A computational study of the chemokine receptor CXCR1 bound with interleukin-8

Yang Wang; Cecylia Severin Lupala; Ting Wang; Xuanxuan Li; Ji Hye Yun; Jae Hyun Park; Zeyu Jin; Weontae Lee; Leihan Tan; Haiguang Liu

doi:10.1088/1674-1056/27/3/038702

A computational study of the chemokine receptor CXCR1 bound with interleukin-8

Yang Wang, Cecylia Severin Lupala, Ting Wang, Xuanxuan Li, Ji Hye Yun, Jae Hyun Park, Zeyu Jin, Weontae Lee, Leihan Tan, Haiguang Liu

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 (IL8) molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCR1-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCR1-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCR1-IL8 binding poses were investigated in detail. Furthermore, the role of the N-terminal of CXCR1 receptor was studied by comparing four complex models differing in the N-terminal sequences. The results indicate that the receptor N-terminal affects the binding of IL8 significantly. With a shorter N-terminal domain, the binding of IL8 to CXCR1 becomes unstable. The homology modeling and simulations also reveal the key receptor-ligand residues involved in the electrostatic interactions known to be vital for complex formation.

Original language	English
Article number	038702
Journal	Chinese Physics B
Volume	27
Issue number	3
DOIs	https://doi.org/10.1088/1674-1056/27/3/038702
Publication status	Published - 2018 Mar

Bibliographical note

Funding Information:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213).

Funding Information:
∗Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213). †Corresponding author. E-mail: hgliu@csrc.ac.cn

Funding Information:
This computational work is supported by the Tianhe-2JK computing time award at the Beijing Computational Research Center (CSRC) and Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase) under Grant No. U1501501.

Publisher Copyright:
© 2018 Chinese Physical Society and IOP Publishing Ltd.

All Science Journal Classification (ASJC) codes

Physics and Astronomy(all)

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10.1088/1674-1056/27/3/038702

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title = "A computational study of the chemokine receptor CXCR1 bound with interleukin-8",

abstract = "CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 (IL8) molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCR1-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCR1-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCR1-IL8 binding poses were investigated in detail. Furthermore, the role of the N-terminal of CXCR1 receptor was studied by comparing four complex models differing in the N-terminal sequences. The results indicate that the receptor N-terminal affects the binding of IL8 significantly. With a shorter N-terminal domain, the binding of IL8 to CXCR1 becomes unstable. The homology modeling and simulations also reveal the key receptor-ligand residues involved in the electrostatic interactions known to be vital for complex formation.",

author = "Yang Wang and {Severin Lupala}, Cecylia and Ting Wang and Xuanxuan Li and Yun, {Ji Hye} and Park, {Jae Hyun} and Zeyu Jin and Weontae Lee and Leihan Tan and Haiguang Liu",

note = "Funding Information: Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213). Funding Information: ∗Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213). †Corresponding author. E-mail: hgliu@csrc.ac.cn Funding Information: This computational work is supported by the Tianhe-2JK computing time award at the Beijing Computational Research Center (CSRC) and Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase) under Grant No. U1501501. Publisher Copyright: {\textcopyright} 2018 Chinese Physical Society and IOP Publishing Ltd.",

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month = mar,

doi = "10.1088/1674-1056/27/3/038702",

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AU - Wang, Yang

AU - Severin Lupala, Cecylia

AU - Wang, Ting

AU - Li, Xuanxuan

AU - Yun, Ji Hye

AU - Park, Jae Hyun

AU - Jin, Zeyu

AU - Lee, Weontae

AU - Tan, Leihan

AU - Liu, Haiguang

N1 - Funding Information: Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213). Funding Information: ∗Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213). †Corresponding author. E-mail: hgliu@csrc.ac.cn Funding Information: This computational work is supported by the Tianhe-2JK computing time award at the Beijing Computational Research Center (CSRC) and Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase) under Grant No. U1501501. Publisher Copyright: © 2018 Chinese Physical Society and IOP Publishing Ltd.

PY - 2018/3

Y1 - 2018/3

N2 - CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 (IL8) molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCR1-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCR1-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCR1-IL8 binding poses were investigated in detail. Furthermore, the role of the N-terminal of CXCR1 receptor was studied by comparing four complex models differing in the N-terminal sequences. The results indicate that the receptor N-terminal affects the binding of IL8 significantly. With a shorter N-terminal domain, the binding of IL8 to CXCR1 becomes unstable. The homology modeling and simulations also reveal the key receptor-ligand residues involved in the electrostatic interactions known to be vital for complex formation.

AB - CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 (IL8) molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCR1-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCR1-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCR1-IL8 binding poses were investigated in detail. Furthermore, the role of the N-terminal of CXCR1 receptor was studied by comparing four complex models differing in the N-terminal sequences. The results indicate that the receptor N-terminal affects the binding of IL8 significantly. With a shorter N-terminal domain, the binding of IL8 to CXCR1 becomes unstable. The homology modeling and simulations also reveal the key receptor-ligand residues involved in the electrostatic interactions known to be vital for complex formation.

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A computational study of the chemokine receptor CXCR1 bound with interleukin-8

Abstract

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