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

Abstract

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 contributemore » to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.« less

Authors:
 [1];  [2];  [1]; ORCiD logo [3]; ORCiD logo [4];  [1];  [1];  [4];  [5];  [5];  [5];  [6];  [6];  [6];  [6];  [7];  [5];  [3];  [3];  [1]
  1. Yonsei Univ., Seoul (South Korea). Dept. of Biochemistry, College of Life Science & Biotechnology
  2. Beijing Computational Science Research Center, Haidian District, Beijing (China). Complex Systems Division; Tsinghua Univ., Beijing (China). Dept. of Engineering Physics
  3. Beijing Computational Science Research Center, Haidian District, Beijing (China). Complex Systems Division
  4. Yokohama City Univ., Tsurumi, Yokohama (Japan). Graduate School of Medical Life Science, Drug Design Lab.
  5. Arizona State Univ., Tempe, AZ (United States). Physics Dept., and Biodesign Center for Applied Structural Discovery
  6. SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
  7. Yonsei Univ., Seoul (South Korea). Dept. of Systems Biology and Division of Life Sciences
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE; National Research Foundation of Korea (NRF); National Natural Science Foundation of China (NNSFC)
OSTI Identifier:
1503558
Grant/Contract Number:  
AC02-76SF00515; NRF-2017R1A2B2008483; NRF-2016R1A6A3A04010213; NRF-2017M3A9F6029755; 11575021; U1530401; U1430237
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 294; Journal Issue: 3; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

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, and Lee, Weontae. Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency. United States: N. p., 2018. Web. doi:10.1074/jbc.ra118.004038.
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. Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency. United States. doi:10.1074/jbc.ra118.004038.
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, and Lee, Weontae. Mon . "Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency". United States. doi:10.1074/jbc.ra118.004038. https://www.osti.gov/servlets/purl/1503558.
@article{osti_1503558,
title = {Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency},
author = {Yun, Ji-Hye and Li, Xuanxuan and Park, Jae-Hyun and Wang, Yang and Ohki, Mio and Jin, Zeyu and Lee, Wonbin and Park, Sam-Yong and Hu, Hao and Li, Chufeng and Zatsepin, Nadia and Hunter, Mark S. and Sierra, Raymond G. and Koralek, Jake and Yoon, Chun Hong and Cho, Hyun-Soo and Weierstall, Uwe and Tang, Leihan and Liu, Haiguang and Lee, Weontae},
abstractNote = {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.},
doi = {10.1074/jbc.ra118.004038},
journal = {Journal of Biological Chemistry},
number = 3,
volume = 294,
place = {United States},
year = {2018},
month = {11}
}

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    Molecular mechanism of light-driven sodium pumping
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