Topography of the free-energy landscape probed via mechanical unfolding of proteins

Serdal Kirmizialtin, Lei Huang, Dmitrii E. Makarov

Research output: Contribution to journalArticle

Abstract

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G (z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G (z) -fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G (z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.

Original languageEnglish (US)
Article number234915
JournalJournal of Chemical Physics
Volume122
Issue number23
DOIs
StatePublished - Jun 15 2005

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Topography
Free energy
topography
free energy
proteins
Stretching
Proteins
chemical reactions
Trajectories
trajectories
Polyproteins
Denaturation
biopolymer denaturation
Experiments
pulling
Ubiquitin
Chemical reactions
Molecules
estimates
profiles

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Topography of the free-energy landscape probed via mechanical unfolding of proteins. / Kirmizialtin, Serdal; Huang, Lei; Makarov, Dmitrii E.

In: Journal of Chemical Physics, Vol. 122, No. 23, 234915, 15.06.2005.

Research output: Contribution to journalArticle

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