title: Biofunctionalization and immobilization of a membrane via peptide binding (CR3-1, S2) by a Monte Carlo simulation.
abstract: A coarse-grained computer simulation model is used to study the immobilization of a dynamic tethered membrane (representation of a clay platelet) in a matrix of mobile peptide chains CR3-1: 1Trp-2Pro-3Ser-4Ser-5Tyr-6Leu-7Ser-8Pro-9Ile-10Pro-11Tyr-12Ser and S2: 1His-2Gly-3Ile-4Asn-5Thr-6Thr-7Lys-8Pro-9Phe-10Lys-11Ser-12Val on a cubic lattice. Each residue interacts with the membrane nodes with appropriate interaction and executes their stochastic motion with the Metropolis algorithm. Density profiles, binding energy of each residue, mobility, and targeted structural profile are analyzed as a function of peptide concentration. We find that the binding of peptides S2 is anchored by lysine residues (7Lys, 10Lys) while peptides CR3-1 do not bind to membrane. The membrane slows down as peptides S2 continues to bind leading to its eventual pinning. How fast the immobilization of the membrane occurs depends on peptide concentration. Binding of peptide S2 modulates the morphology of the membrane. The immobilization of membrane occurs faster if peptides S2 are replaced by the homopolymer of lysine ([Lys]12 of the same molecular weight), the strongest binding residue. The surface of membrane can be patterned with somewhat reduced roughness with the homopolymer of lysine than that with peptide S2
authors.affiliation: Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA. ras.pandey@usm.edu
authors.forename: R B
authors.initials: RB
authors.lastname: Pandey
authors.forename: Hendrik
authors.initials: H
authors.lastname: Heinz
authors.forename: Jie
authors.initials: J
authors.lastname: Feng
authors.forename: Barry L
authors.initials: BL
authors.lastname: Farmer
mesh_terms: D000595:Amino Acid Sequence; D002462:Cell Membrane / Q000378:metabolism*; D003198:Computer Simulation; D008239:Lysine / Q000378:metabolism; D008954:Models, Biological; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000378:metabolism*; D011485:Protein Binding
chemical_list: D010455:Peptides; D008239:Lysine