title: Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments.
abstract: We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (P(fold)=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that P(fold) is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles.
authors.affiliation: School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Greg
authors.initials: G
authors.lastname: Morrison
authors.forename: Changbong
authors.initials: C
authors.lastname: Hyeon
authors.forename: Michael
authors.initials: M
authors.lastname: Hinczewski
authors.forename: D
authors.initials: D
authors.lastname: Thirumalai
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D055029:Inverted Repeat Sequences; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry; D013718:Tensile Strength
chemical_list: D001704:Biopolymers; D012313:RNA