A fast algorithm to estimate the binding free energy of peptides on solid surfaces

Bongwe Ngwenyama

Biomineralization is the production of inorganic composites by organisms. These inorganic composites are usually hierarchical structures such as shells, bones and teeth. The properties of these inorganic structures including morphology are controlled by certain proteins that have the ability to bind to the solid. These solid binding peptides(SBPs) have been harnessed and used in the production of inorganic nanomaterials which have a wide range of uses including drug delivery. The binding free energy of SBPs to the inorganic surface is an important factor in determining which peptides to use in biomineralization. Therefore, the mining of SBPs has been experimentally time consuming and computational methods such as biased sampling are computationally expensive. In this research, we aim to introduce a new algorithm of calculating the binding free energy of SBPs by establishing that : the binding free energy of a polypeptide chain can be estimated from a linear combination of the free energy contribution of each residue at its equilibrium positions. Plain molecular dynamics simulations of Car9 (a 12-amino acid residue peptide) were combined with the binding free energies of individual amino acids obtained from meta dynamics studies to speed up the calculation of the binding free energy of Car9 to quartz. Quartz is a form of silica that is an important inorganic material whose nanostructures are widely utilized in materials science.

• Bongwe Ngwenyama is junior chemistry major with an emphasis in health sciences. In addition to being part of the Honors College, Bongwe is a member of the Student Alumni Association and a student worker at the Admissions Office. She completed this research as part of a National Science Foundation Research Experience for Undergraduates during the summer of 2021.