Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro

The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X-ray scattering (SAXS) is an experimental technique for obtaining low resolution structural information in solution. While not sufficient on its own to uniquely predict complex structures, accounting for SAXS data improves the ranking of models and facilitates the identification of the most accurate structure. Although SAXS profiles are currently available only for a small number of complexes, due to its simplicity the method is becoming increasingly popular. Since combining docking with SAXS experiments will provide a viable strategy for fairly high-throughput determination of protein complex structures, the option of using SAXS restraints is added to the ClusPro server. © 2015 Wiley Periodicals, Inc.status: publishe

Computational modeling of protein-protein and protein-peptide interactions

Protein-protein and protein-peptide interactions play a central role in various aspects of the structural and functional organization of the cell. While the most complete structural characterization is provided by X-ray crystallography, many biological interactions occur in complexes that will not be amenable to direct experimental analysis. Therefore, it is important to develop computational docking methods that start from the structures of component proteins and predict the structure of their complexes, preferably with accuracy close to that provided by X-ray crystallography. This thesis details three applications of computational protein modeling, including the study of antibody maturation mechanisms, and the development of protocols for peptide-protein interaction prediction and template-based modeling of protein complexes. The first project, a comparative analysis of docking an antigen structure to antibodies across a lineage, reveals insights into antibody maturation mechanisms. A linear relationship between near-native docking results and changes in binding free energy is established, and used to investigate changes in binding affinity following mutation across two antibody-antigen systems: influenza and anthrax. The second project demonstrates that a motif-based search of available protein crystal structures is sufficient to adequately represent the conformational space sampled by a flexible peptide, compared to that of a rigid globular protein. This observation forms the basis for a global peptide-protein docking protocol that has since been implemented into the Structural Bioinformatics Laboratory’s docking web server, ClusPro. Finally, as structure availability remains a roadblock to many studies, researchers turn to homology modeling, in which the desired protein sequence is modeled onto a related structure. This is particularly challenging when the target is a protein complex, further restricting template availability. To address this problem, the third project details the development of a new template-based modeling protocol to be integrated into the ClusPro server. The implementation of a novel template-based search enables users to model both homomeric and heteromeric complexes, greatly expanding ClusPro server functionality.2020-08-30T00:00:00