Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond

Proteins: Structure, Function and Bioinformatics

Volumn 81, Issue 12, 2013, Pages 2229-2236

  Qin, Sanbo ^a   Zhou, Huan Xiang ^a  

^a Florida State University   (United States)

Author keywords

Binding affinity; Interaction energy landscape; Protein association; Protein docking; Transient complex

Indexed keywords

ARTICLE; BINDING AFFINITY; CALCULATION; COMPLEX FORMATION; CRYSTALLOGRAPHY; ENERGY; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STATIC ELECTRICITY;

BINDING AFFINITY; INTERACTION ENERGY LANDSCAPE; PROTEIN ASSOCIATION; PROTEIN DOCKING; TRANSIENT COMPLEX;

DATABASES, PROTEIN; ENERGY METABOLISM; INTERNET; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPS; PROTEINS; SOFTWARE; STATIC ELECTRICITY; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84888299375     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24366     Document Type: Article

References (37)

1. Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002;99:5896-5901.
2. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 2012;490:556-560.
3. Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J. A structure-based benchmark for protein-protein binding affinity. Protein Sci 2011;20:482-491.
4. Moal IH, Agius R, Bates PA. Protein-protein binding affinity prediction on a diverse set of structures. Bioinformatics 2011;27:3002-3009.
5. Malod-Dognin N, Bansal A, Cazals F. Characterizing the morphology of protein binding patches. Proteins 2012;80:2652-2665.
6. Vreven T, Hwang H, Pierce BG, Weng Z. Prediction of protein-protein binding free energies. Protein Sci 2012;21:396-404.
7. Shen Y, Paschalidis I, Vakili P, Vajda S. Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLoS Comput Biol 2008;4:e1000191.
8. Alsallaq R, Zhou HX. Energy landscape and transition state of protein-protein association. Biophys J 2007;92:1486-1502.
9. Alsallaq R, Zhou HX. Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 2008;71:320-335.
10. Qin S, Pang X, Zhou HX. Automated prediction of protein association rate constants. Structure 2011;19:1744-1751.
11. Qin S, Zhou HX. A holistic approach to protein docking. Proteins 2007;69:743-749.
12. Qin S, Zhou HX. Selection of near-native poses in CAPRI rounds 13-19. Proteins 2010;78:3166-3173.
13. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 2001;98:10037-10041.
14. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using Modeller. Curr Protoc Protein Sci 2007;50:2.9.1-2.9.31.
15. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
16. Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
17. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010;31:455-461.
18. Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins 2010;78:3111-3114.
19. Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Aze J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Perez-Cano L, Pons C, Fernandez-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodriguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol 2011;414:289-302.
20. Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JPGLM, Trellet M, Bonvin AMJJ, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Kilambi KP, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ONA, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou H-X, Huang S-Y, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins, doi: 10.1002/prot.24356.
21. Sheinerman FB, Norel R, Honig B. Electrostatic aspects of protein-protein interactions. Curr Opin Struct Biol 2000;10:153-159.
22. Vijayakumar M, Zhou HX. Salt bridges stabilize the folded structure of barnase. J Phys Chem B 2001;105:7334-7340.
23. Dong F, Zhou HX. Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges. Biophys J 2002;83:1341-1347.
24. Dong F, Vijayakumar M, Zhou HX. Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophys J 2003;85:49-60.
25. Dong F, Zhou HX. Electrostatic contribution to the binding stability of protein-protein complexes. Proteins 2006;65:87-102.
26. Qin S, Zhou HX. Do electrostatic interactions destabilize protein-nucleic acid binding? Biopolymers 2007;86:112-118.
27. Pang X, Zhou HX. Poisson-Boltzmann calculations: van der Waals or molecular surface? Commun Comput Phys 2013;13:1-12.
28. Schreiber G, Haran G, Zhou HX. Fundamental aspects of protein-protein association kinetics. Chem Rev 2009;109:839-860.
29. Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, Montelione GT, Spiegel CP, Liu DR, Baker D. A de novo protein binding pair by computational design and directed evolution. Mol Cell 2011;42:250-260.
30. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008;73:705-709.
31. Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, Myers CA, Kamisetty H, Blair P, Wilson IA, Baker D. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol 2012;30:543-548.
32. Wojdyla JA, Fleishman SJ, Baker D, Kleanthous C. Structure of the ultra-high-affinity colicin E2 DNase-Im2 complex. J Mol Biol 2012;417:79-94.
33. Li W, Keeble AH, Giffard C, James R, Moore GR, Kleanthous C. Highly discriminating protein-protein interaction specificities in the context of a conserved binding energy hotspot. J Mol Biol 2004;337:743-759.
34. Bailey LJ, McCoy JG, Phillips GN Jr, Fox BG. Structural consequences of effector protein complex formation in a diiron hydroxylase. Proc Natl Acad Sci USA 2008;105:19194-19198.
35. Leysen S, Vanderkelen L, Weeks SD, Michiels CW, Strelkov SV. Structural basis of bacterial defense against g-type lysozyme-based innate immunity. Cell Mol Life Sci 2012;70:1113-1122.
36. Leysen S, Vanderkelen L, Van Asten K, Vanheuverzwijn S, Theuwis V, Michiels CW, Strelkov SV. Structural characterization of the PliG lysozyme inhibitor family. J Struct Biol 2012;180:235-242.
37. Qin S, Zhou HX. meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics 2007;23:3386-3387.