Abstract
Peptide-mediated interactions are involved in many signaling and regulatory pathways as well as the DNA replication machinery and are linked to many pathological disorders. Many research groups are currently working towards a more detailed understanding of these important interactions by characterizing the 3D complex structures with experimental methods like X-ray crystallography and NMR. However, for a large number of peptide-protein complexes such atomistic structural information is lacking to date. Computational peptide docking methods can yield information complementary to experimental information by predicting the protein-peptide complex structure from the 3D structure of the protein and the peptide sequence. This approach can also be used to study interactions between folded and disordered proteins/protein regions (e.g., the interactions of the disordered regions in tumor suppressor p53 with its different partners). Here, we describe the development and usage of the fully blind, flexible peptide-protein docking protocol pepATTRACT. The ATTRACT docking engine is implemented as a suite of command line tools and options that can be combined at will. Therefore, ATTRACT protocols like pepATTRACT are typically invoked via a custom, hand-written shell script. Although this approach is very flexible, it limits the accessibility of ATTRACT to expert users only. To make pepATTRACT easily accessible to non-expert users, we created a web-interface which helps the user set up a peptide docking protocol by editing parameters in a web browser (www.attract.ph.tum.de/peptide.html). pepATTRACT docking scripts can then executed on the user's local machine, once the ATTRACT software has been installed. Here, we describe all the steps necessary for setting up a pepATTRACT docking run via the web-interface including installation of the ATTRACT software.
Keywords: Protein-peptide interaction, Disordered protein binding, Protein-peptide complex structure, Peptide binding prediction, Binding site prediction
Materials and Reagents
Equipment
Software
Procedure
Predicting the structure of a peptide-protein complex with the fully blind docking protocol pepATTRACT requires the following steps:
Instructions and the main parts of the pepATTRACT docking protocol are visualized in Figure 1. In the following, the individual steps are described in more detail.
Representative data
As an example application, we predict the complex of a peptide derived from type 1 human immunodeficiency virus (HIV-1) capsid protein with a cellular protein, cyclophilin A (CypA). The HIV-1 virion forms by assembly of the Gag polyprotein. Approximately 2,000 Gag molecules bind to the host cell membrane and assemble into budding virions. The HIV-1 virion also contains about 200 copies of the cytosolic CypA protein. These are essential for virus replication and are packaged into the virion by a direct interaction between Gag and CypA. Previous studies have characterized both the 3D complex structure of CypA and the His87-Ala-Gly-Pro-Ile-Ala92 sequence from the capsid protein (PDB code: 1AWR) (Vajdos et al., 1997) and the apo cypA structure (PDB code: 2ALF). We use these structures to test the pepATTRACT protocol refining the top 1,000 rigid body docking models with iATTRACT. One of the final top 10 ranked models is shown in Figure 3. It correctly predicts the binding site and an extended conformation for the peptide (IRMSD 1.15 A°, fraction of native contacts 0.67). Figure 3. Results for docking cyclophilin A to the HAGPIA sequence of HIV-1 capsid protein. The protein is drawn in surface representation (gray), the peptide in stick representation (red: docking model, black: reference from the crystal structure). The protein residues involved in binding are shown in yellow. This figure was generated with PyMOL.
Notes
Acknowledgments
This protocol was adapted from the previously published studies of de Vries et al. (2015) and Schindler et al. (2015a). The authors acknowledge funding by the Center for Integrated Protein Science Munich (CIPSM). This work was performed on computational resources provided by a CIPSMWomen’s consumables grant.
References
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