Exploring and Engineering the Conformational Landscape of Calmodulin through Specific Interactions

Abstract

Conformational fluctuations often play paramount role in the function and activity of proteins. Calmodulin (CaM) is a calcium sensing protein that shows significant conformational flexibility on going from a ligand-free open state to a ligand-bound closed state. By employing large-scale equilibrium molecular dynamics simulations and free energy calculations, we have shown that apo CaM frequently visits a state that is neither fully open nor fully closed and referred to as half-open half-closed (HOHC) state. Such states are functionally relevant as they structurally resemble a ligand-bound closed state. Here, we have envisaged that the inherent conformational dynamics of CaM is primarily triggered by a dual salt bridge interaction between the glutamates and lysine at two different domains (N- and C-terminal domains) of the protein. Upon abolition of the dual salt bridge interaction, conformational dynamics is restricted and centered only near the open state. When a cation−π interaction is introduced while replacing the dual salt bridge interaction, the HOHC state tends to reappear as a stable state. Since salt bridge and cation−π interactions are frequently encountered in the protein dynasty, our work may illuminate an interesting direction toward controlling the conformational landscape of proteins through the modulation of minimal specific interactions.

Inter-Domain Repulsion of Dumbbell-Shaped Calmodulin during Electrospray Ionization Revealed by Molecular Dynamics Simulations

“… During the early simulation, all Cl – had been ejected out, and the decreased droplet size allowed the net charge of the protein to be less efficiently projected onto the droplet surface. , Accordingly, the mutual repulsion of the two highly charged domains stretched the flexible linker, and thus the protein structure extended, finally leading to the DRM behavior (Figure A). The effect of the repulsion on the protein structure could be revealed by the distance fluctuation of salt bridges (D93-R90, E47-K75, D87-K94, and E78-K75) more intuitively on the atomic scale, which were forced by electrostatic interactions and played a key role in maintaining the structure of CAM (Figure B, line in red). − We noted that in the absence of Ca 2+ , the distance of the salt bridge formed on the linker all increased when droplet splitting occurred (∼27 ns), and residues moved apart from each other eventually (the inset in Figure B), indicating that these salt bridges underwent dissociation. These dissociation events promoted the unwinding of the helix linker, and thus the protein unfolded.…”

Role of the Residue Q1919 in Increasing Kinase Activity of G2019S LRRK2 Kinase: A Computational Study

“…AMBER 18 software package provides the facility to perform umbrella sampling in GPU version and also, this method has its technical advantage of parallel efficiency. Distance between two particular atoms was considered as a collective variable (CV) [37] . Umbrella windows were kept 0.1Å apart, and a force constant of 100 kcal/mol/Å 2 (restraint potential) was used in these analyses.…”

“…Distance between two particular atoms was considered as a collective variable (CV). [37] Umbrella windows were kept 0.1Å apart, and a force constant of 100 kcal/ mol/Å 2 (restraint potential) was used in these analyses. Each window for all the systems was equilibrated (NPT) for 2 ns and for each system two different production duration run were performed (3 and 5 ns) at 300 K temperature and 1 atm pressure.…”

Comparative study of the unbinding process of some HTLV-1 protease inhibitors using unbiased molecular dynamics simulations

“…Therefore, besides the importance of one particular drug’s binding affinity to a target protein in the traditional drug design, the binding and unbinding processes and the residence time of the compound that interacts with the protein in each intermediate state are just as important. So by a complete understanding of the unbinding mechanism, we can uncover the key elements in the protein-ligand complex interactions [ 18 ], ligand flexibility, and solvation effects that are more critical in the rational drug design. The vital information will ultimately appear in a scenario with fully atomistic details [ 19 ].…”