Stretching Biomolecules

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Biomolecular self-assembly is the complicated processes characterized by broad and hierarchical structure of energy, length, and time scales. Various experimental tools have, for decades, been used to understand the principles governing the dynamics of biomolecular systems.
The recent advent of single molecule force experiments has expanded our perspective on the energetics of biomolecules, explicitly showing the diverse traces of the individual molecules undergoing heterogeneous processes.

Based on theoretical arguments and Langevin dynamics simulations of coarse-grained models, I suggest that the following aspects of biomolecules can be elucidated through the force experiments. (1) The energy landscape roughness can be directly measured if the force experiment is performed in varying temperature. (2) The diverse nature of biomolecular energetics, reflecting the underlying complexity of energy landscape, manifests itself when the molecule is subject to various conditions. As a simple example, thermodynamic and kinetic properties of two-state folding RNA hairpins are investigated at varying temperature and force. We show the thermal and the force induced unfolding/refolding dynamics are vastly different. (3) The free energy landscape of a molecule deforms its terrain differently depending on the nature of external control variable. Force plays a different role from temperature when it is exerted on the molecule. The explicit computations and comparisons of free energy profiles along the reaction coordinate find a Hammond behavior in force but not in temperature. (4) Native topology and polymeric nature of biomolecule determines the force-induced unfolding pathway. (5) There exist pulling speed-dependent unfolding pathways in biomolecules if the molecule consists of multiple subdomains.

When combined with theory, single molecule force experiments can unravel the rich nature of biomolecular free energy landscape. All of the theoretical predictions made in the present work are amenable to the future experiments.