Assembly of heteropolymers via a network of reaction coordinates.

Abstract

In biochemistry, heteropolymers encoding biological information are assembled out of equilibrium by sequentially incorporating available monomers found in the environment. Current models of polymerization treat monomer incorporation as a sequence of discrete chemical reactions between intermediate metastable states. In this paper, we use ideas from reaction rate theory and describe nonequilibrium assembly of a heteropolymer via a continuous reaction coordinate. Our approach allows for estimating the copy error and incorporation speed from the Gibbs free energy landscape of the process. We apply our theory to several examples from a simple reaction characterized by a free energy barrier to more complex cases incorporating error correction mechanisms, such as kinetic proofreading.