Computational Studies of Photochemistry in Phytochrome Proteins

Jonathan R. Church, Aditya G. Rao, Avishai Barnoy, Christian Wiebeler, Igor Schapiro

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


In this book chapter, the computational research which has been performed when studying the photochemistry of phytochrome proteins is reviewed. Phytochromes represent a large family of ubiquitous photoreceptor proteins that are considered for various biotechnological applications. A comprehensive understanding of their photochemical properties is essential for their utilization. A brief introduction to phytochromes is given followed by an array of computational studies that cover different aspects of their photochemical properties. This includes the choice of different quantum chemical methods which have been used to calculate the excitation energies, as well as how to accurately model the protein environmental itself and its interaction with the chromophore. Several benchmarking studies with various quantum chemical methods used in excitation energy calculations and their comparisons are summarized. Further benchmarks include the determination of the correct structure of the chromophores found in the protein. Another issue which has been encountered in these studies is accounting for the high dimensionality of the protein environment in calculation of excitation energies. Several procedures used to alleviate this problem, including conformational sampling and the optimization procedures, are discussed. Eventually, new insights from computer simulations such as the resolution of the chromophore conformation or its protonation state are highlighted, augmented by the molecular mechanism for spectral tuning.

Original languageAmerican English
Title of host publicationChallenges and Advances in Computational Chemistry and Physics
Number of pages30
StatePublished - 2021

Publication series

NameChallenges and Advances in Computational Chemistry and Physics


  • CBCRs
  • Conformational sampling
  • Excitation energies
  • Phytochromes
  • QM/MM

All Science Journal Classification (ASJC) codes

  • Chemistry (miscellaneous)
  • Physics and Astronomy (miscellaneous)
  • Computer Science Applications


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