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A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site
Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular d...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619770/ https://www.ncbi.nlm.nih.gov/pubmed/31291328 http://dx.doi.org/10.1371/journal.pone.0219473 |
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author | Nguyen, Crystal Yamazaki, Takeshi Kovalenko, Andriy Case, David A. Gilson, Michael K. Kurtzman, Tom Luchko, Tyler |
author_facet | Nguyen, Crystal Yamazaki, Takeshi Kovalenko, Andriy Case, David A. Gilson, Michael K. Kurtzman, Tom Luchko, Tyler |
author_sort | Nguyen, Crystal |
collection | PubMed |
description | Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic-site density distributions. Furthermore, we assess the quality of the resulting solvation thermodynamics density distributions by analyzing the binding site of coagulation Factor Xa with both GIST and 3D-RISM. We find good qualitative agreement between the methods for oxygen and hydrogen densities as well as direct solute-solvent energetic interactions. However, 3D-RISM predicts lower energetic and entropic penalties for moving water from the bulk to the binding site. |
format | Online Article Text |
id | pubmed-6619770 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-66197702019-07-25 A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site Nguyen, Crystal Yamazaki, Takeshi Kovalenko, Andriy Case, David A. Gilson, Michael K. Kurtzman, Tom Luchko, Tyler PLoS One Research Article Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic-site density distributions. Furthermore, we assess the quality of the resulting solvation thermodynamics density distributions by analyzing the binding site of coagulation Factor Xa with both GIST and 3D-RISM. We find good qualitative agreement between the methods for oxygen and hydrogen densities as well as direct solute-solvent energetic interactions. However, 3D-RISM predicts lower energetic and entropic penalties for moving water from the bulk to the binding site. Public Library of Science 2019-07-10 /pmc/articles/PMC6619770/ /pubmed/31291328 http://dx.doi.org/10.1371/journal.pone.0219473 Text en © 2019 Nguyen et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Nguyen, Crystal Yamazaki, Takeshi Kovalenko, Andriy Case, David A. Gilson, Michael K. Kurtzman, Tom Luchko, Tyler A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site |
title | A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site |
title_full | A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site |
title_fullStr | A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site |
title_full_unstemmed | A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site |
title_short | A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site |
title_sort | molecular reconstruction approach to site-based 3d-rism and comparison to gist hydration thermodynamic maps in an enzyme active site |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619770/ https://www.ncbi.nlm.nih.gov/pubmed/31291328 http://dx.doi.org/10.1371/journal.pone.0219473 |
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