The solvent at antigen-binding site regulated C3d–CR2 interactions through the C-terminal tail of C3d at different ion strengths: insights from molecular dynamics simulation

• Published in: Biochimica et biophysica acta Vol. 1860; no. 10; pp. 2220 - 2231
• Main Authors: Zhang, Yan, Guo, Jingjing, Li, Lanlan, Liu, Xuewei, Yao, Xiaojun, Liu, Huanxiang
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2016
• Subjects: Adaptive Immunity - immunology; Antigens - chemistry; Antigens - immunology; binding sites; Binding Sites - immunology; C3d; Complement; Complement C3 - chemistry; Complement C3 - immunology; Complement C3 - metabolism; CR2; Humans; immune system; Immunity, Innate - immunology; ionic strength; ions; Ions - chemistry; Ions - metabolism; MM-GBSA; molecular dynamics; Molecular Dynamics Simulation; Multiprotein Complexes - chemistry; Multiprotein Complexes - immunology; Multiprotein Complexes - metabolism; Osmolar Concentration; Protein Binding; Protein Conformation; Receptors, Complement 3d - chemistry; Receptors, Complement 3d - immunology; Receptors, Complement 3d - metabolism; solvents; vaccine development; Vaccines - chemistry; Vaccines - immunology; CR2; Complement; Molecular dynamics simulation; C3d; MM-GBSA
• DOI: 10.1016/j.bbagen.2016.05.002
• ISSN: 0304-4165; 0006-3002

The interactions of complement receptor 2 (CR2) and the degradation fragment C3d of complement component C3 play important links between the innate and adaptive immune systems. Due to the importance of C3d–CR2 interaction in the design of vaccines and inhibitors, a number of studies have been performed to investigate C3d–CR2 interaction. Many studies have indicated C3d–CR2 interactions are ionic strength-dependent. To investigate the molecular mechanism of C3d–CR2 interaction and the origin of effects of ionic strength, molecular dynamics simulations for C3d–CR2 complex together with the energetic and structural analysis were performed. Our results revealed the increased interactions between charged protein and ions weaken C3d–CR2 association, as ionic strengths increase. Moreover, ion strengths have similar effects on antigen-binding site and CR2 binding site. Meanwhile, Ala17 and Gln20 will transform between the activated and non-activated states mediated by His133 and Glu135 at different ion strengths. Our results reveal the origins of the effects of ionic strengths on C3d–CR2 interactions are due to the changes of water, ion occupancies and distributions. This study uncovers the origin of the effect of ionic strength on C3d–CR2 interaction and deepens the understanding of the molecular mechanism of their interaction, which is valuable for the design of vaccines and small molecule inhibitors. [Display omitted] •The solvent occupancies and distributions at antigen-binding site are largely influenced by ionic strengths.•High ionic strengths enhances polar interactions of antigen-binding site and leads to the deviation of Lys291-Pro294 from CR2.•Lys291-Pro294 regulates the interdomain contact region of V-shape structure of CR2.•Ala17 and Gln20 transforms between the activated and non-activated states mediated by His133 and Glu135.