Scientific Analysis of Synthetic Collagen Compounds using Computational Molecular Modeling Methods

Scientists have proven that the health regimen you follow can have a significant impact on the human body. Collagen is found on multiple parts of the body such as skin, bones, lymphatic, cardiovascular, liver, lung, spline, and intestinal tissue. (Spano, 2019) Although it is prevalent that people lose 1% of collagen each year, there is a way to improve this by maintaining a healthy diet. “Collagen-derived dietary proteins are most commonly extracted from porcine skin (45%), bovine hide (30%), and the bones of both animals (23%) Chicken (bones) and fish (scales and bones) byproducts are also used as production sources of collagen-derived dietary protein” (Holwerda and Loon, 2022). In this research, a biomodel of three synthetic collagen molecules is used to bind biomarker properties including Aptamers, CNA, and Silk. Pymol is a molecular visualization tool that provides an ethically pleasing environment for a three-dimensional structure of a protein molecule to be cleaned by removing water, removing repeated molecules, and retrieving the model sequences. The results from PyMOL are then incorporated into the Basic Local Alignment Search Tool (BLASTp) to generate alignments between a protein sequence (Wheeler, Bhagwat, 2007). The binding energy is calculated along with a visual model of the structural changes of the collagens reaction to its biomarker using HDOCK and PATCHDOCK servers. When docking with PatchDock, the results are collected and refined with a software named FireDock to retrieve the binding energies. The best conformations were compared with differing peptides to see which ligand showed the highest affinity. “While enzyme driven crosslinking plateaus at maturation, connective tissue stiffness has been shown to further increase with age and diabetes. This tissue stiffening has been associated with non-enzymatic, oxidative reactions between glucose and collagen which increases with increased plasma glucose end concentrations associated with advanced aging” (Snedeker, 2014). Further research will utilize molecular dynamics to explore conformational space and explicitly treat structural flexibility and entropic effects of synthetic collagen.