Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes

Abstract

Remarkable success in engineering novel efficient biomarkers based on fluorescent and photoactive proteins provokes a question of whether computational modeling of their properties can contribute to this important field. In this Feature Article, we analyze selected papers devoted to computer simulations of three types of photoactive systems: the green fluorescent protein and its derivatives, the flavin-binding proteins, and the phytochrome domains. The main emphasis is on structures, optical spectra, and chemical reactions in the chromophore-containing pockets. Quantum chemistry, quantum mechanics/molecular mechanics, and molecular dynamics methods are effective tools in these simulations. We highlight both the success stories and the persisting challenges, discussing the ways of elevating theoretical approaches to the level of testable predictions.

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang

“…We added hydrogen atoms The choice of the QM subsystem for the quantum mechanics/molecular mechanics (QM/MM) calculations 20,21 was based on the previous studies of the GFP-like proteins. 9,13,22,23 A large fraction of the chromophore-containing pocket was assigned to QM-part: side chains from Chro, Gln94, Arg96, His145, Tyr203, Ser205, Glu222 and 7 water molecules were included.…”

“…Vertical excitation energies S0 → S1 at selected points on the ground state potential energy surface were computed using XMCQDPT2 26 with the cc-pVDZ basis set, the protocol that we verified earlier and used extensively in our studies of the photoreceptor proteins. 13 Here, the perturbation theory calculations were based on the CASSCF wavefunctions obtained by distributing 16 electrons over 12 orbitals and using density averaging over 11 states. The analysis of the corresponding wave functions allowed us to assign the characters of the computed states to locally excited and charge-transfer ones.…”

Stalling chromophore maturation of the fluorescent protein Venus reveals the molecular basis of the final oxidation step

“…To model the system in the triplet electronic state, the unrestricted DFT approach was used. Vertical excitation energies at selected points on the ground state potential energy surface were computed using the extended multiconfigurational quasi-degenerate perturbation theory in the second order (XMCQDPT2) 52 the protocol that we verified earlier and used extensively in studies of the photoreceptor proteins 53 . Here, the perturbation theory calculations were based on the complete active space selfconsistent field (CASSCF) wavefunctions obtained by distributing 16 electrons over 12 orbitals and using density averaging over 15 states.…”

Direct Measurement of the Visible to UV Photodissociation Processes for the PhotoCORM TryptoCORM

“…However, progress is currently hampered by a sparsity of experimental measurements on photoCORMs that can be straightforwardly compared to results from the computational approaches. Gas‐phase experiments would offer considerable benefits in this context, since results could be directly linked to computational results without deploying the very advanced calculations that are necessary to properly account for solvent effects on the photochemistry …”