Electrostatic exploration of the C3d-FH4 interaction using a computational alanine scan

The complement system is a component of innate immunity and is activated by a cascade of protein interactions whose function is vital to our ability to fight infection. When proper regulation fails, the complement system is unable to recognize "self" from "nonself" and, therefore, attacks own tissues leading to autoimmune diseases. The central protein of the complement system is C3, which is the convergence point of three independently activated but communicating pathways. Regulation of C3 occurs through modular proteins which consist of many repeats of complement control protein (CCP) modules. CCP modules have diverse sequences, similar structures, and diverse physicochemical compositions, with excess of charge being a predominant characteristic. The goal of our study is to understand the electrostatic mechanism that underlies the interaction between the C3d domain of C3 and the fourth module of the complement regulator Factor H (FH4). We have performed a computational alanine scan in which we have replaced every ionizable amino acid, one at a time, with an alanine to generate a family of mutants for the C3d-FH4 complex. We have used Poisson-Boltzmann electrostatic calculations in combination with clustering of spatial distributions of electrostatic potentials and free energy calculations to delineate the contribution of each replaced amino acid to the C3d-FH4 interaction. We have analyzed our data in view of a two-step model which separates association into long-range recognition and short-range binding and we have identified key amino acids that contribute to association. We discuss the complex role of C3d in binding FH4 and the bacterial proteins Efb/Ehp from Staphylococcus aureus.