title: Helix/coil nucleation: a local response to global demands.
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.
authors: Department of Physics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA.
authors: Oleg K
authors: OK
authors: Vorov
authors: Dennis R
authors: DR
authors: Livesay
authors: Donald J
authors: DJ
authors: Jacobs
mesh_terms: D001696:Biomechanical Phenomena; D019277:Entropy; D006358:Hot Temperature; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D010455:Peptides; D011506:Proteins