Nonexponential kinetics captured in sequential unfolding of polyproteins over a range of loads

Einat Chetrit; Sabita Sharma; Uri Maayan; Maya Georgia Pelah; Ziv Klausner; Ionel Popa; Ronen Berkovich

doi:10.1016/j.crstbi.2022.04.003

Nonexponential kinetics captured in sequential unfolding of polyproteins over a range of loads

Curr Res Struct Biol. 2022 Apr 28:4:106-117. doi: 10.1016/j.crstbi.2022.04.003. eCollection 2022.

Authors

Einat Chetrit¹, Sabita Sharma², Uri Maayan¹, Maya Georgia Pelah¹, Ziv Klausner³, Ionel Popa², Ronen Berkovich^{1

4}

Affiliations

¹ Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
² Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA.
³ Department of Applied Mathematics, Israel Institute for Biological Research, P.O. Box 19, Ness-Ziona, 7410001, Israel.
⁴ The Ilze Katz Institute for Nanoscience and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.

Abstract

While performing under mechanical loads in vivo, polyproteins are vitally involved in cellular mechanisms such as regulation of tissue elasticity and mechano-transduction by unfolding their comprising domains and extending them. It is widely thought that the process of sequential unfolding of polyproteins follows an exponential kinetics as the individual unfolding events exhibit identical and identically distributed (iid) Poisson behavior. However, it was shown that under high loads, the sequential unfolding kinetics displays nonexponential kinetics that alludes to aging by a subdiffusion process. Statistical order analysis of this kinetics indicated that the individual unfolding events are not iid, and cannot be defined as a Poisson (memoryless) process. Based on numerical simulations it was argued that this behavior becomes less pronounced with lowering the load, therefore it is to be expected that polyproteins unfolding under lower forces will follow a Poisson behavior. This expectation serves as the motivation of the current study, in which we investigate the effect of force lowering on the unfolding kinetics of Poly-L₈ under varying loads, specifically high (150, 100 pN) and moderate-low (45, 30, 20 pN) forces. We found that a hierarchy among the unfolding events still exists even under low loads, again resulting in nonexponential behavior. We observe that analyzing the dwell-time distributions with stretched-exponentials and power laws give rise to different phenomenological trends. Using statistical order analysis, we demonstrated that even under the lowest load, the sequential unfolding cannot be considered as iid, in accord with the power law distribution. Additional free energy analysis revealed the contribution of the unfolded segments elasticity that scales with the force on the overall one-dimensional contour of the energy landscape, but more importantly, it discloses the hierarchy within the activation barriers during sequential unfolding that account for the observed nonexponentiality.

Keywords: Correlations; Energy landscape; Nonexponential kinetics; Polyprotein; Single-molecule force-spectroscopy.