Isolation, Characterization, and Molecular Modeling of a Rheumatoid Factor from a Hepatitis C Virus Infected Patient with Sjögren's Syndrome

Lee, Yu-Ching; Tsai, Keng-Chang; Leu, Sy-Jye; Wang, Tuan-Jen; Liu, Chia-Yu; Yang, Yi-Yuan

The RFL11 CDR-H3 loop has three more amino acids than the RF61 CDR-H3 loop, and these three amino acids belong to the four amino acids (Thr102, Thr103, Asp104, and Phe105) of RFL11 produced by somatic mutation. H-bonding and hydrophobic and ion interactions are formed between IgG Fc and the four amino acids, among which Asp104 forms a critical strong ion interaction with IgG Fc Arg355. Moreover, Tyr106 and Tyr107 also both contribute to the formation of cation-pi interaction with Arg355. As shown in Table 1 , ion interaction is formed between RF61 and Arg355 of IgG Fc via Asp98 and Asp100c. Thus, Arg355 is a key residue to the IgG Fc epitope. Based on the comparison made according to Table 1 , it is inferred that the RFL11 CDR-H3 loop has a binding affinity to IgG Fc similar to that of the RF61 CDR-H3 loop, but there might be some difference in the Fc epitope. Also, from the structure model, it is observed that the RFL11 CDR-H3 loop forms a finger-like structure extending into the bottom of a deep pocket of IgG Fc, which is different from the ellipse-like structure bound to the IgG Fc formed by RF61. Due to the finger-like structure, the CDR-H3 loops of RFL11 can interact with each other as a dimer and together form interactions with IgG Fc (See Figure 7) , providing a binding affinity to the CDR-H3 loops of RFL11 higher than the RF61-H3 loops. From the binding structure of RFL11 and RF61 with Fc, although a novel epitope was not found, we confirmed that IgG type RF is different from IgM type RF and discovered a different CDR loop, particularly a substantial difference between H2 and H3 paratopes. Our study showed that RFL11 has a stronger binding affinity than RF61, and both the somatic mutation and computational structural biology investigation are in line with the experiments.