L.; Zhang, Y.; Glasfeld, E.; Haney, S.; Stahl, M.; Seehra, J.; Somers, W. S. The bacterial cell-division protein ZipA and its interaction with an FtsZ fragment revealed by X-ray crystallography EMBO J. 2000, 19, 3179-3191
19. Bhat, T. N.; Bentley, G. A.; Boulot, G.; Greene, M. I.; Tello, D.; Dallacqua, W.; Souchon, H.; Schwarz, F. P.; Mariuzza, R. A.; Poljak, R. J. Bound water molecules and conformational stabilization help mediate an antigen-antibody association Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 1089-1093
20. Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.; Baker, N. A. PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res. 2004, 32, W665-W667
21. Bas, D. C.; Rogers, D. M.; Jensen, J. H. Very fast prediction and rationalization of pKa values for protein-ligand complexes Proteins 2008, 73, 765-783
22. a values Proteins 2005, 61, 704-721
23. a predictions J. Chem. Theory Comput. 2011, 7, 525-537
24. Case, D. A.; Darden, T.; Cheatham, T. E., III; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER 9; University of California: San Francisco, 2006.
25. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J. M.; Kollman, P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 2003, 24, 1999-2012
26. Tsui, V.; Case, D. A. Theory and applications of the generalized Born solvation model in macromolecular simulations Biopolymers 2001, 56, 275-291
27. Izaguirre, J. A. Langevin stabilization of molecular dynamics J. Chem. Phys. 2001, 114, 2090-2098
28. Loncharich, R. J.; Brooks, B. R.; Pastor, R. W. Langevin dynamics of peptides-The frictional dependence of isomerization rates of n -acetylalanyl- n -methylamide Biopolymers 1992, 32, 523-535
29. 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
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. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Detailed microscopic study of the full ZipA: FtsZ interface Proteins 2006, 63, 811-821
32. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Unraveling the importance of protein-protein interaction: Application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex J. Phys. Chem. B 2006, 110, 10962-10969
33. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Unravelling hot spots: A comprehensive computational mutagenesis study Theor. Chem. Acc. 2007, 117, 99-113
34. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL-10 Int. J. Quantum Chem. 2007, 107, 299-310
35. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Backbone importance for protein-protein binding J. Chem. Theory Comput. 2007, 3, 885-893
36. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Hot spot occlusion from bulk water: A comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3 J. Phys. Chem. B 2007, 111, 2697-2706
37. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Protein-protein recognition: A computational mutagenesis study of the MDM2-P53 complex Theor. Chem. Acc. 2008, 120, 533-542
38. Chong, L. T.; Duan, Y.; Wang, L.; Massova, I.; Kollman, P. A. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7 Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14330-14335
39. Bradshaw, R. T.; Patel, B. H.; Tate, E. W.; Leatherbarrow, R. J.; Gould, I. R. Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction Protein Eng. Des. Sel. 2011, 24, 197-207
40. Rocchia, W.; Alexov, E.; Honig, B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions J. Phys. Chem. B 2001, 105, 6507-6514
41. Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects J. Comput. Chem. 2002, 23, 128-137
42. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Accuracy of the numerical solution of the Poisson-Boltzmann equation J. Mol. Struc.-Theochem 2005, 729, 11-18
43. Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate calculation of hydration free-energies using macroscopic solvent models J. Phys. Chem. 1994, 98, 1978-1988
44. Connolly, M. L. Analytical molecular surface calculation J. Appl. Crystallogr. 1983, 16, 548-558
45. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics J. Mol. Graphics Modell. 1996, 14, 33-38
46. Ribeiro, J. V.; Cerqueira, N. M. F. S. A.; Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. CompASM: an Amber-VMD alanine scanning mutagenesis plug-in Theor. Chem. Acc. 2012, 131, 1271
47. Case, D. A.; Darden, T.; Cheatham, T. E., III; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R.; 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.
48. Hawkins, R. E.; Russell, S. J.; Baier, M.; Winter, G. The contribution of contact and noncontact residues of antibody in the affinity of binding to antigen-The interaction of mutant D1.3 antibodies with lysozyme J. Mol. Biol. 1993, 234, 958-964
49. DallAcqua, W.; Goldman, E. R.; Eisenstein, E.; Mariuzza, R. A. A mutational analysis of the binding of two different proteins to the same antibody Biochemistry 1996, 35, 9667-9676
50. Schreiber, G.; Fersht, A. R. Interaction of Barnase with its polypeptide inhibitor Barstar studied by protein engineering Biochemistry 1993, 32, 5145-5150
51. Keyt, B. A.; Nguyen, H. V.; Berleau, L. T.; Duarte, C. M.; Park, J.; Chen, H.; Ferrara, N. Identification of vascular endothelial growth factor determinants for binding KDR and FLT-1 receptors-Generation of receptor-selective VEGF variants by site-directed mutagenesis J. Biol. Chem. 1996, 271, 5638-5646
52. Schreiber, G.; Fersht, A. R. Energetics of protein-protein interactions-Analysis of the Barnase-Barstar interface by single mutations and double mutant cycles J. Mol. Biol. 1995, 248, 478-486
53. Perez, M. A.; Sousa, S. F.; Oliveira, E. F.; Fernandes, P. A.; Ramos, M. J. Detection of farnesyltransferase interface hot spots through computational alanine scanning mutagenesis J. Phys. Chem. B 2011, 115, 15339-15354