Molecular Docking of Nanoscale Collagen Mimetic Peptides

Document Type


Publication Date

Spring 2023


Collagen, which is a structural protein that joins conjunctive and connective tissues, plays an integral role in many physiological contexts, including tissue engineering and regenerative medicine. Natural collagen’s extraction from natural sources is time consuming, sometimes costly, and it is also difficult to render and could prompt undesired biological and pathogenic changes. Nanoscale collagen mimetic peptides have been shown to mimic the unique properties that are present in natural collagen, however molecular level binding studies of these molecules have been limited. In this work, the molecular level binding capabilities of synthetic collagen with known natural binding partners was explored using computational methods. The implications of the binding properties and capabilities of synthetic collagen significantly enhances the number of applications for collagen and its synthetic variants. Using structures from the RCSB databank, PyMOL and molecular docking software packages we determined viable binding conformations and interactions between synthetic collagen, a collagen binding protein vWF, and an RNA aptamer. Each molecule was viewed and properly formatted for HDOCK using PyMOL. Using both the template and template free options in HDOCK, we performed two experiments per combination: 1) collagen - aptamer and 2) collagen - vWF. Generating these values allows us to interpret our results numerically and builds the knowledge of the structure and data. Using computational methods we were able to determine that synthetic collagen can bind with natural collagen binding partners. In the future additional insights into the chemical and physical properties binding products will be explored.

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