Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions

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...

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Autores principales: Martinez-Gonzalez, José Angel, Nandi, Prithwish K., English, Niall J., Gowen, Aoife
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9785973/
https://www.ncbi.nlm.nih.gov/pubmed/36555590
http://dx.doi.org/10.3390/ijms232415949
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author Martinez-Gonzalez, José Angel
Nandi, Prithwish K.
English, Niall J.
Gowen, Aoife
author_facet Martinez-Gonzalez, José Angel
Nandi, Prithwish K.
English, Niall J.
Gowen, Aoife
author_sort Martinez-Gonzalez, José Angel
collection PubMed
description 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.
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spelling pubmed-97859732022-12-24 Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions Martinez-Gonzalez, José Angel Nandi, Prithwish K. English, Niall J. Gowen, Aoife Int J Mol Sci Article 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. MDPI 2022-12-15 /pmc/articles/PMC9785973/ /pubmed/36555590 http://dx.doi.org/10.3390/ijms232415949 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Martinez-Gonzalez, José Angel
Nandi, Prithwish K.
English, Niall J.
Gowen, Aoife
Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions
title Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions
title_full Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions
title_fullStr Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions
title_full_unstemmed Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions
title_short Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions
title_sort vibrational analysis of hydration-layer water around ubiquitin, unpeeled layer by layer: molecular-dynamics perceptions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9785973/
https://www.ncbi.nlm.nih.gov/pubmed/36555590
http://dx.doi.org/10.3390/ijms232415949
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