Binding hot-spots in an antibody–ssDNA interface: a molecular dynamics study

Abstract

Simulating antigen–antibody interactions is essential for elucidating antigen–antibody mechanics. Proteins interactions are vital for elucidating antibody–ssDNA associations in immunology. Therefore, this study investigated the dissociation of the human systemic lupus erythematosus antibody–ssDNA complex structure. Dissociation (i.e. the distance between the center of mass of the ssDNA and the antibody) is also studied using the potential of mean force calculations based on molecular dynamics and the explicit water model. The MM-PBSA method is also used to prove our dissociation simulations. With 605 nanosecond molecular dynamics simulations, the results indicate that the 8 residues (i.e. Gly44 (HCDR2), Asn54 (HCDR2), Arg98 (HCDR3), Tyr100 (HCDR3), Asp101 (HCDR3), Tyr32 (LCDR1), Tyr49 (LCDR2) and Asn50 (LCDR2)), and the five inter-protein molecular hydrogen bonds may profoundly impact the antibody–ssDNA interaction, a finding which may be useful for protein engineering of this antibody–ssDNA structure. Experimental binding affinity of this antibody–ssDNA complex equals 7.00 kcal mol⁻¹. Our dissociation binding affinity is 7.96 ± 0.33 kcal mol⁻¹ and MM-PBSA binding affinity is 9.12 ± 1.65 kcal mol⁻¹, which is close to the experimental value. Additionally, the 8 residues Gly44 (HCDR2), Asn54 (HCDR2), Arg98 (HCDR3), Tyr100 (HCDR3), Asp101 (HCDR3), Tyr32 (LCDR1), Tyr49 (LCDR2) and Asn50 (LCDR2) may play a more significant role in developing bioactive antibody analogues.