Development and Validation of a Virtual Gelatin Model Using Molecular Modeling Computational Tools

• Published in: Molecules (Basel, Switzerland) Switzerland), 2019-09, Vol.24 (18), p.3365
• Main Authors: Radosinski, Lukasz, Labus, Karolina, Zemojtel, Piotr, Wojciechowski, Jakub W
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acid Sequence; Analysis of Variance; Bioactive compounds; Biocompatibility; Biomedical materials; Biopolymers; Biopolymers - chemistry; Collagen; Computer applications; Design optimization; Enzymes; Experimental methods; functional polymeric matrices; Gelatin; Gelatin - chemistry; hydrogel; Hydrogels; Hydrogels - chemistry; Immobilization; Mechanical properties; Models, Molecular; Molecular dynamics; Molecular modelling; Polymers; Protein Conformation; Simulation; Software; Solubility coefficient; Solvents; Temperature; Thermal expansion; Transition temperature; Transition temperatures
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules24183365

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.