Predicting Protein-Protein Interactions Using BiGGER: Case Studies

Abstract

The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three Case Studies: (Case Study A) in which no specific contact data is available; (Case Study B) when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling) on one of the partners is available; and (Case Study C) when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields.

Keywords: BiGGER; NMR; docking; electron transfer complexes; molecular recognition; protein-protein interactions.

Figure 1

Docking grids. (A) Part of the core grid superimposed on the cartoon representation of the Annexin 24 monomer (PDB ID 1dk5) [38]; and in (B) is shown the surface cells. The surface contact is scored from the overlap of surface cells between the grid representations of both partners, while the overlap of core regions is not allowed.

Figure 2

Soft docking grid. Using Annexin 24 monomer (PDB ID 1dk5) [38] as an example, this figure shows the core grid cells removed at the locations corresponding to the exposed side-chains of Asp27 and Lys30. Surface grid cells, represented in a darker color, still conform to the specific configuration of these residues in the PDB file. As an additional detail, note that the surface cells actually define an external shell of the protein shape. This is deliberate, so that the maximum overlap of surface cells from two grids corresponds to a realistic distance between the atoms from the two partners.

Figure 3

BiGGER Docking Process. Diagram explaining the approach used in molecular docking simulations using BiGGER. The atomic coordinates of the free proteins are entered into the protein docking algorithm [24]. Initial ab initio calculations by BiGGER produce 10⁷ to 10⁹ complexes, which are filtered and scored according to BiGGER Scoring function and 1000 putative docked positions are retained. These complexes are then scored and ranked using experimental restraints (e.g., NMR chemical shift perturbation). The highest ranked complexes are analyzed and a model structure for the complex is obtained. Adapted from Morelli, et al. [48].

Figure 4

Modeling AoR-Flavodoxin complex. Cofactor arrangement on Xanthine Oxidase (A); CO dehydrogenase (B) and Aldehyde Oxido-Reductase (C,D), with each domain or subunit colored accordingly. Panels (C) and (D) depict the result for the docking of D. gigas Flavodoxin to Aldehyde Oxido-Reductase; (C) Structure of the highest ranking model and the placement of the FMN group in the 10 top ranking models; (D) A close up on the redox centers. In all the panels the [Fe-S] binding domain is represented in green, the Mo-binding domain in cyan and the FMN or FAD binding domains in orange. Figure prepared using UCSF Chimera [69].

Figure 5

Electron transfer complex between Nitrous Oxide Reductase and cytochrome c₅₅₂ from Marinobacter hydrocarbonoclasticus. Panels (A) and (B) depict the backbone structure of Marinobacter hydrocarbonoclasticus N₂OR and cytochrome c₅₅₂, respectively. Metal centers (CuA and CuZ center for N₂OR and heme for cytochrome c₅₅₂) are represented in red; Panel (C) 200 top docking solutions ranked by hydrophobic score of N₂OR—cytochrome c₅₅₂ electron transfer complex. The iron atom in the heme of each cytochrome c₅₅₂ putative docking position is represented as a red sphere; Panel (D) A top model structure for the electron transfer complex obtained by BiGGER is represented (probe 2, Table S1 [54]). N₂OR is colored cyan and cytochrome c₅₅₂ is colored green. Figure prepared using UCSF Chimera [69].

Figure 6

Electron transfer complex between Hydrogenase and cytochrome c₅₅₃ from D. desulfuricans. Panels (A) and (B) depict the backbone structure of Hydrogenase and cytochrome c₅₅₃, respectively. Metal cofactors ([4Fe-4S] clusters and binuclear iron H cluster for Hydrogenase and c-type heme for cytochrome c₅₅₃) are represented in red. Grey colored residues in cytochrome c₅₅₃ are the most affected in a ¹H-¹⁵N HSQC NMR titration, and are clearly marked on the picture Panel (C) Top model structure for the electron transfer complex obtained combining NMR and soft-docking (PDB ID 1E08) [40]. Hydrogenase surface is colored cyan, while cytochrome c₅₅₃ surface is colored green. Figure prepared using UCSF Chimera [69].

Figure 7

Electron transfer complex between cytochrome c₃ and rubredoxin from D. gigas. Panels (A) and (B) depict the backbone structure of the cytochrome c₃ and rubredoxin, respectively. Metal centers (c-type heme for cytochrome c₃ and Fe for rubredoxin) are represented in red. Rubredoxin residues whose ^NH resonances are most affected in a ¹H-¹⁵N HSQC NMR titration are shown in light grey; Panel (C) The top 200 docking solutions ranked by electrostatic energy minimization score of the cytochrome c₃—rubredoxin electron transfer complex. The iron atom of each rubredoxin putative docking position is represented as a red sphere; Panel (D) Top model structure for the electron transfer complex obtained by BiGGER is represented. Cytochrome c₃ is colored cyan and rubredoxin is colored dark red. Figures prepared using UCSF Chimera [69].