Separating the role of protein restraints and local metal-site interaction chemistry in the thermodynamics of a zinc finger protein.

ABSTRACT: We express the effective Hamiltonian of an ion-binding site in a protein as a combination of the Hamiltonian of the ion-bound site in vacuum and the restraints of the protein on the site. The protein restraints are described by the quadratic elastic network model. The Hamiltonian of the ion-bound site in vacuum is approximated as a generalized Hessian around the minimum energy configuration. The resultant of the two quadratic Hamiltonians is cast into a pure quadratic form. In the canonical ensemble, the quadratic nature of the resultant Hamiltonian allows us to express analytically the excess free energy, enthalpy, and entropy of ion binding to the protein. The analytical expressions allow us to separate the roles of the dynamic restraints imposed by the protein on the binding site and th

SUBMITTER: Dixit PD 

PROVIDER: S-EPMC3177046 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature