Understanding the Effects of Confinement on Proteins

Eric Jakobsson, University of Illinois at Urbana-Champaign

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Proteins are essential components of living cells. Understanding structure-function relationships of proteins is a major goal of basic biology, biomedicine, and biotechnology. Understanding has been limited by the ability replicate the environment of the cellular interior. For soluble proteins—which constitute the majority of proteins—dynamic simulations, structure determinations, and detailed kinetic characterization are done in aqueous environment, essentially assuming that the molecules are in a bath of infinite size. Our collaborator Jie Sun is pioneering in experiments that show the effects on protein reaction kinetics of being confined in silica compartments that mimic confinement in living cells. We propose to complement these experimental studies with simulations on the proteins confined in silica-bounded cavities. Blue Waters is essential for this work because we must sample systematic deviations of confined protein structures from their experimentally determined value in bulk, thus requiring much more extensive conformational sampling than most molecular dynamics simulations.