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https://hdl.handle.net/2440/125069
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Type: | Journal article |
Title: | Energy landscape mapping and replica exchange molecular dynamics of an adsorbed peptide |
Author: | Ross-Naylor, J.A. Mijajlovic, M. Biggs, M.J. |
Citation: | The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter, 2020; 124(13):2527-2538 |
Publisher: | American Chemical Society |
Issue Date: | 2020 |
ISSN: | 1520-5207 1520-5207 |
Statement of Responsibility: | James A. Ross-Naylor, Milan Mijajlovic and Mark J. Biggs |
Abstract: | Adsorption of peptides at the interface between a fluid and a solid occurs widely in both nature and applications. Knowing the dominant conformations of adsorbed peptides and the energy barriers between them is of interest for a variety of reasons. Molecular dynamics (MD) simulation is a widely used technique that can yield such understanding. However, the complexity of the energy landscapes of adsorbed peptides means that comprehensive exploration of the energy landscape by MD simulation is challenging. An alternative approach is energy landscape mapping (ELM), which involves the location of stationary points on the potential energy surface, and its analysis to determine, for example, the pathways and energy barriers between them. In the study reported here, a comparison is made between this technique and replica exchange molecular dynamics (REMD) for met-enkephalin adsorbed at the interface between graphite and the gas phase: the first ever direct comparison of these techniques for adsorbed peptides. Both methods yield the dominant adsorbed peptide conformations. Unlike REMD, however, ELM readily allows the identification of the connectivity and energy barriers between the favored conformations, transition paths, and structures between these conformations and the impact of entropy. It also permits the calculation of the constant volume heat capacity although the accuracy of this is limited by the sampling of high-energy minima. Overall, compared to REMD, ELM provides additional insights into the adsorbed peptide system provided sufficient care is taken to ensure that key parts of the landscape are adequately sampled. |
Keywords: | Enkephalin, Methionine Molecular Conformation Adsorption Entropy Molecular Dynamics Simulation |
Rights: | © 2020 American Chemical Society |
DOI: | 10.1021/acs.jpcb.9b10568 |
Grant ID: | http://purl.org/au-research/grants/arc/DP130101714 |
Published version: | http://dx.doi.org/10.1021/acs.jpcb.9b10568 |
Appears in Collections: | Aurora harvest 4 Physics publications |
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