Bacteriorhodopsin electronic structure and its modification during all-trans → 13-cis photoisomerisation

Kudriavtsev, A.V.; Novoseletsky, V.N.; Armeev, G.A.; Shaitan, K.V.; Kirpichnikov, M.P.

Авторы: Kudriavtsev A.V., Novoseletsky V.N., Armeev G.A., Shaitan K.V., Kirpichnikov M.P.
Журнал: Journal of Bioenergetics and Biomembranes
Том: 50
Номер: 6
Год издания: 2018
Издательство: Springer/Plenum Publishers
Местоположение издательства: New York, USA
DOI: 10.1007/s10863-018-9775-7
Аннотация: 1 Lomonosov Moscow State University, Biological Faculty, Moscow, Russia 2 Emanuel Institute of Biochemical Phisics, RAS, Moscow, Russia 3 Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia e-mail: aleks.kudriavtsev@gmail.com Photoisomerisation of retinal is the fastest reaction in the nature and this is the common reaction for retinal-binding proteins – visual rhodopsins and microbial rhodopsins. Electronic structure defines spectral and kinetic properties of this reaction. For the understanding how electronic structure changes during photoisomerisation we chose 3D structure of bacteriorhodopsin (BR) as a commonly used model object. We have done QM/MM analysis of the BR structure before and after illumination (structures are obtained from SFX-studies [1]). We found that electronic structure of the BR was crucially changing during excitation and electron density was highly shifted to Schiff base for excited state compared to ground state. We suggest that polar aromatic residues Y185 and W86, W182 share electron density with retinal as a result of their affinity to electron, which located on retinal. Mutations in active center, Y185F and Y185F/W182F, impact on ground state delocalization of electron density from the retinal to protein environment, especially from amino-acid residues that was be mutated. These mutations also lead to the shift of the calculated maximum of absorption. In opposite to tyrosine and tryptophan residues non-polar phenylalanine residues can not accept electron from retinal and it is main cause of this changes. Results of this study will be used for experimental studies based on the recombinant BR expression system in E.coli [2]. It could be important for further development of new spectral-shifted forms of retinal-binding proteins and for understanding mechanism of regulation photoisomerisation of retinal. The research is carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University [3]. The work is ongoing with the support of RFBR grant 17-00-00167K (KOMFI 17-00-00166). 1. Nakane, Takanori, et al. "Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent." Proceedings of the National Academy of Sciences 113.46 (2016): 13039-13044. 2. Smitienko, O. A., et al. "Femtosecond and picosecond dynamics of recombinant bacteriorhodopsin primary reactions compared to the native protein in trimeric and monomeric forms." Biochemistry (Moscow) 82.4 (2017): 490-500. 3. Sadovnichy, V., et al. "AT (2013).“Lomonosov”: Supercomputing at Moscow State University." Contemporary High Performance Computing: From Petascale toward Exascale (2013): 283-307.
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