Thermodynamics and kinetics of protein folding under confinement Export

@article{citeulike:3823328, abstract = {10.1073/pnas.0807742105 Understanding the effects of confinement on protein stability and folding kinetics is important for describing protein folding in the cellular environment. We have investigated the effects of confinement on two structurally distinct proteins as a function of the dimension and characteristic size of the confining boundary. We find that the stabilization of the folded state relative to bulk conditions is quantitatively described by , where the exponent \^{I}³ is \^{a}‰ˆ5/3 independent of the dimension of confinement (cylindrical, planar, or spherical). Moreover, we find that the logarithm of the folding rates also scale as , with deviations only being seen for very small confining geometries, where folding is downhill; for both stability and kinetics, the dominant effect is the change in the free energy of the unfolded state. A secondary effect on the kinetics is a slight destabilization of the transition state by confinement, although the contacts present in the confined transition state are essentially identical to the bulk case. We investigate the effect of confinement on the position-dependent diffusion coefficients () for dynamics along the reaction coordinate (fraction of native contacts). The diffusion coefficients only change in the unfolded state basin, where they are increased because of compaction.}, author = {Mittal, Jeetain and Best, Robert B.}, booktitle = {Proceedings of the National Academy of Sciences}, citeulike-article-id = {3823328}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0807742105}, citeulike-linkout-1 = {http://www.pnas.org/content/105/51/20233.short.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/105/51/20233.short.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19073911}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19073911}, day = {23}, doi = {10.1073/pnas.0807742105}, journal = {Proceedings of the National Academy of Sciences}, keywords = {confinement, crowding, diffusion, folding, protein, simulation}, month = {December}, number = {51}, pages = {20233--20238}, posted-at = {2009-01-20 07:47:58}, priority = {2}, title = {Thermodynamics and kinetics of protein folding under confinement}, url = {http://dx.doi.org/10.1073/pnas.0807742105}, volume = {105}, year = {2008} }

TY - JOUR ID - citeulike:3823328 L3 - citeulike-article-id:3823328 N2 - 10.1073/pnas.0807742105 Understanding the effects of confinement on protein stability and folding kinetics is important for describing protein folding in the cellular environment. We have investigated the effects of confinement on two structurally distinct proteins as a function of the dimension and characteristic size of the confining boundary. We find that the stabilization of the folded state relative to bulk conditions is quantitatively described by , where the exponent γ is ≈5/3 independent of the dimension of confinement (cylindrical, planar, or spherical). Moreover, we find that the logarithm of the folding rates also scale as , with deviations only being seen for very small confining geometries, where folding is downhill; for both stability and kinetics, the dominant effect is the change in the free energy of the unfolded state. A secondary effect on the kinetics is a slight destabilization of the transition state by confinement, although the contacts present in the confined transition state are essentially identical to the bulk case. We investigate the effect of confinement on the position-dependent diffusion coefficients () for dynamics along the reaction coordinate (fraction of native contacts). The diffusion coefficients only change in the unfolded state basin, where they are increased because of compaction. IS - 51 JF - Proceedings of the National Academy of Sciences EP - 20238 TI - Thermodynamics and kinetics of protein folding under confinement VL - 105 T2 - Proceedings of the National Academy of Sciences SP - 20233 KW - confinement KW - crowding KW - diffusion KW - folding KW - protein KW - simulation AU - Mittal, Jeetain AU - Best, Robert PY - 2008/12/23/ UR - http://dx.doi.org/10.1073/pnas.0807742105 ER -