Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions
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Published:2022-12-15
Issue:24
Volume:23
Page:15949
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ISSN:1422-0067
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Container-title:International Journal of Molecular Sciences
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language:en
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Short-container-title:IJMS
Author:
Martinez-Gonzalez José AngelORCID,
Nandi Prithwish K.,
English Niall J.ORCID,
Gowen AoifeORCID
Abstract
Classical molecular-dynamics simulations have been performed to examine the interplay between ubiquitin and its hydration-water sub-layers, chiefly from a vibrational-mode and IR viewpoint—where we analyse individual sub-layers characteristics. The vibrational Density of States (VDOS) revealed that the first solvation sub-shell indicates a confined character therein. For layers of increasing distance from the surface, the adoption of greater bulk-like spectral behaviour was evident, suggesting that vibrational harmonisation to bulk occurs within 6–7 Å of the surface.
Funder
Science Foundation Ireland
European Research Council Starting Grant Programme
European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie grant agreement
Subject
Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis
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