Analysis of the dynamical flexibility of bis-peptide nanostructures

We present an approach to predict the overall structure and flexibility of bis-peptide nanostructures from electron spin resonance (ESR) distance measurements. These molecules are composed of conformationally restricted monomers, and results on a series of bis-peptide oligomers containing four to eight monomers are presented. On the basis of molecular dynamics (MD), a joint-stiff segment model is generated to represent the bis-peptide backbones. A scheme is established to exploit information on end-to-end distance distribution functions obtained by ESR to optimize the force fields used in the joint-stiff segment model. The model provides end-to-end distribution functions for the oligomers that better fit the ESR results than those originally obtained from MD simulations. The results also provide information on the distribution of orientations of a monomer with respect to the preceding monomer. An optimized orientational angle of γγ₀ was -21.06°. The other angles were consistent with MD predictions. The optimized force constants of k_α = 2.144 kcal/(mol· rad²), k _β = 3.245 kcal/(mol·rad²), k_γ = 2.876 kcal/(mol·rad²), and k_ββ = 3.041 kcal/(mol·rad²) were found. Information of these orientational parameters enhances our ability to predict the shapes and flexibility of new oligomers constructed using an arbitrary number of this monomer.