Abstract
Protein–protein interfaces regulate many critical processes for cellular function. The ability to accurately control and regulate these molecular interactions is of major interest for biomedical and synthetic biology applications, as well as to address fundamental biological questions. In recent years, computational protein design has emerged as a tool for designing novel protein–protein interactions with functional relevance. Although attractive, these computational tools carry a steep learning curve. In order to make some of these methods more accessible, we present detailed descriptions and examples of ROSETTA computational protocols for the design of functional protein binders using seeded protein interface design. In these protocols, a motif of known structure that interacts with the target site is grafted into a scaffold protein, followed by design of the surrounding interaction surface.
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References
Procko E, Hedman R, Hamilton K et al (2013) Computational design of a protein-based enzyme inhibitor. J Mol Biol 425:3563–3575. doi:10.1016/j.jmb.2013.06.035
Fleishman SJ, Whitehead TA, Ekiert DC et al (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332:816–821. doi:10.1126/science.1202617
Procko E, Berguig GY, Shen BW et al (2014) A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Cell 157:1644–1656. doi:10.1016/j.cell.2014.04.034
Leaver-Fay A, Tyka M, Lewis SM et al (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487:545–574. doi:10.1016/B978-0-12-381270-4.00019-6
Das R, Baker D (2008) Macromolecular modeling with rosetta. Annu Rev Biochem 77:363–382. doi:10.1146/annurev.biochem.77.062906.171838
Fleishman SJ, Leaver-Fay A, Corn JE et al (2011) RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS ONE 6, e20161. doi:10.1371/journal.pone.0020161
Wärnmark A, Treuter E, Gustafsson J-A et al (2002) Interaction of transcriptional intermediary factor 2 nuclear receptor box peptides with the coactivator binding site of estrogen receptor alpha. J Biol Chem 277:21862–21868. doi:10.1074/jbc.M200764200
Savkur RS, Burris TP (2004) The coactivator LXXLL nuclear receptor recognition motif. J Pept Res 63:207–212. doi:10.1111/j.1399-3011.2004.00126.x
Ofek G, Guenaga FJ, Schief WR et al (2010) Elicitation of structure-specific antibodies by epitope scaffolds. Proc Natl Acad Sci U S A 107:17880–17887. doi:10.1073/pnas.1004728107
Correia BE, Ban Y-EA, Holmes MA et al (2010) Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure 18:1116–1126. doi:10.1016/j.str.2010.06.010
Azoitei ML, Ban Y-EA, Julien J-P et al (2012) Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. J Mol Biol 415:175–192. doi:10.1016/j.jmb.2011.10.003
Azoitei ML, Correia BE, Ban Y-EA et al (2011) Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science 334:373–376. doi:10.1126/science.1209368
Fleishman SJ, Whitehead TA, Strauch E-M et al (2011) Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol 414:289–302. doi:10.1016/j.jmb.2011.09.031
Cooper S, Khatib F, Treuille A et al (2010) Predicting protein structures with a multiplayer online game. Nature 466:756–760. doi:10.1038/nature09304
Whitehead TA, Chevalier A, Song Y et al (2012) Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol 30:543–548. doi:10.1038/nbt.2214
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Silva, DA., Correia, B.E., Procko, E. (2016). Motif-Driven Design of Protein–Protein Interfaces. In: Stoddard, B. (eds) Computational Design of Ligand Binding Proteins. Methods in Molecular Biology, vol 1414. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3569-7_17
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DOI: https://doi.org/10.1007/978-1-4939-3569-7_17
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