Cargando…
Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools
To successfully design and optimize the application of hydrogel matrices one has to effectively combine computational design tools with experimental methods. In this context, one of the most promising techniques is molecular modeling, which requires however accurate molecular models representing the...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6767189/ https://www.ncbi.nlm.nih.gov/pubmed/31527447 http://dx.doi.org/10.3390/molecules24183365 |
_version_ | 1783454859483152384 |
---|---|
author | Radosinski, Lukasz Labus, Karolina Zemojtel, Piotr Wojciechowski, Jakub W. |
author_facet | Radosinski, Lukasz Labus, Karolina Zemojtel, Piotr Wojciechowski, Jakub W. |
author_sort | Radosinski, Lukasz |
collection | PubMed |
description | To successfully design and optimize the application of hydrogel matrices one has to effectively combine computational design tools with experimental methods. In this context, one of the most promising techniques is molecular modeling, which requires however accurate molecular models representing the investigated material. Although this method has been successfully used over the years for predicting the properties of polymers, its application to biopolymers, including gelatin, is limited. In this paper we provide a method for creating an atomistic representation of gelatin based on the modified FASTA codes of natural collagen. We show that the model created in this manner reproduces known experimental values of gelatin properties like density, glass-rubber transition temperature, WAXS profile and isobaric thermal expansion coefficient. We also present that molecular dynamics using the INTERFACE force field provides enough accuracy to track changes of density, fractional free volume and Hansen solubility coefficient over a narrow temperature regime (273–318 K) with 1 K accuracy. Thus we depict that using molecular dynamics one can predict properties of gelatin biopolymer as an efficient matrix for immobilization of various bioactive compounds, including enzymes. |
format | Online Article Text |
id | pubmed-6767189 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-67671892019-10-02 Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools Radosinski, Lukasz Labus, Karolina Zemojtel, Piotr Wojciechowski, Jakub W. Molecules Article To successfully design and optimize the application of hydrogel matrices one has to effectively combine computational design tools with experimental methods. In this context, one of the most promising techniques is molecular modeling, which requires however accurate molecular models representing the investigated material. Although this method has been successfully used over the years for predicting the properties of polymers, its application to biopolymers, including gelatin, is limited. In this paper we provide a method for creating an atomistic representation of gelatin based on the modified FASTA codes of natural collagen. We show that the model created in this manner reproduces known experimental values of gelatin properties like density, glass-rubber transition temperature, WAXS profile and isobaric thermal expansion coefficient. We also present that molecular dynamics using the INTERFACE force field provides enough accuracy to track changes of density, fractional free volume and Hansen solubility coefficient over a narrow temperature regime (273–318 K) with 1 K accuracy. Thus we depict that using molecular dynamics one can predict properties of gelatin biopolymer as an efficient matrix for immobilization of various bioactive compounds, including enzymes. MDPI 2019-09-16 /pmc/articles/PMC6767189/ /pubmed/31527447 http://dx.doi.org/10.3390/molecules24183365 Text en © 2019 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Radosinski, Lukasz Labus, Karolina Zemojtel, Piotr Wojciechowski, Jakub W. Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools |
title | Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools |
title_full | Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools |
title_fullStr | Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools |
title_full_unstemmed | Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools |
title_short | Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools |
title_sort | development and validation of a virtual gelatin model using molecular modeling computational tools |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6767189/ https://www.ncbi.nlm.nih.gov/pubmed/31527447 http://dx.doi.org/10.3390/molecules24183365 |
work_keys_str_mv | AT radosinskilukasz developmentandvalidationofavirtualgelatinmodelusingmolecularmodelingcomputationaltools AT labuskarolina developmentandvalidationofavirtualgelatinmodelusingmolecularmodelingcomputationaltools AT zemojtelpiotr developmentandvalidationofavirtualgelatinmodelusingmolecularmodelingcomputationaltools AT wojciechowskijakubw developmentandvalidationofavirtualgelatinmodelusingmolecularmodelingcomputationaltools |