Protein-protein interactions are integral to virtually all biological pathways. Many important interactions occur in weak, transient complexes that will not be amenable to direct experimental analysis, even when both proteins can be isolated and their structures determined. Thus, it is important to develop computational docking methods which, starting from the structures of component proteins, can determine the structure of their complexes. We have developed a multistage docking algorithm that provided the best results in the latest rounds of the CAPRI (Critical Assessment of Predicted Interactions) worldwide docking experiment. In addition, our docking server ClusPro was the best among automated servers. Although the CAPRI results demonstrate progress, a number of major problems remain unsolved. First, docking homology models is a challenge and all methods used in CAPRI performed poorly for such targets. Docking unbound structures is also difficult if binding is accompanied by substantial backbone conformational change. Second, it is not clear whether a model generated by docking represents a specific and stable complex. Third, the interface may include regions that are disordered in the separate proteins, challenging docking methods. We address these problems by pursuing three specific aims. First, we develop a novel algorithm for docking homology models and proteins with substantial backbone flexibility. The method is based on the hypothesis that the interface in complexes is sequentially and structurally more conserved than the rest of the proteins. Since such regions are frequently sufficient for recognition, identification and correct docking of the key segments can yield near-native docked structures. For homology models this implies that one can dock the regions that can be reliably modeled, and then expand the models by adding back the removed parts using the docked structures as constraints. The problem of docking """"""""difficult cases"""""""" with substantial backbone conformational change can also be addressed by identifying and docking the structurally most conserved regions. Once clusters of the docked rigid fragments are obtained, the models are expanded by rebuilding the more flexible parts. Second, we use a two-step approach to examine the stability of protein complexes, first by removing small and hence unlikely clusters of low energy docked structures, and then by calculating dissociation rates by stochastic roadmap simulation. The method will be validated on a benchmark set that includes models of real protein complexes and decoys generated by docking non-interacting protein pairs. The approach will also be used to determine whether complex structures deposited to the PDB are biologically relevant. Third, we consider the problem of determining the structure of flexible loops and/or disordered regions when they become parts of a protein- protein interface. Rather than attempting to predict and to dock the most likely conformation of the flexible fragment, we build their bound structure directly into binding hot spots of the partner protein. Flexible peptide docking methods will be used to expand the docked fragments by adding further residues.
Many biologically important interactions occur in weak, transient complexes that are not amenable to direct experimental analysis, and hence it is important to develop computational docking methods that, starting from the structures of unbound proteins, can determine the structure of their complexes. The goal of this proposal is to solve some of the most important outstanding problems of protein docking, i.e., docking homology models and flexible proteins, and predicting the stability of complexes.
| Zarbafian, Shahrooz; Moghadasi, Mohammad; Roshandelpoor, Athar et al. (2018) Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes. Sci Rep 8:5896 |
| Yueh, Christine; Hall, David R; Xia, Bing et al. (2017) ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking. J Mol Biol 429:372-381 |
| Kozakov, Dima; Hall, David R; Xia, Bing et al. (2017) The ClusPro web server for protein-protein docking. Nat Protoc 12:255-278 |
| Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J et al. (2017) A benchmark testing ground for integrating homology modeling and protein docking. Proteins 85:10-16 |
| Vajda, Sandor; Yueh, Christine; Beglov, Dmitri et al. (2017) New additions to the ClusPro server motivated by CAPRI. Proteins 85:435-444 |
| Xia, Bing; Vajda, Sandor; Kozakov, Dima (2016) Accounting for pairwise distance restraints in FFT-based protein-protein docking. Bioinformatics 32:3342-3344 |
| Padhorny, Dzmitry; Kazennov, Andrey; Zerbe, Brandon S et al. (2016) Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. Proc Natl Acad Sci U S A 113:E4286-93 |
| Im, Wonpil; Liang, Jie; Olson, Arthur et al. (2016) Challenges in structural approaches to cell modeling. J Mol Biol 428:2943-64 |
| Lensink, Marc F; Velankar, Sameer; Kryshtafovych, Andriy et al. (2016) Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins 84 Suppl 1:323-48 |
| Mamonov, Artem B; Moghadasi, Mohammad; Mirzaei, Hanieh et al. (2016) Focused grid-based resampling for protein docking and mapping. J Comput Chem 37:961-70 |
Showing the most recent 10 out of 68 publications
