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Chin. Phys. B, 2018, Vol. 27(3): 038702    DOI: 10.1088/1674-1056/27/3/038702
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev   Next  

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
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.
Keywords:  CXCR1-IL8 complex      homology modeling      ligand binding      molecular dynamics  
Received:  24 October 2017      Revised:  07 December 2017      Accepted manuscript online: 
PACS:  87.15.K- (Molecular interactions; membrane-protein interactions)  
  31.15.at (Molecule transport characteristics; molecular dynamics; electronic structure of polymers)  
  82.20.Wt (Computational modeling; simulation)  
Fund: 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 Authors:  Haiguang Liu     E-mail:  hgliu@csrc.ac.cn

Cite this article: 

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 2018 Chin. Phys. B 27 038702

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