# Effect of Nanohydroxyapatite on Silk Fibroin-Chitosan Interactions--Molecular Dynamics Study
## 4 Conclusions  
The study focused on the intermolecular interactions in fibroin-chitosan complexes in the presence of Ca2+ and \(\text{HPO}_{4}{}^{2-}\) ions, which simulate nanohydroxyapatite, and in the presence of acetic acid. As we found, molecular dynamics simulations performed using the YASARA program revealed a chemically intuitive description of the structural features and interactions between the studied biomolecules. Our analysis showed that the formation of fibroin-chitosan complexes are highly energetically favorable. Furthermore, these systems are much more stable than the previously studied chitosan-collagen complexes. In order to  
Figure 7: The distributions of hydrophobic contacts in the case of fibroin–chitosan complexes stabilized by \(\text{HPO}_{4}{}^{2-}/\text{Ca}^{2+}\) (**left panel**) and acetic acid aqueous solution (**right panel**). explain the exceptionally high affinity of fibroin for chitosan, the distributions and structural features of the key interaction types were analyzed. All molecular systems considered in this study were found to have a dense network of intermolecular contacts. Additionally, the optimized structural analysis indicated that the complexation of fibroin with chitosan maintains the \(\beta\)-sheet conformation. Although the obtained results were found to be consistent with various empirical observations, additional experimental studies could provide further confirmation and refinement of the structural and energetical features determined in this study. Molecular dynamics simulations of biomolecule pairs offer valuable insights into the properties of new materials. The promising results obtained for fibroin-chitosan complexes in the presence of Ca\({}^{2+}\)/HPO\({}_{4}\)\({}^{2-}\) and acetic acid suggest the need for further research on the effects of other ions or molecules. These studies could lead to the development of novel fibroin composites with tailored properties for a variety of applications, such as bone regeneration, dentistry and wound dressings. The following supporting information can be downloaded at: [[https://www.mdpi.com/article/10.3390/app14104131/s1](https://www.mdpi.com/article/10.3390/app14104131/s1)]([https://www.mdpi.com/article/10.3390/app14104131/s1](https://www.mdpi.com/article/10.3390/app14104131/s1)), Figure S1: Left: RMSD of all atoms evolution (RMSDALL parameter) in time for both cases. Right: the radius gyration analysis of the silk fibroin-chitosan complexes in the presence of HPO\({}_{4}\)\({}^{2-}\) and calcium ions (HPO) and acetic acid aqueous solution (Acetic). Figure S2: The frequency of particular types of interactions appearance during MD simulations; Table S1: Description of H-bonds between chitosan and silk fibroins' amino acids along with binding energy values per silk fibroin molecule for both cases; Table S2: Description of ionic interactions between chitosan and silk fibroins' amino acids; Table S3: Distances between groups carried by ion bridges; Table S4: Description of hydrophobic (HP) interactions between chitosan and silk fibroins' amino acids; Table S5: Description of CationPi interactions between chitosan and silk fibroins' amino acids. Conceptualization, A.T. and P.B. ; methodology, P.B. ; software, P.B. ; validation, M.P., I.B. and P.B. ; formal analysis, M.P., A.T., S.S. and P.B. ; investigation, M.P. and P.B. ; resources, D.L. and P.B. ; data curation, P.B. ; writing--original draft preparation, M.P., A.T., D.L., S.S., A.S., I.B. and P.B. ; writing--review and editing, M.P., A.T., D.L., S.S., A.S., I.B. and P.B. ; visualization, D.L. and P.B. ; supervision, A.S.; project administration, M.P. and A.S. All authors have read and agreed to the published version of the manuscript. This research received no external funding. Not applicable. The raw/processed data required to reproduce these findings are available on request. Author [PERSON] was employed by the company CosmetoSAFE Consulting LLC.