title: Conformational diversity and computational enzyme design.
abstract: The application of computational protein design methods to the design of enzyme active sites offers potential routes to new catalysts and new reaction specificities. Computational design methods have typically treated the protein backbone as a rigid structure for the sake of computational tractability. However, this fixed-backbone approximation introduces its own special challenges for enzyme design and it contrasts with an emerging picture of natural enzymes as dynamic ensembles with multiple conformations and motions throughout a reaction cycle. This review considers the impact of conformational variation and dynamics on computational enzyme design and it highlights new approaches to addressing protein conformational diversity in enzyme design including recent advances in multi-state design, backbone flexibility, and computational library design.
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. jklassila@gmail.com
authors.forename: Jonathan K
authors.initials: JK
authors.lastname: Lassila
mesh_terms: D003198:Computer Simulation; D015195:Drug Design; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D004798:Enzymes; D011506:Proteins