Document Type
Article
Publication Date
5-28-2014
Department
Physics and Astronomy
School
Mathematics and Natural Sciences
Abstract
Binding of a solvated peptide A1 (1E 2P 3L 4Q 5L 6K 7M) 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, 1E, 4Q, and 6K (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.
Publication Title
Journal of Chemical Physics
Volume
140
Issue
20
Recommended Citation
Sheikholeslami, S.,
Pandey, R.,
Dragneva, N.,
Floriano, W.,
Rubel, O.,
Barr, S.,
Kuang, Z.,
Berry, R.,
Naik, R.,
Farmer, B.
(2014). Binding of Solvated Peptide (EPLQLKM) With a Graphene Sheet Via Simulated Coarse-Grained Approach. Journal of Chemical Physics, 140(20).
Available at: https://aquila.usm.edu/fac_pubs/19918
Comments
This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in [Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach. The Journal of Chemical Physics 140, 20 p204901 (2014)] and may be found at https://doi.org/10.1063/1.4876716.