title: Computer-assisted re-design of spectrin SH3 residue clusters.
abstract: We have developed a protein design computer program, called Perla, which performs searches in sequence space to uncover optimal amino acid sequences for desired protein three-dimensional structures. Optimal sequences are localised at the minima of a sequence-structure energy landscape defined using a complex scoring function (an all-atom molecular mechanics force field plus statistical terms including entropy and solvation) measured with respect to a reference state simulating a denatured protein. Sequence choices eventually optimise side chain packing, secondary structure propensities, and hydrogen bonding and electrostatics interactions. Perla was used to re-design clusters of residues of the SH3 domain of alpha-spectrin. Several mutant proteins were produced and characterised. Some of our designed proteins have significantly higher stabilities (stability enhancements about 0.25, 0.70 and 1.0 kcal mol(-1)) than the wild-type protein. These successful protein re-designs, and similar examples found in the literature, establish the quality of the structure-based computational approach to protein design.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117, Heidelberg, Germany.
authors.forename: I
authors.initials: I
authors.lastname: Angrand
authors.forename: L
authors.initials: L
authors.lastname: Serrano
authors.forename: E
authors.initials: E
authors.lastname: Lacroix
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002942:Circular Dichroism; D003198:Computer Simulation; D017076:Computer-Aided Design; D016208:Databases, Factual; D004591:Electrophoresis, Polyacrylamide Gel; D019277:Entropy; D005822:Genetic Vectors; D013058:Mass Spectrometry; D008958:Models, Molecular; D009154:Mutation; D015202:Protein Engineering / Q000379:methods*; D017433:Protein Structure, Secondary; D017421:Sequence Analysis / Q000379:methods*; D012995:Solubility; D013049:Spectrin / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D018909:src Homology Domains
chemical_list: D013049:Spectrin