Abstract
Knowledge about protein interaction sites provides detailed information of protein–protein interactions (PPIs). To date, nearly 20,000 of PPIs from Arabidopsis thaliana have been identified. Nevertheless, the interaction site information has been largely missed by previously published PPI databases. Here, AraPPISite, a database that presents fine-grained interaction details for A. thaliana PPIs is established. First, the experimentally determined 3D structures of 27 A. thaliana PPIs are collected from the Protein Data Bank database and the predicted 3D structures of 3023 A. thaliana PPIs are modeled by using two well-established template-based docking methods. For each experimental/predicted complex structure, AraPPISite not only provides an interactive user interface for browsing interaction sites, but also lists detailed evolutionary and physicochemical properties of these sites. Second, AraPPISite assigns domain–domain interactions or domain–motif interactions to 4286 PPIs whose 3D structures cannot be modeled. In this case, users can easily query protein interaction regions at the sequence level. AraPPISite is a free and user-friendly database, which does not require user registration or any configuration on local machines. We anticipate AraPPISite can serve as a helpful database resource for the users with less experience in structural biology or protein bioinformatics to probe the details of PPIs, and thus accelerate the studies of plant genetics and functional genomics. AraPPISite is available at http://systbio.cau.edu.cn/arappisite/index.html.
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References
Altenhoff AM et al (2015) The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res 43:D240–D249. doi:10.1093/nar/gku1158
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. doi:10.1016/S0022-2836(05)80360-2
Arabidopsis Interactome Mapping Consortium (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333:601–607. doi:10.1126/science.1203877
Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A (2014) PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes. Nucleic Acids Res 42:W285–W289. doi:10.1093/nar/gku397
Braun P, Aubourg S, Van Leene J, De Jaeger G, Lurin C (2013) Plant protein interactomes. Annu Rev Plant Biol 64:161–187. doi:10.1146/annurev-arplant-050312-120140
Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES (2004) Are protein–protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13:190–202. doi:10.1110/ps.03323604
Chatr-Aryamontri A et al (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res 41:D816–D823. doi:10.1093/nar/gks1158
Dinkel H et al (2014) The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res 42:D259–D266. doi:10.1093/nar/gkt1047
Finn RD et al (2014a) Pfam: the protein families database. Nucleic Acids Res 42:D222–D230. doi:10.1093/nar/gkt1223
Finn RD, Miller BL, Clements J, Bateman A (2014b) iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Res 42:D364–D373. doi:10.1093/nar/gkt1210
Fukuhara N, Kawabata T (2008) HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Nucleic Acids Res 36:W185–W189. doi:10.1093/nar/gkn218
Gallivan JP, Dougherty DA (1999) Cation–pi interactions in structural biology. Proc Natl Acad Sci USA 96:9459–9464
Gu H, Zhu P, Jiao Y, Meng Y, Chen M (2011) PRIN: a predicted rice interactome network. BMC Bioinform 12:161. doi:10.1186/1471-2105-12-161
Hashimoto K et al (2012) Phosphorylation of calcineurin B-like (CBL) calcium sensor proteins by their CBL-interacting protein kinases (CIPKs) is required for full activity of CBL-CIPK complexes toward their target proteins. J Biol Chem 287:7956–7968. doi:10.1074/jbc.M111.279331
He F, Zhou Y, Zhang Z (2010) Deciphering the Arabidopsis floral transition process by integrating a protein–protein interaction network and gene expression data. Plant Physiol 153:1492–1505. doi:10.1104/pp.110.153650
Higurashi M, Ishida T, Kinoshita K (2009) PiSite: a database of protein interaction sites using multiple binding states in the PDB. Nucleic Acids Res 37:D360–D364. doi:10.1093/nar/gkn659
Kortemme T, Kim DE, Baker D (2004) Computational alanine scanning of protein–protein interfaces. Sci STKE 2004:pl2. doi:10.1126/stke.2192004pl2
Krissinel E (2010) Crystal contacts as nature’s docking solutions. J Comput Chem 31:133–143. doi:10.1002/jcc.21303
Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774–797. doi:10.1016/j.jmb.2007.05.022
Kundrotas PJ, Vakser IA (2010) Accuracy of protein–protein binding sites in high-throughput template-based modeling. PLoS Comput Biol 6:e1000727. doi:10.1371/journal.pcbi.1000727
Kundrotas PJ, Zhu Z, Janin J, Vakser IA (2012) Templates are available to model nearly all complexes of structurally characterized proteins. Proc Natl Acad Sci USA 109:9438–9441. doi:10.1073/pnas.1200678109
Lamesch P et al (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210. doi:10.1093/nar/gkr1090
Li H, Zhou Y, Zhang Z (2015) Competition–cooperation relationship networks characterize the competition and cooperation between proteins. Sci Rep 5:11619. doi:10.1038/srep11619
Lin M, Zhou X, Shen X, Mao C, Chen X (2011) The predicted Arabidopsis interactome resource and network topology-based systems biology analyses. Plant Cell 23:911–922. doi:10.1105/tpc.110.082529
Mendez R, Leplae R, De Maria L, Wodak SJ (2003) Assessment of blind predictions of protein–protein interactions: current status of docking methods. Proteins 52:51–67. doi:10.1002/prot.10393
Morrow JK, Zhang S (2012) Computational prediction of protein hot spot residues. Curr Pharm Des 18:1255–1265
Mosca R, Ceol A, Aloy P (2013) Interactome3D: adding structural details to protein networks. Nat Methods 10:47–53. doi:10.1038/nmeth.2289
Mosca R, Ceol A, Stein A, Olivella R, Aloy P (2014) 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res 42:D374–D379. doi:10.1093/nar/gkt887
Mukherjee S, Zhang Y (2009) MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Res 37:e83. doi:10.1093/nar/gkp318
Orchard S et al (2014) The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42:D358–D363. doi:10.1093/nar/gkt1115
Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18(Suppl 1):S71–S77
Rego N, Koes D (2015) 3Dmol.js: molecular visualization with WebGL. Bioinformatics 31:1322–1324. doi:10.1093/bioinformatics/btu829
Rose PW et al (2015) The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res 43:D345–D356. doi:10.1093/nar/gku1214
Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815. doi:10.1006/jmbi.1993.1626
Sievers F et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. doi:10.1038/msb.2011.75
Sinha R, Kundrotas PJ, Vakser IA (2010) Docking by structural similarity at protein–protein interfaces. Proteins 78:3235–3241. doi:10.1002/prot.22812
Tuncbag N, Gursoy A, Nussinov R, Keskin O (2011) Predicting protein–protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc 6:1341–1354. doi:10.1038/nprot.2011.367
UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res 43:D204–D212. doi:10.1093/nar/gku989
Westermarck J, Ivaska J, Corthals GL (2013) Identification of protein interactions involved in cellular signaling. Mol Cell Proteomics 12:1752–1763. doi:10.1074/mcp.R113.027771
Yan T et al (2005) PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res 33:W262–W266. doi:10.1093/nar/gki368
Yao Q et al (2014) P(3)DB 3.0: From plant phosphorylation sites to protein networks. Nucleic Acids Res 42:D1206–D1213. doi:10.1093/nar/gkt1135
Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33:2302–2309. doi:10.1093/nar/gki524
Acknowledgments
We are also grateful to Xin Yi from Prof. Zhen Su’s Lab and Dr. Xiaobao Dong for valuable comments on the construction of the database.
Funding
This work was supported by grants from the National Natural Science Foundation of China (31471249 and 31271414).
Author contributions
H.L. performed the analyses and drafted the manuscript. S.Y. constructed the database. Y.Z. and Z.Z. supervised the study. C.W., Y.Z. and Z.Z. revised the manuscript. H.L., C.W., Y.Z. and Z.Z. provided suggestions for the database construction.
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Hong Li and Shiping Yang have contributed equally to the work.
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Li, H., Yang, S., Wang, C. et al. AraPPISite: a database of fine-grained protein–protein interaction site annotations for Arabidopsis thaliana . Plant Mol Biol 92, 105–116 (2016). https://doi.org/10.1007/s11103-016-0498-z
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DOI: https://doi.org/10.1007/s11103-016-0498-z