Molecular crowding enhances native state stability and refolding rates of globular proteins

Abstract

The presence of macromolecules in cells geometrically restricts the available space for poplypeptide chains. To study the effects of macromolecular crowding on folding thermodynamics and kinetics, we used an off-lattice model of the all-β-sheet WW domain in the presence of large spherical particles whose interaction with the polypeptide chain is purely repulsive. At all volume fractions, ϕ c , of the crowding agents the stability of the native state is enhanced. Remarkably, the refolding rates, which are larger than the value at ϕ c = 0, increase nonmonotonically as ϕ c increases, reaching a maximum at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\varphi}_{{\mathrm{c}}}={\varphi}_{{\mathrm{c}}}^{*}\end{equation*}\end{document} . At high values of ϕ c , the depletion-induced intramolecular attraction produces compact structures with considerable structure in the denatured state. Changes in native state stability and folding kinetics at ϕ c can be quantitatively mapped onto confinement in a volume-fraction-dependent spherical pore with radius R s ≈ (4π/3ϕ c ) 1/3 R c ( R c is the radius of the crowding particles) as long as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\varphi}_{{\mathrm{c}}}{\leq}{\varphi}_{{\mathrm{c}}}^{*}\end{equation*}\end{document} . We show that the extent of native state stabilization at finite ϕ c is comparable with that in a spherical pore. In both situations, rate enhancement is due to destabilization of the denatured states with respect to ϕ c = 0.