Calculations on folding of segment B1 of streptococcal protein G

Abstract

We present an investigation of the folding thermodynamics and mechanism of segment B1 of streptococcal protein G. Molecular dynamics simulations of the fully solvated protein are used to probe thermodynamically significant states at different stages of folding. We performed several unfolding simulations to generate a database of initial conditions. The database is analyzed and clustered. The cluster centers extracted from this database were then used as starting points for umbrella sampling of the folding free energy landscape under folding conditions. The resulting sampling was combined with the weighted histogram analysis method. One and two-dimensional free energy surfaces were constructed along several order parameters and used to analyze the folding process. Our findings indicate that an initial collapse precedes the formation of significant native structure. Elements of local structure originate in the regions of the protein shown to have higher H/2H exchange protection factors in early stages of folding. A non-native contact, observed experimentally at the N terminus of the alpha-helix in a peptide excised from the protein, is seen to pre-organize the chain in early stages of folding. Collapse and early structure formation yields a compact globule with a significant number of water molecules present. Desolvation of the protein core is coincident with the final stages of folding from the compact state.