title: Direct Calculation of Protein Fitness Landscapes through Computational Protein Design.
abstract: Naturally selected amino-acid sequences or experimentally derived ones are often the basis for understanding how protein three-dimensional conformation and function are determined by primary structure. Such sequences for a protein family comprise only a small fraction of all possible variants, however, representing the fitness landscape with limited scope. Explicitly sampling and characterizing alternative, unexplored protein sequences would directly identify fundamental reasons for sequence robustness (or variability), and we demonstrate that computational methods offer an efficient mechanism toward this end, on a large scale. The dead-end elimination and A(∗) search algorithms were used here to find all low-energy single mutant variants, and corresponding structures of a G-protein heterotrimer, to measure changes in structural stability and binding interactions to define a protein fitness landscape. We established consistency between these algorithms with known biophysical and evolutionary trends for amino-acid substitutions, and could thus recapitulate known protein side-chain interactions and predict novel ones.
authors.affiliation: Department of Statistics, The University of Chicago, Chicago, Illinois. Electronic address: lorettaau@uchicago.edu.
authors.forename: Loretta
authors.initials: L
authors.lastname: Au
authors.affiliation: Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York.
authors.forename: David F
authors.initials: DF
authors.lastname: Green
mesh_terms: D000465:Algorithms; D017076:Computer-Aided Design; D019204:GTP-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D016296:Mutagenesis; D009154:Mutation; D015202:Protein Engineering / Q000379:methods*; D055503:Protein Multimerization; D055550:Protein Stability; D020836:Protein Structure, Quaternary
chemical_list: D019204:GTP-Binding Proteins