Rational Protein Design via Structure-Energetics-Function Relationships in the Photoactive Yellow Protein (PYP) Model System

Abstract

Rational protein design uses biophysical principles to inform the generation of new, purpose-built proteins. However, this methodology is hampered by our limited understanding of these biophysical principles relating a protein's structure to its function. In an initial attempt at using structure-energetics-function relationships to rationally design protein function, we recently developed a model that guides qualitative suggestions for engineering light-activated dissociation of split GFPs [1]. We analyzed the potential energy surface of the photodissociation reaction coordinate to identify critical energetics features like barriers and population branching ratios, which can be tuned to increase the photoswitching quantum yield and decrease the fluorescence quantum yield. To develop this structure-energetics-function design methodology further, we are using QM/MM non-adiabatic dynamics studies to predict the effects of mutating key residues in the PYP chromophore environment on observable photoactivated processes. These predictions will then be evaluated by comparisons to spectroscopic measurements.