Distinction in Binding of Peptides (P2E) and Its Mutations (P2G, P2Q) to a Graphene Sheet via a Hierarchical Coarse-Grained Monte Carlo Simulation
Document Type
Article
Publication Date
10-28-2013
Department
Physics and Astronomy
School
Mathematics and Natural Sciences
Abstract
A hierarchical coarse-grained approach is used to study the binding of peptides (P2E: (1)E(2)P(3)L(4)Q(5)L(6)K(7)M) and variants (P2G: (1)G(2)P(3)L(4)Q(5)L(6)K(7)M and P2Q: (1)Q(2)L(3)P(4)M(5)E(6)K(7)L) with a graphene sheet. Simulation-based residue-substrate and hydropathy index-based residue-residue interaction is used as input to a phenomenological interaction potential for peptide chains to execute the stochastic motion with a graphene sheet at the center of a box. Large-scale Monte Carlo simulations are performed at a range (low to high) of temperatures to identify peptides binding with the graphene sheet with a constant peptide concentration (C-p = 0.01). A number of local (energy, mobility, and substrate contact profiles) and global (density profiles, mean square displacement of the center of mass of a peptide and its radius of gyration) physical quantities are examined to monitor the patterns. We find that each peptide can bind to a graphene sheet at low temperatures but the residues that can anchor their binding vary among these three peptides. For example, P2E is anchored by E-1, (4)Q, and K-6, P2Q by (1)Q, E-5, and K-6, and P2G by nearly all its residues with about the same strength except (1)G and P-2. The site-specific binding is reflected in the thermal response of the radius of gyration of the peptides. Despite the lack of a large difference in binding patterns, a systematic variation in radius of gyration and surface binding profile with the temperature reveals the distinction in their binding: the probability of P2E binding is the highest and that of P2G is the lowest. (C) 2013 AIP Publishing LLC.
Publication Title
Journal of Chemical Physics
Volume
139
Issue
16
Recommended Citation
Pandey, R. B.,
Farmer, B. L.
(2013). Distinction in Binding of Peptides (P2E) and Its Mutations (P2G, P2Q) to a Graphene Sheet via a Hierarchical Coarse-Grained Monte Carlo Simulation. Journal of Chemical Physics, 139(16).
Available at: https://aquila.usm.edu/fac_pubs/7950