Exploring the changes in the structure of α-helical peptides adsorbed onto a single walled carbon nanotube using classical molecular dynamics simulation

Balamurugan, K. ; Gopalakrishnan, R. ; Raman, S. Sundar ; Subramanian, V. (2010) Exploring the changes in the structure of α-helical peptides adsorbed onto a single walled carbon nanotube using classical molecular dynamics simulation Journal of Physical Chemistry B, 114 (44). pp. 14048-14058. ISSN 1520-6106

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Official URL: http://pubs.acs.org/doi/abs/10.1021/jp106177n

Related URL: http://dx.doi.org/10.1021/jp106177n

Abstract

Classical molecular dynamics (MD) simulation has been carried out in an explicit solvent environment to understand the interaction between the single walled carbon nanotube (SWCNT) and α-helix. A polyalanine peptide consisting of 40 alanine residues has been chosen as the model for the α-helix (PA40). Results reveal that the SWCNT induces conformational changes in PA40. Furthermore, breakage of hydrogen bonds in the chosen model peptides has been observed, which leads to conformational transitions (α → turns) in different parts of the PA40. Owing to these transitions, regions of different structural and energetic stability are generated in PA40 which enable the PA40 to curl around the surface of the SWCNT. The overall observations obtained from the MD simulations are not significantly influenced by the starting geometry and the choice of the force field. Although the qualities of structural information obtained from the MD simulation using ff03 and OPLS are different, the overall observation derived from the ff03 is similar to that of OPLS. Results from the MD simulation on the interaction of the α-helical fragment of the SNARES protein with the SWCNT elicit that the amino acid composition influences the interaction pattern. The wrapping of the α-helical fragment of the SNARES onto the SWCNT is similar to that of PA40. Overall, there is a considerable decrease in the helical content of peptides upon interaction with SWCNTs, in agreement with the experimental findings.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society.
ID Code:107659
Deposited On:01 Dec 2017 12:31
Last Modified:01 Dec 2017 12:31

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