ArticleScience (New York, N.Y.)2015
Transition states. Trapping a transition state in a computationally designed protein bottle.
Article in Science (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 46 citations in OpenAlex.
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- Coumarin luciferins and mutant luciferases for robust multi-component bioluminescence imaging.Chemical science · 2021Article
- Titrating bacterial growth and chemical biosynthesis for efficient N-acetylglucosamine and N-acetylneuraminic acid bioproduction.Nature communications · 2020Article
- Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore.Biochemistry · 2020Article
- Multicomponent Bioluminescence Imaging with a π-Extended Luciferin.Journal of the American Chemical Society · 2020Article
- Development and Testing of Force Field Parameters for Phenylalanine and Tyrosine Derivatives.Frontiers in molecular biosciences · 2020Article
- A genetically encoded photosensitizer protein facilitates the rational design of a miniature photocatalytic CONature chemistry · 2018Article
- Article
- Playing with the Molecules of Life.ACS chemical biology · 2018Review
- Expanding and reprogramming the genetic code.Nature · 2017Review
- Rewriting the Genetic Code.Annual review of microbiology · 2017Review
- Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences.Journal of the American Chemical Society · 2017Article
- At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code.Cold Spring Harbor perspectives in biology · 2016Review
- Designed metalloprotein stabilizes a semiquinone radical.Nature chemistry · 2016Article
- Human DNMT1 transition state structure.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes.Methods in enzymology · 2016Article
- Article
- Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement.The journal of physical chemistry letters · 2015Article
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.