Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding

The heterogeneous fast side-chain dynamics of proteins plays crucial roles in molecular recognition and binding. Site-specific NMR experiments quantify these motions by measuring the model-free order parameter (O-axis(2)) on a scale of 0 (most flexible) to 1 (least flexible) for each methyl-containing residue of proteins. Here, we have examined ligand-induced variations in the fast side-chain dynamics and conformational entropy of calmodulin (CaM) using five different CaM-peptide complexes. O-axis(2) of CaM in the ligand-free (O-axis,U(2)) and ligand-bound (O-axis,B(2)) states are calculated from molecular dynamics trajectories and conformational energy surfaces obtained using the adaptive biasing force (ABF) method. Delta O-axis(2) = O-axis,B(2) - O-axis,U(2) follows a Gaussian-like unimodal distribution whose second moment is a potential indicator of the binding affinity of these complexes. The probability for the binding-induced O-axis,U(2) -> O-axis,B(2) transition decreases with increasing magnitude of Delta O-axis(2), indicating that large flexibility changes are improbable for side chains of CaM after ligand binding. A linear correlation established between Delta O-axis(2) and the conformational entropy change of the protein makes possible the determination of the conformational entropy of binding of protein-ligand complexes. The results not only underscore the functional importance of fast side-chain fluctuations but also highlight key motional and thermodynamic correlates of protein-ligand binding.

Automated summary

The study focuses on the fast side-chain dynamics and conformational entropy changes during protein binding, demonstrating that significant flexibility changes are unlikely after ligand binding and establishing a linear correlation between O-axis(2) and conformational entropy changes for protein-ligand complexes.