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

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

中国物理B ›› 2018, Vol. 27 ›› Issue (3): 38702-038702.doi: 10.1088/1674-1056/27/3/038702

• INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY • 上一篇下一篇

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

Yang Wang(王洋), Cecylia Severin Lupala, Ting Wang(王亭), Xuanxuan Li(李选选), Ji-Hye Yun, Jae-hyun Park, Zeyu Jin(金泽宇), Weontae Lee, Leihan Tan(汤雷翰), Haiguang Liu(刘海广)

1 Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China;
2 Genome Center, University of California, Davis, 451 East Health Science Drive, Davis, CA, 95616, USA;
3 Department of Engineering physics, Tsinghua University, Beijing 100086, China;
4 Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea;
5 Department of Physics and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong, China

收稿日期:2017-10-24 修回日期:2017-12-07 出版日期:2018-03-05 发布日期:2018-03-05
通讯作者: Haiguang Liu E-mail:hgliu@csrc.ac.cn
基金资助:
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).

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

Yang Wang(王洋)¹, Cecylia Severin Lupala¹, Ting Wang(王亭)², Xuanxuan Li(李选选)^1,3, Ji-Hye Yun⁴, Jae-hyun Park⁴, Zeyu Jin(金泽宇)⁴, Weontae Lee⁴, Leihan Tan(汤雷翰)^1,5, Haiguang Liu(刘海广)¹

1 Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China;
2 Genome Center, University of California, Davis, 451 East Health Science Drive, Davis, CA, 95616, USA;
3 Department of Engineering physics, Tsinghua University, Beijing 100086, China;
4 Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea;
5 Department of Physics and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong, China

Received:2017-10-24 Revised:2017-12-07 Online:2018-03-05 Published:2018-03-05
Contact: Haiguang Liu E-mail:hgliu@csrc.ac.cn
Supported by:
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).

摘要/Abstract

摘要： 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.

关键词: CXCR1-IL8 complex, homology modeling, ligand binding, molecular dynamics

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.

Key words: CXCR1-IL8 complex, homology modeling, ligand binding, molecular dynamics

中图分类号: (Molecular interactions; membrane-protein interactions)

87.15.K-

31.15.at (Molecule transport characteristics; molecular dynamics; electronic structure of polymers) 82.20.Wt (Computational modeling; simulation)

王洋, 王亭, 李选选, 金泽宇, 汤雷翰, 刘海广. A computational study of the chemokine receptor CXCR1 bound with interleukin-8[J]. 中国物理B, 2018, 27(3): 38702-038702.

Yang Wang(王洋), Cecylia Severin Lupala, Ting Wang(王亭), Xuanxuan Li(李选选), Ji-Hye Yun, Jae-hyun Park, Zeyu Jin(金泽宇), Weontae Lee, Leihan Tan(汤雷翰), Haiguang Liu(刘海广). A computational study of the chemokine receptor CXCR1 bound with interleukin-8[J]. Chin. Phys. B, 2018, 27(3): 38702-038702.

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

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

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