ScaPD: a database for human scaffold proteins
© The Author(s). 2017
Published: 3 October 2017
Scaffold proteins play a critical role in an increasing number of biological signaling processes, including simple tethering mechanism, regulating selectivity in pathways, shaping cellular behaviors. While many databases document the signaling pathways, few databases are devoted to the scaffold proteins that medicate signal transduction.
Here, we have developed a user-friendly database, ScaPD, to describe computationally predicted, experimentally validated scaffold proteins and associated signaling pathways. It currently contains 273 scaffold proteins and 1118 associated signaling pathways. The database allows users to search, navigate and download the scaffold protein-mediated signaling networks.
Manually curated and predicted scaffold protein data will be a foundation for further investigation of the scaffold protein in the signal transduction. With maintained up-to-date data, ScaPD (http://bioinfo.wilmer.jhu.edu/ScaPD) will be a valuable resource for understanding how individual signaling pathways are regulated.
About 10% of proteins expressed in human cells are involved in the signal transduction . How can signaling proteins interact with the correct partners and avoid wrong proteins? One principle is that cells achieve well in the signal transduction networks by tethering subset proteins in space and time. More than 20 years ago, the first set of scaffold proteins were discovered, which assemble components of diverse pathways at the plasma membrane or subcellular compartments [2–6]. For example, scaffold protein Ste5 tethers multiple protein kinases in the MAP kinase cascade, such as Ste11, Ste7 and Fus3. The spatial organization achieves high efficacy information transfer on cellular information flow.
The scaffold proteins link multiple signaling proteins together to facilitate signal transduction [6, 7]. These proteins mediate a linear pathway among many partner proteins, and mediate pathway branching to multiple outputs as well [8, 9]. One central role of scaffold proteins is to coordinate feedback loops in signaling pathways, and thus to regulate the signaling response [10, 11]. They enhance signaling specificity or increase the signaling efficiency by increasing the local concentration of signaling components. Thus, the scaffold proteins play a crucial role in the signal transduction.
Although various signaling pathways are the central topics in many biological fields, researchers pay much less attention on the scaffold proteins. One possible reason is that identification of scaffold proteins is challenging, which requires multiple steps using traditional biochemical techniques, including selection of a candidate scaffold protein, testing the protein-protein interaction and assessment of the signaling pathway. The systematic study of scaffold proteins can greatly enhance the understanding of the protein regulation that occurs in eukaryotic organisms [12–14].
While many databases were constructed to collect the information of signaling pathways (e.g. KEGG, phosphonetworks, phosphoGRID) [15–17], these databases often contain little information of the scaffold proteins. We believe that a central portal specifically designed for scaffold proteins will provide a useful resource to the research community. To facilitate usage of the information of scaffold proteins, we created a scaffold protein database, ScaPD, an integrated information system for the storage and visualization of human scaffold proteins as well as the corresponding signaling pathway data.
The content of the database has two major sources. First, we performed a manual curation of the literatures to collect experimentally determined scaffold proteins. We first searched papers containing the keyword “scaffold protein” through Google Scholar and PubMed. We then manually examined the papers and collected the known scaffold proteins. In total, we collected 82 scaffold proteins. Second, we collected predicted scaffold proteins generated from a recent project, in which we developed a bioinformatics approach to predict scaffold proteins . In brief, we constructed a composite network, including 55,048 protein-protein interactions and 1103 kinase-substrate relationship in human. We then identified the proteins that interact with multiple components in a signaling pathway. Based on our analysis, 212 proteins were predicted as scaffold proteins with statistical significance.
Discussion and Conclusion
Recent studies have revealed that the scaffold proteins play a versatile and important role in many signaling pathways. However, only a few scaffold proteins have been extensively characterized. Furthermore, no database has been developed for analyzing scaffold proteins, although many databases exist for signaling pathways. To our knowledge, ScaPD is the most comprehensive database focused on the scaffold proteins and associated signaling pathways. It holds a significant number of predicted scaffold proteins and their associated signaling pathways, which were previously completely uncharacterized. In addition, the database is more than a list of scaffold proteins. The users can search for scaffold proteins or singlaing pathways and their associated scaffold proteins. We will continuously update the scaffold proteins as new data are brought forth. Therefore, the ScaPD should provide additional information on the function of the scaffold proteins and pathways in signal transduction.
This work was funded by: EY024580, GM111514 (National Institutes of Health) to JQ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The article’s publication costs were supported by these grants.
Availability of data and materials
About this supplement
This article has been published as part of BMC Bioinformatics Volume 18 Supplement 11, 2017: Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: bioinformatics. The full contents of the supplement are available online at <https://bmcbioinformatics.biomedcentral.com/articles/supplements/volume-18-supplement-11 > .
Conceived and designed the experiments: XH JQ. Performed the experiments: XH. Analyzed the data: XH JW JW SL JH HZ JQ. Wrote the paper: XH JQ. All authors read and approved the manuscript.
Ethics approval and consent to participate
No ethics approval was required for the study.
Consent for publication
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Milo R, Jorgensen P, Moran U, Weber G, Springer M. BioNumbers--the database of key numbers in molecular and cell biology. Nucleic Acids Res. 2010;38(Database issue):D750–3. https://doi.org/10.1093/nar/gkp889.View ArticlePubMedGoogle Scholar
- Choi KY, Satterberg B, Lyons DM, Elion EA. Ste5 tethers multiple protein kinases in the MAP kinase cascade required for mating in S. Cerevisiae. Cell. 1994;78(3):499–512.View ArticlePubMedGoogle Scholar
- Kornau HC, Schenker LT, Kennedy MB, Seeburg PH. Domain interaction between NMDA receptor subunits and the postsynaptic density protein PSD-95. Science. 1995;269(5231):1737–40.View ArticlePubMedGoogle Scholar
- Printen JA, Sprague GF Jr. Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase cascade. Genetics. 1994;138(3):609–19.PubMedPubMed CentralGoogle Scholar
- Therrien M, Morrison DK, Wong AM, Rubin GM. A genetic screen for modifiers of a kinase suppressor of Ras-dependent rough eye phenotype in drosophila. Genetics. 2000;156(3):1231–42.PubMedPubMed CentralGoogle Scholar
- Zhang W, Sloan-Lancaster J, Kitchen J, Trible RP, Samelson LE. LAT: the ZAP-70 tyrosine kinase substrate that links T cell receptor to cellular activation. Cell. 1998;92(1):83–92.View ArticlePubMedGoogle Scholar
- Tsunoda S, Sierralta J, Sun Y, Bodner R, Suzuki E, Becker A, et al. A multivalent PDZ-domain protein assembles signalling complexes in a G-protein-coupled cascade. Nature. 1997;388(6639):243–9. doi:10.1038/40805.View ArticlePubMedGoogle Scholar
- McKay MM, Ritt DA, Morrison DK. Signaling dynamics of the KSR1 scaffold complex. Proc Natl Acad Sci U S A. 2009;106(27):11022–7. doi:10.1073/pnas.0901590106.View ArticlePubMedPubMed CentralGoogle Scholar
- Strickfaden SC, Winters MJ, Ben-Ari G, Lamson RE, Tyers M, Pryciak PM. A mechanism for cell-cycle regulation of MAP kinase signaling in a yeast differentiation pathway. Cell. 2007;128(3):519–31. doi:10.1016/j.cell.2006.12.032.View ArticlePubMedPubMed CentralGoogle Scholar
- Bhattacharyya RP, Remenyi A, Good MC, Bashor CJ, Falick AM, Lim WA. The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway. Science. 2006;311(5762):822–6. doi:10.1126/science.1120941.View ArticlePubMedGoogle Scholar
- Malleshaiah MK, Shahrezaei V, Swain PS, Michnick SW. The scaffold protein Ste5 directly controls a switch-like mating decision in yeast. Nature. 2010;465(7294):101–5. doi:10.1038/nature08946.View ArticlePubMedGoogle Scholar
- Shaw AS, Filbert EL. Scaffold proteins and immune-cell signalling. Nat Rev Immunol. 2009;9(1):47–56. doi:10.1038/nri2473.View ArticlePubMedGoogle Scholar
- Bhattacharyya RP, Remenyi A, Yeh BJ, Lim WA. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem. 2006;75:655–80. doi:10.1146/annurev.biochem.75.103004.142710.View ArticlePubMedGoogle Scholar
- Good MC, Zalatan JG, Lim WA. Scaffold proteins: hubs for controlling the flow of cellular information. Science. 2011;332(6030):680–6. doi:10.1126/science.1198701.View ArticlePubMedPubMed CentralGoogle Scholar
- Hu J, Rho HS, Newman RH, Zhang J, Zhu H, Qian J. PhosphoNetworks: a database for human phosphorylation networks. Bioinformatics. 2014;30(1):141–2. doi:10.1093/bioinformatics/btt627.View ArticlePubMedGoogle Scholar
- Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30.View ArticlePubMedPubMed CentralGoogle Scholar
- Sadowski I, Breitkreutz BJ, Stark C, Su TC, Dahabieh M, Raithatha S, et al. The PhosphoGRID Saccharomyces Cerevisiae protein phosphorylation site database: version 2.0 update. Database. 2013;2013:bat026. doi:10.1093/database/bat026.View ArticlePubMedPubMed CentralGoogle Scholar
- Hu J, Neiswinger J, Zhang J, Zhu H, Qian J. Systematic prediction of scaffold proteins reveals new design principles in scaffold-mediated signal transduction. PLoS Comput Biol. 2015;11(9):e1004508. doi:10.1371/journal.pcbi.1004508.View ArticlePubMedPubMed CentralGoogle Scholar
- Morrison DK, Davis RJ. Regulation of MAP kinase signaling modules by scaffold proteins in mammals. Annu Rev Cell Dev Biol. 2003;19:91–118. doi:10.1146/annurev.cellbio.19.111401.091942.View ArticlePubMedGoogle Scholar