A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory

Abstract

Modeling the structure of natively disordered peptides has proved difficult due to the lack of structural information on these peptides. In this work, we use a novel application of the host-guest method, combining folding theory with experiments, to model the structure of natively disordered polyglutamine peptides. Initially, a minimalist molecular model (CαCβ) of Cl2 is developed with a structurally based potential and captures many of the folding properties of Cl2 determined from experiments. Next, polyglutamine "guest" inserts of increasing length are introduced into the Cl2 "host" model and the polyglutamine is modeled to match the resultant change in Cl2 thermodynamic stability between simulations and experiments. The polyglutamine model that best mimics the experimental changes in Cl2 thermodynamic stability has 1), a β-strand dihedral preference and 2), an attractive energy between polyglutamine atoms 0.75-times the attractive energy between the Cl2 host Go-contacts. When free-energy differences in the Cl2 host-guest system are correctly modeled at varying lengths of polyglutamine guest inserts, the kinetic folding rates and structural perturbation of these Cl2 insert mutants are also correctly captured in simulations without any additional parameter adjustment. In agreement with experiments, the residues showing structural perturbation are located in the immediate vicinity of the loop insert. The simulated polyglutamine loop insert predominantly adopts extended random coil conformations, a structural model consistent with low resolution experimental methods. The agreement between simulation and experimental Cl2 folding rates, Cl2 structural perturbation, and polyglutamine insert structure show that this host-guest method can select a physically realistic model for inserted polyglutamine. If other amyloid peptides can be inserted into stable protein hosts and the stabilities of these host-guest mutants determined, this novel host-guest method may prove useful to determine structural preferences of these intractable but biologically relevant protein fragments.