histidine-mediated ph-sensitive regulation of m-ficolinglcnac binding activity in innate immunity examined by molecular dynamics simulationshistidine-mediated ph-sensitive监管m-ficolinglcnac绑定在先天免疫检查活动分子动力学模拟.pdfVIP

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histidine-mediated ph-sensitive regulation of m-ficolinglcnac binding activity in innate immunity examined by molecular dynamics simulationshistidine-mediated ph-sensitive监管m-ficolinglcnac绑定在先天免疫检查活动分子动力学模拟.pdf

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histidine-mediated ph-sensitive regulation of m-ficolinglcnac binding activity in innate immunity examined by molecular dynamics simulationshistidine-mediated ph-sensitive监管m-ficolinglcnac绑定在先天免疫检查活动分子动力学模拟

Histidine-Mediated pH-Sensitive Regulation of M-Ficolin:GlcNAc Binding Activity in Innate Immunity Examined by Molecular Dynamics Simulations 1,2 2,3 4 1,2 Lifeng Yang , Jing Zhang , Bow Ho , Jeak Ling Ding * 1 Computational and Systems Biology, Singapore-MIT Alliance (SMA), Singapore, Singapore, 2 Department of Biological Sciences, National University of Singapore, Singapore, Singapore, 3 NUS Graduate School for Integrative Science and Engineering (NGS), National University of Singapore, Singapore, Singapore, 4 Department of Microbiology, Yong Loo Lin School of Medicine, Singapore, Singapore Abstract Background: M-ficolin, a pathogen recognition molecule in the innate immune system, binds sugar residues including N- acetyl-D-glucosamine (GlcNAc), which is displayed on invading microbes and on apoptotic cells. The cis and trans Asp282- Cys283 peptide bond in the M-ficolin, which was found to occur at neutral and acidic pH in crystal structures, has been suggested to represent binding and non-binding activity, respectively. A detailed understanding of the pH-dependent conformational changes in M-ficolin and pH-mediated discrimination mechanism of GlcNAc-binding activity are crucial to both immune-surveillance and clearance of apoptotic cells. Methodology/Principal Findings: By immunodetection analysis, we found that the pH-sensitive binding of GlcNAc is regulated by a conformational equilibrium between the active and inactive states of M-ficolin. We performed constant pH molecular dynamics (MD) simulation at a series of pH values to explore the pH effect on the cis-trans isomerization of the Asp282-Cys283 peptide bond in the M-ficolin fibrinogen-like domain (FBG). Analysis of the hydrogen bond occupancy of wild type FBG compar