Helix/coil nucleation: a local response to global demands

Biophys J. 2009 Dec 2;97(11):3000-9. doi: 10.1016/j.bpj.2009.09.013.

Abstract

A complete description of protein structure and function must include a proper treatment of mechanisms that lead to cooperativity. The helix/coil transition serves as a simple example of a cooperative folding process, commonly described by a nucleation-propagation mechanism. The prevalent view is that coil structure must first form a short segment of helix in a localized region despite paying a free energy cost (nucleation). Afterward, helical structure propagates outward from the nucleation site. Both processes entail enthalpy-entropy compensation that derives from the loss in conformational entropy on helix formation with concomitant gain in favorable interactions. Nucleation-propagation models inherently assume that cooperativity arises from a sequential series of local events. An alternative distance constraint model asserts there is a direct link between available degrees of freedom and cooperativity through the nonadditivity in conformational entropy. That is, helix nucleation is a concerted manifestation of rigidity propagating through atomic structure. The link between network rigidity and nonadditivity of conformational entropy is shown in this study by solving the distance constraint model using a simple global constraint counting approximation. Cooperativity arises from competition between excess and deficiency in available degrees of freedom in the coil and helix states respectively.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biomechanical Phenomena
  • Entropy
  • Hot Temperature
  • Models, Molecular
  • Peptides / chemistry
  • Peptides / metabolism
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Proteins / metabolism

Substances

  • Peptides
  • Proteins