Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Yun, Ji-Hye; Li, Xuanxuan; Park, Jae-Hyun; Wang, Yang; Ohki, Mio; Jin, Zeyu; Lee, Wonbin; Park, Sam-Yong; Hu, Hao; Li, Chufeng; Zatsepin, Nadia; Hunter, Mark S.; Sierra, Raymond G.; Koralek, Jake; Yoon, Chun Hong; Cho, Hyun-Soo; Weierstall, Uwe; Tang, Leihan; Liu, Haiguang; Lee, Weontae

doi:10.1074/jbc.ra118.004038

Title: Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Journal Article · 19 November 2018 · Journal of Biological Chemistry

DOI: https://doi.org/10.1074/jbc.ra118.004038 · OSTI ID:1503558

Yun, Ji-Hye ^[1]; Li, Xuanxuan ^[2]; Park, Jae-Hyun ^[1];

^[3];

^[4]; Jin, Zeyu ^[1]; Lee, Wonbin ^[1]; Park, Sam-Yong ^[4]; Hu, Hao ^[5]; Li, Chufeng ^[5]; Zatsepin, Nadia ^[5]; Hunter, Mark S. ^[6]; Sierra, Raymond G. ^[6]; Koralek, Jake ^[6]; Yoon, Chun Hong ^[6]; Cho, Hyun-Soo ^[7]; Weierstall, Uwe ^[5]; Tang, Leihan ^[3]; Liu, Haiguang ^[3]; Lee, Weontae ^[1]

Yonsei Univ., Seoul (South Korea). Dept. of Biochemistry, College of Life Science & Biotechnology
Beijing Computational Science Research Center, Haidian District, Beijing (China). Complex Systems Division; Tsinghua Univ., Beijing (China). Dept. of Engineering Physics
Beijing Computational Science Research Center, Haidian District, Beijing (China). Complex Systems Division
Yokohama City Univ., Tsurumi, Yokohama (Japan). Graduate School of Medical Life Science, Drug Design Lab.
Arizona State Univ., Tempe, AZ (United States). Physics Dept., and Biodesign Center for Applied Structural Discovery
SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
Yonsei Univ., Seoul (South Korea). Dept. of Systems Biology and Division of Life Sciences

Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: National Natural Science Foundation of China (NNSFC); National Research Foundation of Korea (NRF); USDOE

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1503558

Journal Information:: Journal of Biological Chemistry, Journal Name: Journal of Biological Chemistry Journal Issue: 3 Vol. 294; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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