Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation Article

Gerstman, BS. (2013). Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation . Methods in molecular biology (Clifton, N.J.), 932 191-204. 10.1007/978-1-62703-65-6_12

cited authors

  • Gerstman, BS

abstract

  • The dynamics of protein folding are complicated because of the various types of amino acid interactions that create secondary, supersecondary, and tertiary interactions. Computational modeling can be used to simulate the biophysical and biochemical interactions that determine protein folding. Effective folding to a desired protein con fi guration requires a compromise between speed, stability, and speci fi city. If the primary sequence of amino acids emphasizes one of these characteristics, the others might suffer and the folding process may not be optimized. We provide an example of a model peptide whose primary sequence produces a highly stable supersecondary two-helix bundle structure, but at the expense of lower speed and speci fi city of the folding process. We show how computational simulations can be used to discover the con fi guration of the kinetic trap that causes the degradation in the speed and speci fi city of folding. We also show how amino acid sequences can be engineered by speci fi c substitutions to optimize the folding to the desired supersecondary structure. © Springer Science+Business Media New York 2013.

authors

publication date

  • January 1, 2013

published in

Digital Object Identifier (DOI)

start page

  • 191

end page

  • 204

volume

  • 932