COARSE-GRAINED MODELING OF PROTEIN UNFOLDING DYNAMICS.

ABSTRACT: We present a new dynamic elastic network model (DENM) that describes the unfolding process of a force-loaded protein. The protein interaction network and its potentials are constructed based on information of its native-state structure obtained from the Protein Data Bank, with network nodes positioned at the C_α coordinates of the protein backbone. Specifically, to mimic the unfolding process, i.e., to simulate the process of overcoming the local energy barrier on the free energy landscape with force loading, the noncovalent protein network bonds (i.e., hydrogen bonds, salt bridges, hydrophobic contacts, etc.) are broken one-by-one with a certain probability, while the strong covalent bonds along the backbone (i.e., peptide bonds, disulfide bonds, etc.) are kept int

SUBMITTER: Deng M 

PROVIDER: S-EPMC4230303 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature