title: Ribosome exit tunnel can entropically stabilize alpha-helices.
abstract: Several experiments have suggested that newly synthesized polypeptide chains can adopt helical structures deep within the ribosome exit tunnel. We hypothesize that confinement in the roughly cylindrical tunnel can entropically stabilize alpha-helices. The hypothesis is validated by using theory and simulations of coarse-grained off-lattice models. The model helix, which is unstable in the bulk, is stabilized in a cylindrical cavity provided the diameter (D) of the cylinder exceeds a critical value D*. When D < D* both the helical content and the helix-coil transition temperature (T(f)) decrease abruptly. Surprisingly, we find that the stability of the alpha-helix depends on the number (N) of amino acid residues. Entropic stabilization, as measured by changes in T(f), increases nonlinearly as N increases. The simulation results are in quantitative agreement with a standard helix-coil theory that takes into account entropy cost of confining a polypeptide chain in a cylinder. The results of this work are in qualitative accord with most of the findings of a recent experiment in which N-dependent ribosome-induced helix stabilization of transmembrane sequences was measured by fluorescence resonance energy transfer.
authors.affiliation: Department of Chemical Physics, Weizmann Institute of Science, POB 26, Rehovot 76100, Israel.
authors.forename: Guy
authors.initials: G
authors.lastname: Ziv
authors.forename: Gilad
authors.initials: G
authors.lastname: Haran
authors.forename: D
authors.initials: D
authors.lastname: Thirumalai
mesh_terms: D003198:Computer Simulation; D019277:Entropy; D031541:Fluorescence Resonance Energy Transfer; D006860:Hydrogen Bonding; D015233:Models, Statistical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012270:Ribosomes / Q000737:chemistry* / Q000648:ultrastructure; D013816:Thermodynamics
chemical_list: D010455:Peptides