Paper Citing NAMD - Abstract
Pandey, R. B.; Kuang, Zhifeng; Farmer, B. L.; Kim, Steve S.; Naik, Rajesh R.
Stability of peptide (P1 and P2) binding to a graphene sheet via an all-atom to all-residue coarse-grained approach
SOFT MATTER, 8:9101-9109, 2012
Peptide binding to a graphene sheet is studied by a coarse-grained approach. All-atom molecular dynamics (MD) is used to assess the adsorption energy (e. g. binding) of each amino acid with graphene. The relative adsorption energy of each residue is normalized to describe its coarse-grained interactions with graphene which is used as an input to a phenomenological interaction in an all-residue coarse-grained (ARCG) representation of the peptide chain. Large scale Monte Carlo (MC) simulations are performed to study the stability of peptides (P1: H-1-S-2-S-3-Y-4-W-5-Y-6-(7)A-F-8-N-9-N-10-K-11-T-12 and P2: E-1-P-2-L-3-(4)Q-L-5-K-6-M-7) binding to a graphene sheet as a function of temperature. A number of local and global physical quantities are analyzed including mobility and substrate-in-contact profiles of each residue, density profiles, root mean square displacement of the center of mass of each peptide and its radius of gyration. We find that P1 has a higher probability of binding to a graphene sheet than P2 supported by both local and global physical quantities. All residues of P1 can bind to the graphene sheet at low temperatures; however, three residues Y-4-W-5-Y-6 seem to anchor it most strongly at higher temperatures, which is consistent with an all-atom MD simulation.
