bioRxiv ScienceSearch

Biology subjects

Eugene I. Shakhnovich

Publications and source records attributed to Eugene I. Shakhnovich.

2 recordsLinked to original sources

An internal disulfide locks a misfolded aggregation-prone intermediate in cataract-linked mutants of human γD-crystallin

Considerable mechanistic insight has been gained into amyloid aggregation; however, a large class of non-amyloid protein aggregates are considered \"amorphous,\" and in most cases little is known about their mechanisms. Amorphous aggregation of {gamma}-crystallins in the eye lens causes a widespread disease of aging, cataract. We combined simulations and experiments to study the mechanism of aggregation of two {gamma}D-crystallin mutants, W42R and W42Q - the former a congenital cataract mutation, and the latter a mimic of age-related oxidative damage. We found that formation of an internal disulfide was necessary and sufficient for aggregation under physiological conditions. Two-chain all-atom simulations predicted that one non-native disulfide in particular, between Cys32 and Cys41, was likely to stabilize an unfolding intermediate prone to intermolecular interactions. Mass spectrometry and mutagenesis experiments confirmed the presence of this bond in the aggregates and its necessity for oxidative aggregation under physiological conditions in vitro. Mining the simulation data linked formation of this disulfide to extrusion of the N-terminal {beta}-hairpin and rearrangement of the native {beta}-sheet topology. Specific binding between the extruded hairpin and a distal {beta}-sheet, in an intermolecular chain reaction similar to domain swapping, is the most probable mechanism of aggregate propagation.

Biophysics

The role of evolutionary selection in the dynamics of protein structure evolution

Homology modeling is a powerful tool for predicting a proteins structure. This approach is successful because proteins whose sequences are only 30% identical still adopt the same structure, while structure similarity rapidly deteriorates beyond the 30% threshold. By studying the divergence of protein structure as sequence evolves in real proteins and in evolutionary simulations, we show that this non-linear sequence-structure relationship emerges as a result of selection for protein folding stability in divergent evolution. Fitness constraints prevent the emergence of unstable protein evolutionary intermediates thereby enforcing evolutionary paths that preserve protein structure despite broad sequence divergence. However on longer time scales, evolution is punctuated by rare events where the fitness barriers obstructing structure evolution are overcome and discovery of new structures occurs. We outline biophysical and evolutionary rationale for broad variation in protein family sizes, prevalence of compact structures among ancient proteins and more rapid structure evolution of proteins with lower packing density.

Biophysics