Agreement between Experimental and Simulated Circular Dichroic Spectra of a Positively Charged Peptide in Aqueous...

Successfully immobilizing functional proteins on inorganic surfaces has long been a challenge to the biophysics and bioengineering communities. This is due, in part, to a lack of understanding of the effect of nonaqueous environments on protein structure from both experimental and computational perspectives. Because most experimental information about protein structure comes from the Protein Data Bank and is collected from an aqueous solvent environment, modern force fields for molecular dynamics (MD) simulations are parameterized against these data. The applicability of such force fields to biomolecules in different environments, including when in contact with surfaces and substrates, must be validated. Here, we present MD folding simulations of a highly charged peptide solvated in water, solvated in a solution of 2:1 t-BuOH/H₂O and bound to the surface of a methyl-terminated self-assembled monolayer (SAM), and compare the structures predicted by these simulations to previously reported circular dichroism spectra. We show quantitative agreement between experiments and simulations of solvent- and surface-induced conformational changes of a positively charged peptide in these three environments. We show further that the surface-bound peptide must fold before chemically reacting with the surface. Finally, we demonstrate that a well-ordered SAM is critical to the folding process. These results will guide further simulations of peptides and proteins in diverse and complex environments.