Effect of Ionizable Residues on the Folding Energy Landscape of Globular Proteins: Linking Experiment and Computation

Abstract

Ionizable residues play important role in protein structure, stability and function. In globular proteins, majority of ionizable residues are located on the protein surface. We have previously used computational approach to optimized surface charge-charge interactions in several globular proteins: ubiquitin, the activation domain of human procarboxypeptidase A2 (ADA2), the fibronectin typeIII domain (TnfIII), acylphosphatase (ACP), the N-terminal domain of human U1A protein (U1A), Cdc42 GTPase, Fyn SH3 domain, and cold shock protein CspB(1-3). Biophysical studies have shown that all the designed variants have increased thermodynamic stability. Here we have measured experimentally the folding kinetics of the wild-type and designed variants of four proteins: U1A, Ten, ACP and ADA2. We have also performed native topology-based model simulations that correspond to a funneled energy landscape, but explicitly include non-native charge-charge interactions. Analysis of computer simulations provided molecular details for the experimentally observed changes in the folding rates of charge-charge optimized variants.This work was supported by grants from the National Science Foundation MCB-0110396.