UC Riverside

Protein-protein interactions play a crucial role in most biological functions. Structural biology provides a glimpse into the atomic world, helping to further understand the relation between protein structure and function. Computational methods hold promise for understanding the dynamics of proteins and protein-protein interactions, but require careful selection of tools and parameters that are applicable for probing a phenomenon of interest. We describe the utility of Poisson-Boltzmann electrostatic calculations and their applicability in analysis of protein-protein interactions and protein design. We discuss a benchmark of these calculations against experimental mutagenesis data, in order to choose parameters appropriate for calculating free energies of protein association. Poisson-Boltzmann electrostatic calculations, in conjunction with other computational methods, were used to better understand the molecular mechanism by which Staphylococcus aureus evades the complement system. Recent crystallographic structures and experimental work provided insight into the molecular interactions between three secreted staphylococcal virulence factors (Efb, Ecb, and Sbi) and complement protein C3d. Our work elucidated specific residues of Efb and Ecb crucial for C3d binding, and suggested templates for the design of C3d- and Efb/Ecb-derived peptides for therapeutic design. We also used electrostatic calculations and molecular and Brownian dynamics simulations to investigate two distinct binding modes of Sbi (domain IV) to C3d, and provide insight into the physiological contexts in which each binding site may play a role. Finally, we used these data as a basis for therapeutic design. We used molecular dynamics simulations to assess rationally designed peptides aimed at competitively inhibiting interactions between complement C3d and its host and pathogenic ligands. We also describe a comprehensive approach for virtual high- throughput screening of small molecules that can bind to C3d. Our data provide frameworks for the analysis of host-pathogen interactions and drug design, and identify several potential C3d-binding molecules that serve as a foundation for the design of complement-targeted and anti-infective therapeutics.