title: Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach.
abstract: Binding of a solvated peptide A1 ((1)E (2)P (3)L (4)Q (5)L (6)K (7)M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.g., the extent of binding within a temperature range) and qualitative similarities are observed in results from three simulated potentials. Differences in variations of both local and global physical quantities suggest a need for such analysis with multiple inputs in assessing the reliability of both quantitative and qualitative observations. While all three potentials indicate binding at low T and unbinding at high T, the extent of binding of peptide with the temperature differs. Unlike un-solvated peptides (with little variation in binding among residues), solvation accentuates the differences in residue binding. As a result the binding of solvated peptide at low temperatures is found to be anchored by three residues, (1)E, (4)Q, and (6)K (different from that with the un-solvated peptide). Binding to unbinding transition can be described by the variation of the transverse (with respect to graphene sheet) component of the radius of gyration of the peptide (a potential order parameter) as a function of temperature.
authors.affiliation: Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406-0001, USA.
authors.forename: Somayyeh
authors.initials: S
authors.lastname: Sheikholeslami
authors.affiliation: Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406-0001, USA.
authors.forename: R B
authors.initials: RB
authors.lastname: Pandey
authors.affiliation: Thunder Bay Regional Research Institute and Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada.
authors.forename: Nadiya
authors.initials: N
authors.lastname: Dragneva
authors.affiliation: Thunder Bay Regional Research Institute and Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada.
authors.forename: Wely
authors.initials: W
authors.lastname: Floriano
authors.affiliation: Thunder Bay Regional Research Institute and Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada.
authors.forename: Oleg
authors.initials: O
authors.lastname: Rubel
authors.affiliation: Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Barr
authors.affiliation: Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA.
authors.forename: Zhifeng
authors.initials: Z
authors.lastname: Kuang
authors.affiliation: Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA.
authors.forename: Rajiv
authors.initials: R
authors.lastname: Berry
authors.affiliation: Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA.
authors.forename: Rajesh
authors.initials: R
authors.lastname: Naik
authors.affiliation: Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA.
authors.forename: Barry
authors.initials: B
authors.lastname: Farmer
mesh_terms: D055592:Biophysical Phenomena; D006108:Graphite / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D010455:Peptides; D006108:Graphite