1
|
Taguchi S, Niwa S, Dao HA, Tanaka Y, Takeda R, Fukai S, Hasegawa K, Takeda K. Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin. Commun Biol 2023; 6:190. [PMID: 36808185 PMCID: PMC9938236 DOI: 10.1038/s42003-023-04554-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
The K intermediate of proton pumping bacteriorhodopsin is the first intermediate generated after isomerization of retinal to the 13-cis form. Although various structures have been reported for the K intermediate until now, these differ from each other, especially in terms of the conformation of the retinal chromophore and its interaction with surrounding residues. We report here an accurate X-ray crystallographic analysis of the K structure. The polyene chain of 13-cis retinal is observed to be S-shaped. The side chain of Lys216, which is covalently bound to retinal via the Schiff-base linkage, interacts with residues, Asp85 and Thr89. In addition, the Nζ-H of the protonated Schiff-base linkage interacts with a residue, Asp212 and a water molecule, W402. Based on quantum chemical calculations for this K structure, we examine the stabilizing factors of distorted conformation of retinal and propose a relaxation manner to the next L intermediate.
Collapse
Affiliation(s)
- Shoun Taguchi
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Satomi Niwa
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Hoang-Anh Dao
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Yoshihiro Tanaka
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Ryota Takeda
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Shuya Fukai
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku 606-8502 Japan
| | - Kazuya Hasegawa
- grid.410592.b0000 0001 2170 091XStructural Biology Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198 Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku, 606-8502, Japan.
| |
Collapse
|
2
|
Antipin IS, Alfimov MV, Arslanov VV, Burilov VA, Vatsadze SZ, Voloshin YZ, Volcho KP, Gorbatchuk VV, Gorbunova YG, Gromov SP, Dudkin SV, Zaitsev SY, Zakharova LY, Ziganshin MA, Zolotukhina AV, Kalinina MA, Karakhanov EA, Kashapov RR, Koifman OI, Konovalov AI, Korenev VS, Maksimov AL, Mamardashvili NZ, Mamardashvili GM, Martynov AG, Mustafina AR, Nugmanov RI, Ovsyannikov AS, Padnya PL, Potapov AS, Selektor SL, Sokolov MN, Solovieva SE, Stoikov II, Stuzhin PA, Suslov EV, Ushakov EN, Fedin VP, Fedorenko SV, Fedorova OA, Fedorov YV, Chvalun SN, Tsivadze AY, Shtykov SN, Shurpik DN, Shcherbina MA, Yakimova LS. Functional supramolecular systems: design and applications. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5011] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|