Enhanced Sampling Reveals Metastable Conformations Driving K417N-Mediated Class I Antibody Escape.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Emerging SARS-CoV-2 variants possess mutations, such as in the receptor-binding domain (RBD), that reduce neutralizing antibody (nAb) effectiveness and promote immune evasion.
• Characterizing the impact of single-point mutations on antibody binding is difficult due to weak affinities and challenges in conventional structural analysis.

Purpose of the Study:

• To investigate the structural and dynamic effects of the K417N mutation on the binding of a Class I antibody (NT-193) to the SARS-CoV-2 RBD.
• To understand the molecular mechanisms by which mutations drive antibody immune evasion.

Main Methods:

• Utilized enhanced sampling molecular dynamics (MD) simulations with generalized replica exchange with solute tempering (gREST).
• Performed surface plasmon resonance (SPR) experiments to validate simulation findings.

Main Results:

• The K417N mutation significantly alters the transient metastable states of antibody-RBD interaction, despite similar stable binding conformations.
• The substitution of lysine with asparagine disrupts crucial heavy chain interactions in metastable states, leading to faster antibody dissociation.
• SPR experiments confirmed a significantly increased dissociation rate and reduced binding affinity for the K417N mutant.

Conclusions:

• Capturing transient and metastable conformations is crucial for understanding mutation-driven immune evasion.
• The gREST method effectively reveals insights into weakly interacting antibody-antigen complexes.
• Findings facilitate the rational design of next-generation antibody therapeutics to overcome viral immune escape.