title: Achieving stability and conformational specificity in designed proteins via binary patterning.
abstract: We have developed a method to determine the optimal binary pattern (arrangement of hydrophobic and polar amino acids) of a target protein fold prior to amino acid sequence selection in protein design studies. A solvent accessible surface is generated for a target fold using its backbone coordinates and "generic" side-chains, which are constructs whose size and shape are similar to an average amino acid. Each position is classified as hydrophobic or polar according to the solvent exposure of its generic side-chain. The method was tested by analyzing a set of proteins in the Protein Data Bank and by experimentally constructing and analyzing a set of engrailed homeodomain variants whose binary patterns were systematically varied. Selection of the optimal binary pattern results in a designed protein that is monomeric, well-folded, and hyperthermophilic. Homeodomain variants with fewer hydrophobic residues are destabilized, while additional hydrophobic residues induce aggregation. Binary patterning, in conjunction with a force field that models folded state energies, appears sufficient to satisfy two basic goals of protein design: stability and conformational specificity.
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA.
authors.forename: S A
authors.initials: SA
authors.lastname: Marshall
authors.forename: S L
authors.initials: SL
authors.lastname: Mayo
mesh_terms: D000818:Animals; D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D019992:Databases as Topic; D019791:Guanidine / Q000494:pharmacology; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008027:Light; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics; D011487:Protein Conformation / Q000187:drug effects; D011489:Protein Denaturation / Q000187:drug effects; D015202:Protein Engineering; D017510:Protein Folding; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D012542:Scattering, Radiation; D012997:Solvents; D013816:Thermodynamics; D014157:Transcription Factors
chemical_list: D018398:Homeodomain Proteins; D011994:Recombinant Proteins; D012997:Solvents; D014157:Transcription Factors; C106185:engrailed homeobox proteins; D019791:Guanidine