Molecular scale simulations of protein folding for post-genomic applications

Abstract

From sequence information, protein chains are organized into native topology to maintain biological functions. To understand protein folding mechanism remains the essential challenge in structural biology although numerous studies have been performed. It may result from the fact that protein residue motions are strongly governed by incredibly complicated physicochemical interactions directly generated by sequence information. However, if fundamental questions how sequence information codes native state topology and which interaction plays a critical role in determining folding pathways are fully solved, we will make the great progress on many fields: to predict unknown structures from sequence, to design proteins from given structures, and to synthesize new medicine which has a specific biological function. The funnel-like energy landscape theory suggested that naturally evolved protein chains are organized into secondary and tertiary structures compatible to native state via their energy landscape similar to funnel shape toward native basin with rugged surfaces. Of interest, it is found that native interactions existing in native topology substantially contribute to the folding kinetics, stability, and mechanisms of small proteins; many theoretical, computational, and experimental data have supported the importance of native interactions. Nevertheless, several proteins of which folding mechanisms are greatly determined not by native topology but by sequence-specific interactions. In this study, the folding mechanisms of 3 proteins which are mainly governed by different factors are investigated by using molecular scale over-damped Langevin simulations where physical effective energy function (EEF) weakly buttressed to $G\bar{o}-like$ energy is employed to fully realize the folding native contact map of TSE (transition state ensemble) shows that folding nuclei of protein G are mainly distributed in the C terminal β hairpin while protein L conspires to have foldi...