Protein denaturation in wet nanoporous silica gels: Effect of caging and crowding on the dynamics of GFPmut2

Proteins encapsulated in wet, nanoporous silica gels usually maintain their structural and functional properties. However, excluded-volume effects and the perturbation of water structure inside the pores of the gel may influence the kinetics of conformational transitions and the thermodynamics of functionally relevant conformational states. We investigated the unfolding of a mutant of GFP, GFPmut2, in wet nanoporous silica gels. Protein molecules are individually caged in the pores of the gel, avoiding protein aggregation and reproducing some of the effects exerted by molecular crowding and confinement in the cellular environment. Encapsulation in silica gels results in the alteration of the equilibrium distribution of native conformations, so that at least two alternative substates of the protein, spectrally undistinguishable in bulk studies, are significantly populated in the absence of denaturant. The evidence of an altered conformational distribution upon caging indicates that studies in dilute solution can miss functionally relevant structural and dynamic properties, highlighting the importance to carry out experiments under conditions that mimic the intracellular milieu