Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach Academic Article uri icon

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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

  • Sheikholeslami, Somayyeh
  • Pandey, RB
  • Dragneva, Nadiya
  • Floriano, Wely
  • Rubel, Oleg
  • Barr, Stephen A
  • Kuang, Zhifeng
  • Berry, Rajiv
  • Naik, Rajesh
  • Farmer, Barry

publication date

  • May 28, 2014