Elastic netwok models coarse grain proteins into a network of residue beadsconnected by springs. We add dissipative dynamics to this mechanical system byapplying overdamped Langevin equations of motion to normal-mode vibrations ofthe network. In addition, the network is made heterogeneous and softened at theprotein surface by accounting for hydration of the ionized residues. Solvationchanges the network Hessian in two ways. Diagonal solvation terms soften thespring constants and off-diagonal dipole-dipole terms correlate displacementsof the ionized residues. The model is used to formulate the response functionsof the electrostatic potential and electric field appearing in theories ofredox reactions and spectroscopy. We also formulate the dielectric response ofthe protein and find that solvation of the surface ionized residues leads to aslow relaxation peak in the dielectric loss spectrum, about two orders ofmagnitude slower than the main peak of protein relaxation. Finally, thesolvated network is used to formulate the allosteric response of the protein toion binding. The global thermodynamics of ion binding is not strongly affectedby the network solvation, but it dramatically enhances conformational changesin response to placing a charge at the active site of the protein.
展开▼
