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J Biol Chem. 2019 Jan 18;294(3):794-804. doi: 10.1074/jbc.RA118.004038. Epub 2018 Nov 19.

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

Author information

1
From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea.
2
Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.
3
Department of Engineering Physics, Tsinghua University, Beijing 100086, China.
4
Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.
5
Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287.
6
Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and.
7
Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea.
8
Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China, hgliu@csrc.ac.cn.
9
From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, wlee@spin.yonsei.ac.kr.

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 contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.

KEYWORDS:

X-ray crystallography; X-ray free electron laser; anion pump; chloride transport; circular dichroism (CD); light-driven chloride pump; non-cryogenic condition; rhodopsin; serial femtosecond crystallography; structure-function; temperature dependence; time-resolved XFEL; transport efficiency; ultraviolet-visible spectroscopy (UV-Vis spectroscopy)

PMID:
30455349
PMCID:
PMC6341376
[Available on 2020-01-18]
DOI:
10.1074/jbc.RA118.004038
[Indexed for MEDLINE]

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