Free energy simulations are reported for the N31LD mutation, both in the HyHEL-10-HEL antibody-lysozyme complex and in the unliganded antibody, using the thermodynamic-cycle perturbation method. The present study suggests that the mutation would change the free energy of binding of the complex by -5.6 kcal/mol (unrestrained free energy simulations), by -0.5 kcal/mol (free energy simulations with a restrained backbone) and by 1.8 kcal/mol (Poisson-Boltzmann calculations, which also use a restrained geometry model). A detailed structural analysis helps in estimating the contributions from various residues and regions of the system. Enhanced recognition of HEL by the mutant HyHEL-10 would arise from the combination of thermodynamically more favorable conformational changes of the CDR loops upon association and subsequent charge pairing with Lys96 in the antigen.
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