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Trapping a transition state in a computationally designed protein bottle

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Science  20 Feb 2015:
Vol. 347, Issue 6224, pp. 863-867
DOI: 10.1126/science.aaa2424

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A transition state holds a pose

The transition state of a chemical transformation is inherently fleeting because the structure is high in energy. Nonetheless, Pearson et al. trapped a classical example of a bond rotation transition state using a modified protein (see the Perspective by Romney and Miller). The biphenyl molecule passes through an energy maximum when its rings rotate through a parallel position. A pocket within the editing domain of threonyl–transfer RNA synthetase was modified to stabilize parallel biphenyl rings, allowing further characterization of this normally transient structure.

Science, this issue p. 863; see also p. 829

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.

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