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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2019-09-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/24/18/3365 |
| _version_ | 1818544943887548416 |
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| author | Lukasz Radosinski Karolina Labus Piotr Zemojtel Jakub W. Wojciechowski |
| author_facet | Lukasz Radosinski Karolina Labus Piotr Zemojtel Jakub W. Wojciechowski |
| author_sort | Lukasz Radosinski |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-11T22:55:03Z |
| format | Article |
| id | doaj.art-fdbc4dd11c8b402882448f39c53a02b3 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-11T22:55:03Z |
| publishDate | 2019-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-fdbc4dd11c8b402882448f39c53a02b32022-12-22T00:47:17ZengMDPI AGMolecules1420-30492019-09-012418336510.3390/molecules24183365molecules24183365Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational ToolsLukasz Radosinski0Karolina Labus1Piotr Zemojtel2Jakub W. Wojciechowski3Department of Bioprocess and Biochemical Engineering, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, PolandDepartment of Bioprocess and Biochemical Engineering, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, PolandFaculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, PolandFaculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 50-370 Wroclaw, PolandTo 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.https://www.mdpi.com/1420-3049/24/18/3365biopolymersgelatinhydrogelmolecular dynamicsfunctional polymeric matrices |
| spellingShingle | Lukasz Radosinski Karolina Labus Piotr Zemojtel Jakub W. Wojciechowski Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools Molecules biopolymers gelatin hydrogel molecular dynamics functional polymeric matrices |
| 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 | biopolymers gelatin hydrogel molecular dynamics functional polymeric matrices |
| url | https://www.mdpi.com/1420-3049/24/18/3365 |
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