(174v) Development of Transferable Coarse-Grained Models of Amino Acids

Deshmukh, S. A. - Presenter, Virginia Polytechnic Institute and State University
Conway, O., Virginia Tech
An, Y., Virginia Polytechnic Institute and State University
Bejagam, K. K., Virginia Polytechnic Institute and State University
There are twenty standard amino acids that are the structural units of biomolecules and biomaterials such as proteins and peptide amphiphiles (PAs). The goal of this study is to develop accurate transferable coarse-grained (CG) models of those amino acids. Several atoms are represented collectively as a single pseudo-atom or “bead” in CG models, and this can allow the modeling of processes like self-assembly of biomolecules and biomaterials through a reduction in the number of degrees of freedom and a corresponding increase in computational speed. A 2:1 to 4:1 mapping scheme, in which a CG bead is comprised of two to four heavy atoms, respectively, and their associated hydrogens, is used to represent functional groups in the amino acids. The peptide backbone—formed by a condensation reaction between amino acids—is modeled as two beads, while the amino acid side chains are modeled with one to three beads. Each terminus is modeled as one bead. All amino acid side chains and termini are modeled in their neutral forms. The bonded parameters for the CG models were obtained from atomistic distributions from simulations of dipeptides using the CHARMM force-field. Non-bonded parameters were optimized using the particle swarm optimization (PSO) method to reproduce experimental properties (heat of vaporization, surface tension, and density) of analogues of the side chains, termini, and backbone groups of the amino acids. These CG models were used to study the self-assembly pathways and mechanisms of the peptide amphiphile c16-AHL3K3-CO2H in the presence of explicit CG water. Results of our CG MD simulations show good agreement with reported studies.