Multi-scale Simulation Reveals that an Amino Acid Substitution Increases Photosensitizing Reaction Inputs in Rhodopsins

Erix W Hernández-Rodríguez*, Andres M Escorcia Cabrera, Marc W Van Der Kamp, Ana L Montero-Alejo, Julio Caballero

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

1 Citation (Scopus)
85 Downloads (Pure)


Evaluating the availability of molecular oxygen (O2) and energy of excited states in the retinal
binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions
in wild-type (WT) and mutant rhodopsins by absorbing visible light. In the present work, energies
of the ground and excited states related to 11-cis-retinal and the O2 accessibility to the β-ionone
ring are evaluated inside WT and human M207R mutant rhodopsins. Putative O2 pathways within
rhodopsins are identified by using molecular dynamics simulations, Voronoi-diagram analysis,
and implicit ligand sampling while retinal energetic properties are investigated through density
functional theory, and quantum mechanical/molecular mechanical methods. Here, the predictions
reveal that an amino acid substitution can lead to enough energy and O2 accessibility in the core
hosting retinal of mutant rhodopsins to favor the photosensitized singlet oxygen generation, which
can be useful in understanding retinal degeneration mechanisms and in designing blue-lightingabsorbing proteic photosensitizers.
Original languageEnglish
JournalJournal of Computational Chemistry
Publication statusPublished - 5 Aug 2020


  • Photosensitization
  • singlet oxygen
  • retinitis pigmentosa
  • implicit ligand sampling
  • QM/MM calculations


Dive into the research topics of 'Multi-scale Simulation Reveals that an Amino Acid Substitution Increases Photosensitizing Reaction Inputs in Rhodopsins'. Together they form a unique fingerprint.
  • HPC (High Performance Computing) Facility

    Sadaf R Alam (Manager), Steven A Chapman (Manager), Polly E Eccleston (Other), Simon H Atack (Other) & D A G Williams (Manager)

    Facility/equipment: Facility

Cite this