Journal of Physical Chemistry B, Vol.118, No.24, 6380-6392, 2014
Multistage Unfolding of an SH3 Domain: An Initial Urea-Filled Dry Molten Globule Precedes a Wet Molten Globule with Non-Native Structure
The unfolding of the SH3 domain of the P13 kinase in aqueous urea has been studied using a synergistic experiment simulation approach. The experimental observation of a transient wet molten globule intermediate, I-U, with an unusual non-native burial of the sole Trp residue, W53, provides the benchmark for the unfolding simulations performed (eight in total, each at least 0.5 mu s long). The simulations reveal that the partially unfolded I-U ensemble is preceded by an early native-like molten globule intermediate ensemble I*. In the very initial stage of unfolding, dry globule conformations with the protein core filled with urea instead of water are transiently observed within the I* ensemble. Water penetration into the urea-filled core of dry globule conformations is frequently accompanied by very transient burial of W53. Later during gradual unfolding W53 is seen to again become transiently buried in the I-U ensemble for a much longer time. In the structurally heterogeneous I-U ensemble, conformational flexibility of the C-terminal beta-strands enables W53 burial by the formation of non-native, tertiary contacts with hydrophobic residues, which could serve to protect the protein from aggregation during unfolding.