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

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

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Pages (from-to)794-804
Number of pages11
JournalJournal of Biological Chemistry
Volume294
Issue number3
DOIs
Publication statusPublished - 2019 Jan 1

Fingerprint

Chlorides
Pumps
Rhodopsin
X ray lasers
Temperature
Free electron lasers
Lasers
X-Rays
Electrons
Synchrotrons
Ion Pumps
Ions
Crystallography
Molecules
Water
X ray crystallography
X Ray Crystallography
Thermal effects
Cryogenics
Hydrogen

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

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, Weon Tae. / Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency. In: Journal of Biological Chemistry. 2019 ; Vol. 294, No. 3. pp. 794-804.
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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 {\AA}, 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.",
author = "Yun, {Ji Hye} and Xuanxuan Li and Park, {Jae Hyun} and Yang Wang and Mio Ohki and Zeyu Jin and Wonbin Lee and Park, {Sam Yong} and Hao Hu and Chufeng Li and Nadia Zatsepin and Hunter, {Mark S.} and Sierra, {Raymond G.} and Jake Koralek and Yoon, {Chun Hong} and Cho, {Hyun Soo} and Uwe Weierstall and Leihan Tang and Haiguang Liu and Lee, {Weon Tae}",
year = "2019",
month = "1",
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Yun, JH, Li, X, Park, JH, Wang, Y, Ohki, M, Jin, Z, Lee, W, Park, SY, Hu, H, Li, C, Zatsepin, N, Hunter, MS, Sierra, RG, Koralek, J, Yoon, CH, Cho, HS, Weierstall, U, Tang, L, Liu, H & Lee, WT 2019, 'Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency', Journal of Biological Chemistry, vol. 294, no. 3, pp. 794-804. https://doi.org/10.1074/jbc.RA118.004038

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, Weon Tae.

In: Journal of Biological Chemistry, Vol. 294, No. 3, 01.01.2019, p. 794-804.

Research output: Contribution to journalArticle

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T1 - Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

AU - Yun, Ji Hye

AU - Li, Xuanxuan

AU - Park, Jae Hyun

AU - Wang, Yang

AU - Ohki, Mio

AU - Jin, Zeyu

AU - Lee, Wonbin

AU - Park, Sam Yong

AU - Hu, Hao

AU - Li, Chufeng

AU - Zatsepin, Nadia

AU - Hunter, Mark S.

AU - Sierra, Raymond G.

AU - Koralek, Jake

AU - Yoon, Chun Hong

AU - Cho, Hyun Soo

AU - Weierstall, Uwe

AU - Tang, Leihan

AU - Liu, Haiguang

AU - Lee, Weon Tae

PY - 2019/1/1

Y1 - 2019/1/1

N2 - 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.

AB - 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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