Protein–protein interactions lie at the heart of most cellular processes. Determining their high-resolution structures by experimental methods is a nontrivial task, which is why complementary computational approaches have been developed over the years. To gain structural and dynamical insight on an atomic scale in these interactions, computational modeling must often be complemented by low-resolution experimental information. For this purpose, we developed the user-friendly HADDOCK webserver, the interface to our biomolecular docking program, which can make use of a variety of low-resolution data to drive the docking process. In this chapter, we explain the use of the HADDOCK webserver based on the real-life Lys48-linked di-ubiquitin case, which led to the 2BGF PDB model. We demonstrate the use of chemical shift perturbation data in combination with residual dipolar couplings and further highlight a few other cases where our software was successfully used. The HADDOCK webserver is available to the science community for free at haddock.science.uu.nl/services/HADDOCK.
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Financial support from the Dutch Foundation for Scientific Research (NWO) (ECHO grant no. 711.011.009 and VICI grant no. 700.56.442) and the European Union (FP7 e-Infrastructure grant WeNMR no. 261572) is acknowledged.
Moreira IS, Fernandes PA, Ramos MJ (2010) Protein-protein docking dealing with the unknown. J Comput Chem 31:317–342PubMedGoogle Scholar
Dominguez C, Boelens R, Bonvin AMJJ (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125: 1731–1737PubMedCrossRefGoogle Scholar
de Vries SJ, van Dijk ADJ, Krzeminski M et al (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69:726–733PubMedCrossRefGoogle Scholar
van Dijk ADJ, Fushman D, Bonvin AMJJ (2005) Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins 60:367–381PubMedCrossRefGoogle Scholar
van Dijk ADJ, Kaptein R, Boelens R et al (2006) Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking. J Biomol NMR 34: 237–244PubMedCrossRefGoogle Scholar
Lensink MF, Wodak SJ (2013) Docking, scoring and affinity prediction in CAPRI. Proteins 81:2082–2095Google Scholar
Varadan R, Walker O, Pickart C et al (2002) Structural properties of polyubiquitin chains in solution. J Mol Biol 324:637–647PubMedCrossRefGoogle Scholar
Brünger AT, Adams PD, Clore GM et al (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921PubMedCrossRefGoogle Scholar