Protein kinetics: Structures of intermediates and reaction mechanism from time-resolved x-ray data

Marius Schmidt*, Reinhard Pahl, Vukica Srajer, Spencer Anderson, Zhong Ren, Hyotcherl Ihee, Sudarshan Rajagopal, Keith Moffat

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    72 Scopus citations


    We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of time-dependent difference electron density maps spanning the time range from 5 μs to 100 ms. The successful fit of exponentials to right singular vectors derived from a singular value decomposition of the difference maps demonstrates that a chemical kinetic mechanism holds and that structurally distinct intermediates exist. We identify two time-independent difference maps, from which we refine the structures of the corresponding intermediates. We thus demonstrate how structures associated with intermediate states can be extracted from the experimental, time-dependent crystallographic data. Stoichiometric and structural constraints allow the exclusion of one kinetic mechanism proposed for the photocycle but retain other plausible candidate kinetic mechanisms.

    Original languageEnglish (US)
    Pages (from-to)4799-4804
    Number of pages6
    JournalProceedings of the National Academy of Sciences of the United States of America
    Issue number14
    StatePublished - Apr 6 2004


    • Chemical, kinetic mechanism
    • Time-resolved crystallography

    ASJC Scopus subject areas

    • General

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