Molecular crowding enhances native state stability and refolding rates of globular proteins.
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-beta-sheet WW domain in the presence of large spherical particles whose interaction with the polypeptide chain is purely repulsive. At all volume fractions, phi(c), of the crowding agents the stability of the native state is enhanced. Remarkably, the refolding rates, which are larger than the value at phi(c) = 0, increase nonmonotonically as phi(c) increases, reaching a maximum at phi(c)=phi(c)(*). At high values of phi(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 phi(c) can be quantitatively mapped onto confinement in a volume-fraction-dependent spherical pore with radius R(s) approximately (4pi/3phi(c))(1/3) R(c) (R(c) is the radius of the crowding particles) as long as phi(c)< or =phi(c)(*). We show that the extent of native state stabilization at finite phi(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 phi(c) = 0.
Cheung
Margaret S
MS
Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
Klimov
Dmitri
D
Thirumalai
D
D
D003198:Computer Simulation; D007700:Kinetics; D046911:Macromolecular Substances / Q000378:metabolism*; D008863:Microspheres; D008958:Models, Molecular; D010455:Peptides / Q000378:metabolism*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
D046911:Macromolecular Substances; D010455:Peptides