Understanding the change in calcium ion-binding, protein dynamics, and hydration behavior from the wild type for two pathogenic mutants (D3V and G34R) of troponin-C: molecular dynamics simulation and network analysis

The protein Troponin-C is an important player in muscle contraction, and mutations in Cardiac Troponin-C (cTnC) have been associated with inherited cardiomyopathies. Till now, eight mutants of the N-domain of cTnC have been listed in the ClinVar database as pathogenic or likely pathogenic. Understanding the molecular mechanisms of these mutations is crucial for mitigating their effects. Previous work studied mutations A8V, A31S, and I4M and found that changes in the conformational landscape are a key feature of these mutations. In the current work, our focus is on two mutations, D3V and G34R, the only ones out of the eight mentioned that undergo a change of charge on mutation. We have performed molecular dynamics simulation and network analysis to calculate binding affinity between Ca2+ and mutants vis-à-vis the wild type, the change of Ca2+ coordination shell, the effect of water, protein dynamics, and the communication path from the mutation site to the binding site. Our findings show that both electrostatics and the location of the mutation are the key factors for the difference between WT and the two mutants. D3V, in a disordered region, disrupts long-range allostery through electrostatic and hydration changes, whereas G34R, near the binding site, induces local electrostatic and structural perturbations. The changed conformational landscape, as found for the previously studied mutants, is a general feature for these two mutations also; however, specific effects found here illustrate the diversity present in different mutants.