Exploring the energy landscape of biopolymers using single molecule force spectroscopy and molecular simulations

Abstract

In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule force experiments, quantitative analyses of measurements employing sound theoretical models and molecular simulations play central role more than any other field. With a brief description of basic theories for force mechanics and molecular simulation technique using self-organized polymer (SOP) model, this chapter will discuss various issues in single molecule force spectroscopy (SMFS) experiments, which include pulling speed dependent unfolding pathway, measurement of energy landscape roughness, the in uence of molecular handles in optical tweezers on measurement and molecular motion, and folding dynamics of biopolymers under force quench condition.

32 pages, 4 figures, Book Chapter in "Simulations in Nanobiotechnology"

References in corpus (8)

• Mechanical control of the directional stepping dynamics of the kinesin motor
• Forced-unfolding and force-quench refolding of RNA hairpins
• Mechanical unfolding of RNA: From hairpins to structures with internal multiloops
• Force Dependent Hopping Rates of RNA Hairpins can be Estimated from Accurate Measurement of the Folding Landscapes
• Refolding dynamics of stretched biopolymers upon force quench
• Stretching Homopolymers
• Protein-mediated DNA Loop Formation and Breakdown in a Fluctuating Environment
• The role of internal chain dynamics on the rupture kinetics of adhesive contacts