Transferable coarse-grained potential for de novo protein folding and design.

ABSTRACT: Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here we provide evidence of how a novel parametrization of the Caterpillar model may be used for both quantitative protein design and folding. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences require further experimental testing. For an independent set of proteins, previously used as benchmark, the correct folded structure of both the designed and the natural sequences is also demonstrated. The equilibrium folding properties are characterized by free energy calculations.

SUBMITTER: Coluzza I 

PROVIDER: S-EPMC4249799 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature