Thermodynamics of force-dependent folding and unfolding of small protein and nucleic acid structures

Integr Biol (Camb). 2015 Oct;7(10):1154-60. doi: 10.1039/c5ib00038f. Epub 2015 Mar 24.

Abstract

In this paper, we outline the theoretical framework for understanding the equilibrium force-dependent folding and unfolding transitions of protein domains and small nucleic acid structures, both having small rigid folded structures and highly flexible unfolded polymeric chain conformations. A complete statistical description of the state described by the probability function ρ(ξ)(n,x), is obtained, where n is an index denoting the structural state, and x is the extension of the molecule. ξ denotes an external constraint applied to the molecule, which is either a constant force or a harmonic spring attached to one end of the molecule. The extension probability distribution regardless of the structural state: , the free energy landscape: -kBT ln(ρ(ξ)(x)), and the probability of the states regardless of the extension: , are analyzed using the force-dependent structural transitions of the classic titin I27 domain as an example. The impact of different external constraints is also discussed.

MeSH terms

  • Biomechanical Phenomena
  • Connectin / chemistry
  • Connectin / metabolism
  • Kinetics
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nucleic Acids / chemistry*
  • Nucleic Acids / metabolism
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Tertiary
  • Protein Unfolding
  • Proteins / chemistry*
  • Proteins / metabolism
  • Thermodynamics

Substances

  • Connectin
  • Nucleic Acids
  • Proteins