Deciphering the folding kinetics of transmembrane helical proteins

Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. U nderstanding the detailed mechanisms of the folding of membrane proteins is a largely unsolved, key problem in structural biology. Here, we introduce a general model and use computer simulations to study the equilibrium prope rties and the folding kinetics of a C-alpha-based two-helix bundle fragment (comprised of 66 aa) of bacteriorhodopsin. Various intermediates are ident ified and their free energy are calculated together with the free energy ba rrier between them. In 40% of folding trajectories, the folding rate is con siderably increased by the presence of nonobligatory intermediates acting a s traps. In all cases, a substantial portion of the helices is rapidly form ed. This initial stage is followed by a long period of consolidation of the helices accompanied by their correct packing within the membrane. Our resu lts provide the framework for understanding the variety of folding pathways of helical transmembrane proteins.