Low Force Unfolding of a Single-Domain Protein by Parallel Pathways

J Phys Chem B. 2021 Feb 25;125(7):1799-1805. doi: 10.1021/acs.jpcb.0c11308. Epub 2021 Feb 10.

Abstract

Deviations from linearity in the dependence of the logarithm of protein unfolding rates, log ku(f), as a function of mechanical force, f, measurable in single molecule experiments, can arise for many reasons. In particular, upward curvature in log ku(f) as a function of f implies that the underlying energy landscape must be multidimensional with the possibility that unfolding ensues by parallel pathways. Here, simulations using the SOP-SC model of a wild type β-sandwich protein and several mutants, with immunoglobulin folds, show upward curvature in the unfolding kinetics. There are substantial changes in the structures of the transition state ensembles as the force is increased, signaling a switch in the unfolding pathways. Our results, when combined with previous theoretical and experimental studies, show that parallel unfolding of structurally unrelated single domain proteins can be determined from the dependence of log ku(f) as a function of force (or log ku[C] where [C] is the denaturant concentration).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Kinetics
  • Protein Denaturation
  • Protein Folding
  • Protein Unfolding*
  • Proteins* / genetics

Substances

  • Proteins