Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16

• Published in: Scientific reports 2019-12, Vol.9 (1), p.19840-9, Article 19840
• Main Authors: Kondo, Hiroko X., Kiribayashi, Ryo, Kuroda, Daisuke, Kohda, Jiro, Kugimiya, Akimitsu, Nakano, Yasuhisa, Tsumoto, Kouhei, Takano, Yu
• Format: Article
• Language: English
• Subjects: 119/118; 631/45/56; 631/57/2266; 639/638/563/981; 82/1; Amino Acid Sequence; Antibodies, Neutralizing - genetics; Antibodies, Neutralizing - immunology; Antibodies, Neutralizing - metabolism; Antigens; Antigens - genetics; Antigens - immunology; Antigens - metabolism; Binding Sites, Antibody - genetics; Complementarity; Complementarity Determining Regions - genetics; Complementarity Determining Regions - immunology; Complementarity Determining Regions - metabolism; Crystal structure; Crystallography, X-Ray; HIV; HIV Antibodies - chemistry; HIV Antibodies - immunology; HIV Antibodies - metabolism; HIV Infections - immunology; HIV Infections - metabolism; HIV Infections - virology; HIV-1 - genetics; HIV-1 - immunology; HIV-1 - physiology; Human immunodeficiency virus; Humanities and Social Sciences; Humans; Immunoglobulin Fab Fragments - chemistry; Immunoglobulin Fab Fragments - immunology; Immunoglobulin Fab Fragments - metabolism; Molecular Dynamics Simulation; multidisciplinary; Mutation; Neutralization; Protein Conformation; Rigidity; Science; Science (multidisciplinary)
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-56154-y

PG16 is a broadly neutralizing antibody to the human immunodeficiency virus (HIV). A crystal structure of PG16 revealed that the unusually long 28-residue complementarity determining region (CDR) H3 forms a unique subdomain, referred to as a “hammerhead”, that directly contacts the antigen. The hammerhead apparently governs the function of PG16 while a previous experimental assay showed that the mutation of Tyr H100Q to Ala, which does not directly contact the antigen, decreased the neutralization ability of PG16. However, the molecular mechanism by which a remote mutation from the hammerhead or contact paratope affects the neutralization potency has remained unclear. Here, we performed molecular dynamics simulations of the wild-type and variants (Tyr H100Q to Ala, and Tyr H100Q to Phe) of PG16, to clarify the effects of these mutations on the dynamics of CDR-H3. Our simulations revealed that the structural rigidity of the CDR-H3 in PG16 is attributable to the hydrogen bond interaction between Tyr H100Q and Pro H99 , as well as the steric support by Tyr H100Q . The loss of both interactions increases the intrinsic fluctuations of the CDR-H3 in PG16, leading to a conformational transition of CDR-H3 toward an inactive state.