Crowding effects on the mechanical stability and unfolding pathways of Ubiquitin
| dc.creator | Pincus, David L. | |
| dc.creator | Thirumalai, D. | |
| dc.date | 2008-11-05 | |
| dc.date.accessioned | 2026-07-07T12:23:21Z | |
| dc.date.available | 2026-07-07T12:23:21Z | |
| dc.description | The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we probe the mechanical stability of Ubiquitin (Ub) monomers and trimers ((Ub)$_3$) in the presence of monodisperse spherical crowding agents. Crowding increases the volume fraction ($Φ_c$)-dependent average force ($<f_u(Φ_c)>$), relative to the value at $Φ_c = 0$, needed to unfold Ub and the polyprotein. For a given $Φ_c$, the values of $<f_u(Φ_c)>$ increase as the diameter ($σ_c$) of the crowding particles decreases. The average unfolding force $<f_u(Φ_c)>$ depends on the ratio $\frac{D}{R_g}$, where $D \approx σ_c (\fracπ{6 Φ_c})^{1/3}$ with $R_g$ being the radius of gyration of Ub (or (Ub)$_3$) in the unfolded state. Examination of the unfolding pathways shows that, relative to $Φ_c = 0$, crowding promotes reassociation of ruptured secondary structural elements. Both the nature of the unfolding pathways and $<f_u(Φ_c)>$ for (Ub)$_3$ are altered in the presence of crowding particles with the effect being most dramatic for the subunit that unfolds last. We predict, based on SOP simulations and theoretical arguments, that $<f_u(Φ_c) > \sim Φ_c^{\frac{1}{3ν}}$, where $ν$ is the Flory exponent that describes the unfolded (random coil) state of the protein. | |
| dc.description | 31 pages, 8 figures, 1 table. To be published in the Journal of Physical Chemistry B | |
| dc.identifier | https://arxiv.org/abs/0811.0781 | |
| dc.identifier | http://arxiv.org/abs/0811.0781 | |
| dc.identifier | doi:10.1021/jp807755b | |
| dc.identifier.uri | http://salesiana.dossiersoluciones.com/handle/123456789/213959 | |
| dc.subject | Biomolecules | |
| dc.subject | Soft Condensed Matter | |
| dc.title | Crowding effects on the mechanical stability and unfolding pathways of Ubiquitin | |
| dc.type | text |