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

Chinese Physics B 2018年第3期27卷 534-543页

作者： Yang Wang cecylia severin lupala Ting Wang Xuanxuan Li Ji-Hye Yun Jae-hyun Park Zeyu Jin Weontae Lee Leihan Tan Haiguang Liu Complex Systems Division Beijing Computational Science Research Center Beijing 100193 China Genome Center University of California Davis 451 East Health Science Drive Davis CA 95616 USA Department of Engineering physics Tsinghua University Beijing 100086 China Department of Biochemistry College of Life Science ＆ Biotechnology Yonsei University Seou103722 South Korea Department of Physics and Institute of Computational and Theoretical Studies Hong Kong Baptist University Hong Kong China

CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 （1L8） molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCRI-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCRI-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCRI-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： CXCRI-IL8 complex homology modeling ligand binding molecular dynamics

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Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein

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Quantitative Biology 2021年第1期9卷 61-72页

作者： cecylia Slupala Xuanxuan Li Jian Lei Hong Chen Jianxun Qi Haiguang Liu Xiao-Dong Su Complex Systems Division Beijing Computational Science Research CenterBeijing 100193China Engingeering Physics Department Tsinghua UniversityBeijing 100084China State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengdu 610041China School of Life Sciences State Key Laboratory of Protein and Plant Gene Research and Biomedical Pioneering Innovation Center(BIOPIC)Peking UniversityBeijing 100871China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Physics Department Beijing Normal UniversityBeijing 100875China

Background:A novel coronavirus(the SARS-CoV-2)has been identified in January 2020 as the causal pathogen for COVID-19,a pandemic started near the end of *** Angiotensin converting enzyme 2 protein(ACE2)utilized by the SARS-CoV as a receptor was found to facilitate the infection of SARS-CoV-2,initiated by the binding of the spike protein to human ***:Using homology modeling and molecular dynamics(MD)simulation methods,we report here the detailed structure and dynamics of the ACE2 in complex with the receptor binding domain(RBD)of the SARS-CoV-2 spike ***:The predicted model is highly consistent with the experimentally determined structures,validating the homology modeling *** the binding interface reported in the crystal structures,novel binding poses are revealed from all-atom MD *** simulation data are used to identify critical residues at the complex interface and provide more details about the interactions between the SARS-CoV-2 RBD and human ***:Simulations reveal that RBD binds to both open and closed state of *** human ACE2 mutants and rat ACE2 are modeled to study the mutation effects on RBD binding to *** simulations show that the N-terminal helix and the K353 are very important for the tight binding of the complex,the mutants are found to alter the binding modes of the CoV2-RBD to ACE2.

关键词： SARS-CoV-2 COVID-19 ACE2 mutation molecular dynamics simulations

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