title: Transition states. Trapping a transition state in a computationally designed protein bottle.
abstract: The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl. This latter moiety was introduced biosynthetically as the side chain of the noncanonical amino acid p-biphenylalanine. Through iterative rounds of computational design and structural analysis, we identified a protein in which the side chain of p-biphenylalanine is trapped in the energetically disfavored, coplanar conformation of the TS of the bond rotation reaction.
authors.affiliation: Department of Chemistry, and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Aaron D
authors.initials: AD
authors.lastname: Pearson
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Jeremy H
authors.initials: JH
authors.lastname: Mills
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Yifan
authors.initials: Y
authors.lastname: Song
authors.affiliation: Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089.
authors.forename: Fariborz
authors.initials: F
authors.lastname: Nasertorabi
authors.affiliation: Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089.
authors.forename: Gye Won
authors.initials: GW
authors.lastname: Han
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.|Howard Hughes Medical Institute (HHMI), University of Washington, Seattle, WA 98195, USA.
authors.forename: David
authors.initials: D
authors.lastname: Baker
authors.affiliation: Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089.
authors.forename: Raymond C
authors.initials: RC
authors.lastname: Stevens
authors.affiliation: Department of Chemistry, and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Schultz
mesh_terms: D000409:Alanine / Q000031:analogs & derivatives* / Q000737:chemistry; D019843:Archaeal Proteins / Q000737:chemistry*; D001713:Biphenyl Compounds / Q000737:chemistry*; D003198:Computer Simulation; D017076:Computer-Aided Design; D018360:Crystallography, X-Ray; D019277:Entropy; D008956:Models, Chemical; D017433:Protein Structure, Secondary; D043903:Pyrococcus abyssi / Q000201:enzymology*; D012984:Software; D013914:Threonine-tRNA Ligase / Q000737:chemistry*
chemical_list: D019843:Archaeal Proteins; D001713:Biphenyl Compounds; C000595935:p-biphenylalanine; D013914:Threonine-tRNA Ligase; D000409:Alanine