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

76 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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