Extraction of Free Energy Parameters from Dynamic Single-Molecule Force-Extension Measurements

Abstract

Dynamic single molecule force spectroscopy (SMFS) provides a powerful approach for probing the free energy landscape that governs how molecules fold into complex 3D architectures, bind to each other, and undergo conformational transitions. In SMFS experiments, a gradually increasing force is applied to a single molecule or complex and the resulting force-extension behavior is recorded until rupture of the system. The analysis of force-extension measurements to recover the intrinsic energy landscape of the system is an outstanding challenge in SMFS. In this talk, I will describe the development of new theoretical models for extracting the height and location of activation energy barriers and their intrinsic transition rates from SMFS measurements [1, 2]. These models improve on the current state-of-the-art by accounting for both the finite stiffness of the pulling device and the non-linear stretching behavior of the molecular handles connecting the device to the system under study. I will end the talk by reporting the results of steered molecular dynamics simulations in which we successfully applied our theoretical models to extract the free energy parameters of representative ligand-receptor unbinding transitions.