Functional studies and spatial structure of new retinal-binding proteins

Okhrimenko, I.S.; Popov, P.A.; Malyar, N.L.; Chupin, V.V.; Petrovskaya, L.E.; Dolgikh, D.A.; Novoseletsky, V.N.; Kudryavtsev, A.V.; Shaitan, K.V.; Gordeliy, V.I.; Kirpichnikov, M.P.

Авторы: Okhrimenko I.S., Popov P.A., Malyar N.L., Chupin V.V., Petrovskaya L.E., Dolgikh D.A., Novoseletsky V.N., Kudryavtsev A.V., Shaitan K.V., Gordeliy V.I., 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: Structural and functional characteristics of new unexplored microbial rhodopsins, as well as high-resolution data of the structure of these membrane proteins and their mutant variants, are the necessary input information for the development of concepts of the relationship between the structure and function of retinal-containing proteins, using molecular modeling techniques and improving bioengineering designs of photosensitive proteins for solving problems optogenetics and biophotonics. To define the function and to obtain high-resolution structural information for new microbial rhodopsins particularly found by knowledge-based prediction bioinformatics search of microbial rhodopsins [1] we use the well-developed pipeline of methods of heterologous expression, isolation and purification, functional characterization of previously unexplored microbial rhodopsins, determination of their kinetic characteristics and determination of their spatial structure of atomic resolution by X-ray diffraction. Under the study are unexplored rhodopsins of Sphingomonas paucimobilis, Pantoea anthophila, also various mutant forms of rhodopsin from Gram-positive bacteria Exiguobacterium sibiricum (ESR), previously obtained and characterized by the authors of the project [2], Exiguobacterium sp AT1b and Exiguobacterium 7-3 from permafrost. Molecular modeling methods [3] were used to predict the structures and dynamic properties for amino acid substitutions, general stability and thermal stability of unexplored rhodopsins. Based on the proteins’ structures, spectral properties were calculated by QM/MM methods. The work is ongoing with the support of RFBR grant 17-00-00167K (KOMFI 17-00-00166, 17-00-00165, 17-00-00164). 1. Ushakov, A., et al. Knowledge-based prediction model for characterization of microbial rhodopsins for optogenetics. FEBS Journal (2016). Volume 283, P-03.03.2-014
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