Structure-based prediction of protein-peptide specificity in rosetta

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 16, 2010, Pages 3437-3449

  King, Christopher A ^a   Bradley, Philip ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Linear binding motifs; Molecular modeling; Peptide design; Peptide recognition domains; Peptide specificity; Rosetta PepSpec

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; MOLECULAR DOCKING; MOLECULAR MODEL; MOLECULAR RECOGNITION; PEPTIDE ANALYSIS; POINT MUTATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, MOLECULAR; PEPTIDES; PLIABILITY; POSITION-SPECIFIC SCORING MATRICES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN; SUBSTRATE SPECIFICITY;

EID: 78349258533     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22851     Document Type: Article

References (42)

1. Donnes P, Elofsson A. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 2002; 3: 25.
2. Liu W, Meng XS, Xu QQ, Flower DR, Li TB. Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. BMC Bioinformatics 2006; 7: 182.
3. Salomon J, Flower DR. Predicting class II MHC-peptide binding: a kernel based approach using similarity scores. BMC Bioinformatics 2006; 7:501.
4. Chen JR, Chang BH, Allen JE, Stiffler MA, MacBeath G. Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotechnol 2008; 26: 1041-1045.
5. Gan WX, Roux B. Binding specificity of SH2 domains: insight from free energy simulations. Protein-Struct Funct Bioinformatics 2009; 74: 996-1007.
6. Rognan D, Scapozza L, Folkers G, Daser A. Molecular-dynamics simulation of Mhc-peptide complexes as a tool for predicting potential T-cell epitopes. Biochemistry 1994; 33: 11476-11485.
7. Suenaga A, Hatakeyama M, Ichikawa M, Yu X, Futatsugi N, Narumi T, Fukui K, Terada T, Taiji M, Shirouzu M, Yokoyama S, Konagaya A. Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides. Biochemistry 2003; 42: 5195-5200.
8. Zhang J, King CA, Dalby K, Ren P. Conformational preference of ChaK1 binding peptides: a molecular dynamics study. PMC Biophys 2010; 3: 2.
9. Brinkworth RI, Breinl RA, Kobe B. Structural basis and prediction of substrate specificity in protein serine/threonine kinases. Proc Natl Acad Sci USA 2003; 100: 74-79.
10. Hou T, Xu Z, Zhang W, McLaughlin WA, Case DA, Xu Y, Wang W. Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains. Mol Cell Proteomics 2009; 8: 639-649.
11. Sanchez IE, Beltrao P, Stricher F, Schymkowitz J, Ferkinghoff-Borg J, Rousseau F, Serrano L. Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PLoS Comput Biol 2008; 4: e1000052.
12. Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D. Structure prediction for CASP8 with all-atom refinement using Rosetta. Protein-Struct Funct Bioinformatics 2009; 77(Suppl 9): 89-99.
13. Sood VD, Baker D. Recapitulation and design of protein binding peptide structures and sequences. J Mol Biol 2006; 357: 917-927.
14. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-242.
15. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947-2948.
16. Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003; 374: 461-491.
17. Smith CA, Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 2008; 380: 742-756.
18. DeLano WL. The PyMOL molecular graphics system, Available at: 2002. Accessed September 13, 2009.
19. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268: 209-225.
20. Dunbrack RL, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997; 6: 1661-1681.
21. Habib N, Kaplan T, Margalit H, Friedman N. A novel Bayesian DNA motif comparison method for clustering and retrieval. PLoS Comput Biol 2008; 4: e1000010.
22. London N, Movshovitz-Attias D, Schueler-Furman O. The structural basis of peptide-protein binding strategies. Structure 2010; 18: 188-199.
23. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004; 14: 1188-1190.
24. Benos PV, Bulyk ML, Stormo GD. Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 2002; 30: 4442-4451.
25. Yang L, Nolan JP. High-throughput screening and characterization of clones selected from phage display libraries. Cytometry A 2007; 71A: 625-631.
26. Obenauer JC, Cantley LC, Yaffe MB. Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 2003; 31: 3635-3641.
27. Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, Boone C, Bader GD, Sidhu SS. A specificity map for the PDZ domain family. PLoS Biol 2008; 6: e239.
28. Stormo GD, Fields DS. Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci 1998; 23: 109-113.
29. Huse M, Kuriyan J. The conformational plasticity of protein kinases. Cell 2002; 109: 275-282.
30. Gong W, Zhou D, Ren Y, Wang Y, Zuo Z, Shen Y, Xiao F, Zhu Q, Hong A, Zhou X, Gao X, Li T. PepCyber:P PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains. Nucleic Acids Res 2008; 36(Database issue): D679-D683.
31. Tatusova TA, Madden TL. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999; 174: 247-250.
32. Yongkiettrakul S, Byeon IJ, Tsai MD. The ligand specificity of yeast Rad53 FHA domains at the +3 position is determined by nonconserved residues. Biochemistry 2004; 43: 3862-3869.
33. Yuan C, Yongkiettrakul S, Byeon IJ, Zhou S, Tsai MD. Solution structures of two FHA1-phosphothreonine peptide complexes provide insight into the structural basis of the ligand specificity of FHA1 from yeast Rad53. J Mol Biol 2001; 314: 563-575.
34. Petsalaki E, Stark A, Garcia-Urdiales E, Russell RB. Accurate prediction of peptide binding sites on protein surfaces. PLoS Comput Biol 2009; 5: e1000335.
35. Raveh B, London N, Schueler-Furman O. Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins: Struct Funct Bioinformatics 2010; 9999:2029-2040.
36. Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 2009; 25: 621-627.
37. Humphris EL, Kortemme T. Design of multi-specificity in protein interfaces. PLoS Comput Biol 2007; 3: e164.
38. Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H. PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics 2005; 21: 827-828.
39. Diella F, Gould CM, Chica C, Via A, Gibson TJ. Phospho.ELM: a database of phosphorylation sites-update 2008. Nucleic Acids Res 2008; 36(Database issue): D240-D244.
40. Khati M, Pillay TS. Phosphotyrosine phosphoepitopes can be rapidly analyzed by coexpression of a tyrosine kinase in bacteria with a T7 bacteriophage display library. Anal Biochem 2004; 325: 164-167.
41. Schutkowski M, Reimer U, Panse S, Dong L, Lizcano JM, Alessi DR, Schneider-Mergener J. High-content peptide microarrays for deciphering kinase specificity and biology. Angew Chem Int Ed Engl 2004; 43: 2671-2674.
42. Sparks AB, Rider JE, Hoffman NG, Fowlkes DM, Quillam LA, Kay BK. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2. Proc Natl Acad Sci USA 1996; 93: 1540-1544.