Recent advances in proteinprotein interaction prediction: Experimental and computational methods

Expert Opinion on Drug Discovery

Volumn 6, Issue 9, 2011, Pages 921-935

  Jessulat, Matthew ^a   Pitre, Sylvain ^a   Gui, Yuan ^a   Hooshyar, Mohsen ^a   Omidi, Katayoun ^a   Samanfar, Bahram ^a   Tan, Le Hoa ^a   Alamgir, Md ^a   Green, James ^a   Dehne, Frank ^a   Golshani, Ashkan ^a  

^a CARLETON UNIVERSITY   (Canada)

Author keywords

Protein interaction prediction engine; Proteinprotein interactions; Tandem affinity purification; Yeast two hybrid

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; GENE LOCATION; GENOME; HIGH THROUGHPUT SCREENING; HUMAN; NONHUMAN; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; REVIEW; TWO HYBRID SYSTEM;

EID: 80052054208     PISSN: 17460441     EISSN: 1746045X     Source Type: Journal    
DOI: 10.1517/17460441.2011.603722     Document Type: Review

References (123)

1. Hu L, Huang T, Shi X, et al. Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties. PLoS One 2011;6:e14556
2. Sprinzak E, Sattah S, Margalit H. How reliable are protein-protein interaction data? J Mol Biol 2003;327:919-23 (Pubitemid 36363701)
3. Hazbun TR, Fields S. Networking proteins in yeast. Proc Natl Acad Sci USA 2001;98:4277-8 (Pubitemid 32294963)
4. Pitre S, Alamgir M, Green JR, et al. Computational methods for predicting protein-protein interactions. Adv Biochem Eng Biotechnol 2008;110:247-67
5. Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 1989;340:245-6 (Pubitemid 19171591)
6. Suter B, Kittanakom S, Stagljar I. Two-hybrid technologies in proteomics research. Curr Opin Biotechnol 2008;19:316-23
7. Stephens DJ, Banting G. The use of yeast two-hybrid screens in studies of protein:protein interactions involved in trafficking. Traffic 2000;1:763-8
8. Semple JI, Sanderson CM, Campbell RD. The jury is still out on "guilt by association" trials. Brief Funct Genomic Proteomic 2002;1:40-52
9. Lievens S, Lemmens I, Tavernier J. Mammalian two-hybrids come of age. Trends Biochem Sci 2009;34:579-88
10. Kittanakom S, Chuk M, Wong V, et al. Analysis of membrane protein complexes using the Split-Ubiquitin membrane yeast two-hybrid (MYTH) system. Methods Mol Biol 2009;48:247-71
11. Petschnigg J, Snider J, Stagljar I. Interactive proteomics research technologies: recent applications and advances. Curr Opin Biotechnol 2010;22:1-9
12. Chen J, Zhou J, Bae W, et al. A yEGFP-based reporter system for high-throughput yeast two-hybrid assay by flow cytometry. Cytometry 2008;73:312-20 (Pubitemid 351522114)
13. Cormack RS, Hahlbrock K, Somssich IE. Isolation of putative plant transcriptional coactivators using a modified two-hybrid system incorporating a GFP reporter gene. Plant J 1998;14:685-92
14. Chen J, Zhou J, Sanders CK, et al. A surface display yeast two-hybrid screening system for high-throughput protein interactome mapping. Anal Biochem 2009;390:29-37
15. de Almeida RA, Burgess D, Shema R, et al. Saccharomyces cerevisiae cell-based quantitative beta-galactosidase assay compatible with robotic handling and high-throughput screening. Yeast 2008;25:71-6 (Pubitemid 351181640)
16. Hannah R, Stroke I, Betz N. beta-Glo assay system: a luminescent beta-galactosidase assay for multiple cell types and media. Promega Cell Notes 2003;6:16-18
17. Kamiya T, Ojimab T, Sugimotoa K, et al. Quantitative Y2H screening: Cloning and signal peptide engineering of a fungal secretory LacA gene and its application to yeast two-hybrid system as a quantitative reporter. J Biotechnol 2010;146:151-9
18. Mockli N, Auerbach D. Quantitative beta-galactosidase assay suitable for high-throughput applications in the yeast two-hybrid system. Biotechniques 2004;36:872-6 (Pubitemid 38620207)
19. Sekar RB, Periasamy A. Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations. J Cell Biol 2003;160:629-33 (Pubitemid 36298259)
20. Rigaut G, Shevchenko A, Rutz B, et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 1999;17:1030-2 (Pubitemid 29474865)
21. Puig O, Caspary F, Rigaut G, et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 2001;24:218-29 (Pubitemid 32846428)
22. Gully D, Moinier D, Loiseau L, et al. New partners of acyl carrier protein detected in Escherichia coli by tandem affinity purification. FEBS Lett 2003;548:90-6 (Pubitemid 37281256)
23. Rohila JS, Chen M, Cerny R, et al. Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J 2004;38:172-81 (Pubitemid 38448454)
24. Knuesel M, Wan Y, Xiao Z, et al. Identification of novel protein-protein interactions using a versatile mammalian tandem affinity purification expression system. Mol Cell Proteomics 2003;2:1225-33
25. Forler D, Kocher T, Rode M, et al. An efficient protein complex purification method for functional proteomics in higher eukaryotes. Nat Biotechnol 2003;21:89-92 (Pubitemid 36055834)
26. Koch KV, Reinders Y, Ho TH,et al. Identification and isolation of Dictyostelium microtubule-associated protein interactors by tandem affinity purification. Eur J Cell Biol 2006;85:1079-90 (Pubitemid 44317607)
27. Meima ME, Weening KE, Schaap P. Vectors for expression of proteins with single or combinatorial fluorescent protein and tandem affinity purification tags in Dictyostelium. Protein Expr Purif 2007;53:283-8 (Pubitemid 46453209)
28. Butland G, Peregrin-Alvarez J, Li J, et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 2005;433:531-7 (Pubitemid 40204311)
29. Resa-Infante P, Jorba N, Zamarren N, et al. The Host-dependent interaction of a-Importins with influenza PB2 polymerase subunit is required for virus RNA replication. PLoS ONE 2008;3:e3904
30. Nassa G, Tarallo R, Ambrosino C, et al. A large set of estrogen receptor beta-interacting proteins identified by tandem affinity purification in hormone-responsive human breast cancer cell nuclei. Proteomics 2011;11:159-65
31. Rubio V, Shen Y, Saijo Y, et al. An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation. Plant J 2005;41:767-78 (Pubitemid 40336007)
32. Gloeckner CJ, Boldt K, Schumacher A, et al. Tandem affinity purification of protein complexes from mammalian cells by the strep/FLAG (SF)-TAP tag. Methods Mol Biol 2009;564:359-70
33. Gloeckner CJ, Boldt K, Schumacher S, et al. A novel tandem affinity purification strategy for the efficient isolation and characterisation of native protein complexes. Proteomics 2007;7:4228-34 (Pubitemid 350250468)
34. Lehmann R, Meyer J, Schuemann M, et al. A novel S3S-TAP-tag for the isolation of T-cell interaction partners of adhesion and degranulation promoting adaptor protein. Proteomics 2009;9:5288-95
35. Guerrero C, Tagwerker C, Kaiser P, et al. An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol Cell Proteomics 2006;5:366-78 (Pubitemid 43329314)
36. Burckstummer T, Bennett KL, Preradovic A, et al. An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells. Nat Methods 2006;3:1013-19 (Pubitemid 44782701)
37. Honey S, Schneider BL, Schieltz DM, et al. A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin-CDK complex. Nucleic Acids Res 2001;29:24-32
38. Kobayashi T, Morone N, Kashiyama T, et al. Engineering a novel multifunctional green fluorescent protein tag for a wide variety of protein research. PLoS ONE 2008;3:e3822
39. Tomizaki KY, Usui K, Mihara H. Protein-detecting microarrays: current accomplishments and requirements. ChemBioChem 2005;6:782-99 (Pubitemid 40873732)
40. Wolf-Yadlin A, Sevecka M, MacBeath G. Dissecting protein function and signaling using protein microarrays. Curr Opin Chem Biol 2009;13:398-405
41. Weinrich D, Jonkheijm P, Niemeyer CM, et al. Applications of protein biochips in biomedical and biotechnological research. Angew Chem Int Ed Engl 2009;48:7744-51
42. Berrade L, Garcia AE, Camarer JA. Protein microarrays: novel developments and applications. Pharm Res 2010;28:1480-99
43. Chepelev N, Chepelev L, Alamgir MD, et al. Large-scale protein-protein interaction detection approaches: past, present and future. Biotechnol Biotechnol Eq 2008;22:513-29 (Pubitemid 351422047)
44. Camarero JA. Recent developments in the site-specific immobilization of proteins onto solid supports. Biopolymers 2008;90:450-8
45. Mueller C, Liotta LA, Espina V. Reverse phase protein microarrays advance to use in clinical trials. Mol Oncol 2010;4:461-81
46. Hu S, Xie Z, Qian J, et al. Functional protein microarray technology. Wiley Interdiscip Rev Syst Biol Med 2010;3:225-68
47. Zhu H, Bilgin M, Bangham R, et al. Global analysis of protein activities using proteome chips. Science 2001;293:2101-5 (Pubitemid 32848060)
48. Popescu SC, Popescu GV, Bachan S, et al. MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev 2009;23:80-92
49. Merbl Y, Kirschner MW. Protein microarrays for genome-wide posttranslational modification analysis. Wiley Interdiscip Rev Syst Biol Med 2010;3:347-56
50. Miller JC, Zhou H, Kwekel J, et al. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 2003;3:56-63 (Pubitemid 36151068)
51. Kim DH, Bae J, Lee JW, et al. Proteomic analysis of breast cancer tissue reveals upregulation of actin-remodeling proteins and its relevance to cancer invasiveness. Proteomics Clin Appl 2009;3:30-40
52. Pierotti MA, Negri T, Tamborini E, et al. Targeted therapies: the rare cancer paradigm. Mol Oncol 2010;4:19-37
53. Skrabanek L, Saini HK, Bader GD, et al. Computational prediction of protein-protein interactions. Mol Biotechnol 2008;38:1-17 (Pubitemid 351378094)
54. Guarracino MR, Nebbia A, Manna V, et al. Efficient prediction of protein-protein interactions using sequence information. Complex Int Software Intensive Syst 2010;677-82
55. Szilagyi A, Grimm V, Arakaki AK, et al. Prediction of physical protein-protein interactions. Phys Biol 2005;2:S1-16
56. Gomez SM, Nobel WS, Rzhetsky A. Learning to predict protein-protein interactions from protein sequences. Bioinformatics 2003;19:1875-81 (Pubitemid 37322330)
57. Gavin AC, Aloy P, Grandi P, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006;440:631-6
58. Krogan NJ, Cagney G, Yu H, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006;440:637-43
59. Ito T, Chiba T, Ozawa R, et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001;98:4569-74 (Pubitemid 32295017)
60. Uetz P, Giot L, Cagney G, et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000;403:623-7 (Pubitemid 30103994)
61. Guo Y, Yu L, Wen Z, et al. Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucleic Acids Res 2008;9:3025-30 (Pubitemid 351737194)
62. Valencia A, Pazos F. Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 2002;12:368-73 (Pubitemid 34804620)
63. Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-91 (Pubitemid 37038881)
64. Chou KC, Shen HB. Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS One 2010;5:e11335
65. Chou KC, Shen HB. Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat Protocols 2008;3:153-62
66. Fraser HB. Evolutionary rate in the protein. Science 2002;296:750-2
67. Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res 2000;28:235-42 (Pubitemid 30047768)
68. Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002;99:5896-901 (Pubitemid 34493236)
69. Ma B, Elkayam T, Wolfson H, et al. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 2003;100:5772-7 (Pubitemid 36576883)
70. Kundrotas PJ, Vakser IA. Accuracy of protein-protein binding sites in high-throughput template-based modeling. PLoS Comput Biol 2010;6:e1000727
71. Sinha R, Kondrotas PJ, Vakser IA. Docking by structural similarity at protein-protein interfaces. Proteins 2010;78:3235-41
72. Aloy P, Russell RB. InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 2003;19:161-2 (Pubitemid 36150198)
73. Ogmen U, Keskin O, Aytuna AS, et al. PRISM: protein interactions by structural mapping. Nucleic Acids Res 2005;33:W331-6 (Pubitemid 44529938)
74. Lu L, Lu H, Skolnick J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 2002;49:350-64 (Pubitemid 35231471)
75. Moult J, Fidelis K, Kryshtafovych A, et al. Critical assessment of methods of protein structure prediction-round VIII. Proteins 2009;77(S9):1-4
76. Wodak SJ, Mendez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14:242-9 (Pubitemid 38490791)
77. Qi Y, Bar-Joseph Z, Klein-Seetharaman J. Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 2006;63:490-500
78. Licamele K, Getoor L. Predicting protein-protein interactions using relational features. Proc of ICML Workshop on Statistical Network Analysis; 2006. p. 1-7
79. Paradesi MSR, Caragea D, Hsu WH. Structural Prediction of Protein-Protein Interactions in Saccharomyces cerevisiae. Proc of IEEE 7th International Symposium on BioInformatics and BioEngineering; 2007;2:1270-4
80. Liu G, Li J, Wong L. Assessing and predicting protein interactions using both local and global network topological metrics. Genome Inform 2008;21:138-49
81. Mohamed TP, Carbonell JG, Ganapathiraju MK. Active learning for human protein-protein interaction prediction. BMC Bioinformatics 2010;11:S57
82. Yu CY, Chou LC, Chang DT. Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. BMC Bioinformatics 2010;11:167
83. Sprinzak E, Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 2001;311:681-92 (Pubitemid 32803728)
84. Martin S, Roe D, Faulon JL. Predicting protein-protein interactions using signature products. Bioinformatics 2005;21:218-26 (Pubitemid 40202023)
85. Zaki N, Lazarova-Molnar S, El-Hajj W, et al. Protein-protein interaction based on pairwise similarity. BMC Bioinformatics 2009;10:150
86. Shen JW, Zhang J, Luo XM, et al. Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci USA 2007;104:4337-41 (Pubitemid 47186227)
87. Guo Y, Li M, Pu X, et al. PRED-PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment. BMC Res Notes 2010;3:145
88. Najafabadi HS, Salavati R. Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol 2008;9:R87
89. Wang Y, Wang J, Yang Z, et al. Sequence-based potein-protein interaction prediction via support vector machine. J Syst Sci Complex 2010;23:1012-23
90. Roy S, Martinez D, Platero H, et al. Exploiting amino acid composition for predicting protein-protein interactions. PLoS One 2009;4:e7813
91. Nanni L, Lumini A. An ensemble of K-local hyperplanes for predicting protein-protein interactions. Bioinformatics 2006;22:1207-10 (Pubitemid 43779012)
92. Pitre S, Dehne F, Chan A, et al. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics 2006;7:365
93. Pitre S, North C, Alamgir M, et al. Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. Nucleic Acids Res 2008;36:4286-94
94. Pan XY, Zhang YN, Shen HB. Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features. J Proteome Res 2010;9:4992-5001
95. Xia JF, Zhao XM, Huang DS. Predicting protein-protein interactions from protein sequences using meta predictor. Amino Acids 2010;39:1595-9
96. Park Y. Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences. BMC Bioinformatics 2009;10:419
97. Marcotte EM, Pellegrini M, Ng HL, et al. Detecting protein function and protein-protein interactions from genome sequences. Science 1999;285:751-3
98. Bock JR, Gough DA. Predicting protein-protein interactions from primary structure. Bioinformatics 2001;17:455-60 (Pubitemid 32440306)
99. Shi MG, Xia JF, Li XL, et al. Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset. Amino Acids 2010;38:891-9
100. Chang DT-H, Syu Y-T, Lin P-C. Predicting the protein-protein interactions using primary structures with predicted protein surface. BMC Bioinformatics 2010;11(S1):S3
101. Chou KC, Cai YD. Predicting protein-protein interactions from sequences in a hybridization space. J Proteome Res 2006;5:316-22
102. Chou KC. Prediction of protein cellular attributes using pseudo amino acid composition. Proteins 2001;43:246-55
103. Browne F, Zheng H, Wang HY, et al. From experimental approaches to computational techniques: a review on the prediction of protein-protein interactions. Adv Artif Int 2010;924529(2010):1-15
104. Yu J, Guo M, Needham CJ, et al. Simple sequence-based kernels do not predict protein-protein interactions. Bioinformatics 2010;26:2610-14
105. Chou KC, Zhang CT. Review: prediction of protein structural classes. Crit Rev Biochem Mol Biol 1995;30:275-349
106. Chou KC, Shen HB. Cell-PLoc 2.0: An improved package of web-servers for predicting subcellular localization of proteins in various organisms. Nat Sci 2010;2:1090-103
107. Chou KC. Some remarks on protein attribute prediction and pseudo amino acid composition (50th Anniversary Year Review). J Theor Biol 2011;273:236-47
108. Lin H. The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition. J Theor Biol 2008;252:350-6
109. Zeng YH, Guo YZ, Xiao RQ, et al. Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. J Theor Biol 2009;259:366-72
110. Zhou XB, Chen C, Li ZC, et al. Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes. J Theor Biol 2007;248:546-51 (Pubitemid 47368372)
111. Chou KC, Shen HB. Review: recent progresses in protein subcellular location prediction. Anal Biochem 2007;370:1-16
112. Hayat M, Khan A. Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition. J Theor Biol 2011;271:10-17
113. Kandaswamy KK, Chou KC, Martinetz T, et al. AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties. J Theor Biol 2011;270:56-62
114. Lin H, Ding H. Predicting ion channels and their types by the dipeptide mode of pseudo amino acid composition. J Theor Biol 2011;269:64-9
115. Chen C, Chen L, Zou X, et al. Prediction of protein secondary structure content by using the concept of Chou's pseudo amino acid composition and support vector machine. Protein Pept Lett 2009;16:27-31
116. Ding H, Luo L, Lin H. Prediction of cell wall lytic enzymes using Chou's amphiphilic pseudo amino acid composition. Protein Pept Lett 2009;16:351-5
117. Jiang X, Wei R, Zhang TL, et al. Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy. Protein Pept Lett 2008;15:392-6 (Pubitemid 351679342)
118. Li FM, Li QZ. Predicting protein subcellular location using Chou's pseudo amino acid composition and improved hybrid approach. Protein Pept Lett 2008;15:612-16
119. Lin H, Ding H, Guo FB, et al. Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition. Protein Pept Lett 2008;15:739-44
120. Mohabatkar H. Prediction of cyclin proteins using Chou's pseudo amino acid composition. Protein Pept Lett 2010;17:1207-14
121. Xiao X, Wang P, Chou KC. GPCR-2L: Predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions. Mol Biosyst 2011;7:911-19
122. Neduva V, Linding R, Su-Angrand I, et al. Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 2005;3:e405
123. Chou KC, Shen HB. Review: recent advances in developing web-servers for predicting protein attributes. Nat Sci 2009;2:63-92