Knowledge-based design of a soluble bacteriorhodopsin

Abstract

Much knowledge has been accrued from high resolution protein structures. This knowledge provides rules and guidelines for the rational design of soluble proteins. We have extracted these rules and applied them to redesigning the structure of bacteriorhodopsin and to creating blueprints for a monomeric, soluble seven-helix bundle protein. Such a protein is likely to have desirable properties, such as ready crystallization, which membrane proteins lack and an internal structure similar to that of the native protein. While preserving residues shown to be necessary for protein function, we made modifications to the rest of the sequence, distributing polar and charged residues over the surface of the protein to achieve an amino acid composition as akin to that of soluble helical proteins as possible. A secondary goal was to increase apolar contacts in the helix intercalation regions of the protein. The scheme used to design the model sequences requires knowledge of the number and orientation of helices and some information about interior contacts, but detailed structural knowledge is not required to use a scheme of this type.