Cargando…
Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network
Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobici...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954116/ https://www.ncbi.nlm.nih.gov/pubmed/33718433 http://dx.doi.org/10.3389/fmolb.2021.626837 |
_version_ | 1783664021457600512 |
---|---|
author | Di Rienzo, Lorenzo Miotto, Mattia Bò, Leonardo Ruocco, Giancarlo Raimondo, Domenico Milanetti, Edoardo |
author_facet | Di Rienzo, Lorenzo Miotto, Mattia Bò, Leonardo Ruocco, Giancarlo Raimondo, Domenico Milanetti, Edoardo |
author_sort | Di Rienzo, Lorenzo |
collection | PubMed |
description | Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues. |
format | Online Article Text |
id | pubmed-7954116 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-79541162021-03-13 Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network Di Rienzo, Lorenzo Miotto, Mattia Bò, Leonardo Ruocco, Giancarlo Raimondo, Domenico Milanetti, Edoardo Front Mol Biosci Molecular Biosciences Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues. Frontiers Media S.A. 2021-02-26 /pmc/articles/PMC7954116/ /pubmed/33718433 http://dx.doi.org/10.3389/fmolb.2021.626837 Text en Copyright © 2021 Di Rienzo, Miotto, Bò, Ruocco, Raimondo and Milanetti. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Molecular Biosciences Di Rienzo, Lorenzo Miotto, Mattia Bò, Leonardo Ruocco, Giancarlo Raimondo, Domenico Milanetti, Edoardo Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network |
title | Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network |
title_full | Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network |
title_fullStr | Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network |
title_full_unstemmed | Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network |
title_short | Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network |
title_sort | characterizing hydropathy of amino acid side chain in a protein environment by investigating the structural changes of water molecules network |
topic | Molecular Biosciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954116/ https://www.ncbi.nlm.nih.gov/pubmed/33718433 http://dx.doi.org/10.3389/fmolb.2021.626837 |
work_keys_str_mv | AT dirienzolorenzo characterizinghydropathyofaminoacidsidechaininaproteinenvironmentbyinvestigatingthestructuralchangesofwatermoleculesnetwork AT miottomattia characterizinghydropathyofaminoacidsidechaininaproteinenvironmentbyinvestigatingthestructuralchangesofwatermoleculesnetwork AT boleonardo characterizinghydropathyofaminoacidsidechaininaproteinenvironmentbyinvestigatingthestructuralchangesofwatermoleculesnetwork AT ruoccogiancarlo characterizinghydropathyofaminoacidsidechaininaproteinenvironmentbyinvestigatingthestructuralchangesofwatermoleculesnetwork AT raimondodomenico characterizinghydropathyofaminoacidsidechaininaproteinenvironmentbyinvestigatingthestructuralchangesofwatermoleculesnetwork AT milanettiedoardo characterizinghydropathyofaminoacidsidechaininaproteinenvironmentbyinvestigatingthestructuralchangesofwatermoleculesnetwork |