Due to the limitations posed by the static images and molecular viewers currently used by researchers, there is a strong need for a visual tool that accurately depicts the theoretical structural changes that occur during complex molecular interactions. In the case of collagen I, visual synthesis of structural data is extremely difficult due to the complexity of collagen’s structure and its size on a macromolecular scale.
An animation reflecting current collagen structure research was created, allowing for the synthesis of information to be compiled into a single dynamic visualization. This animation of the interaction between collagen I and Matrix Metalloproteinase I, or MMP1, may allow individuals studying collagen research to better understand the way specific molecular reactions influence collagen structure and facilitate additional functional ligand interactions.
The initial intent of this project was to create an interactive environment in which researchers could study an animation depicting the interaction between MMP1 and collagen I from multiple angles. Three different interactive authoring tools, WebGL, Unity, and Unreal Engine were compared in terms of which tool was best suited for creating an interactive environment and Unity Pro was chosen for production.
A comparison of three popular 3D interactive authoring tools: Unity, Unreal Engine, and WebGL.
Screen shot taken from the testing process in Unreal Development Kit (UDK). The molecule used for testing was Crambin.
Screen shot taken while testing interactive development in Unity Pro. The molecule Crambin was used for the testing process.
However, when the theoretical collagen I research data used in this project was placed into modern molecular viewers, gaps were found in the bonds of the secondary protein structure. It is believed that these gaps were caused by the specific ways in which modern molecular viewers such as Visual Molecular Dynamics (VMD), Chimera, and PyMOL define secondary protein structure.
The secondary focus of the project then shifted from interactivity and focused instead on the investigation of methods for troubleshooting theoretical data in modern molecular viewers and mining the capabilities of PyMOL to provide a methodology for biomedical visualization professionals who experience similar situations with theoretical data in the future.
Licorice representation of collagen I monomers 1-5. Gaps can be seen in each of the individual alpha chains making up each monomer.
Stick representation of collagen I monomer 4. Gaps can be seen in each of the monomer alpha chains.
The PyMOL bond command was implemented using the PyMOL command line to manually bridge the gaps in each of the three alpha chains that makes up a single collagen I monomer.
After PyMOL troubleshooting proved successful, assets were exported into 3D Studio Max and ZBrush for modeling and animation. The final animation produced depicts collagen structure from the most basic level, the collagen monomer, to the most complex, the collagen fiber while illustrating the way in which the collagen I/MMP1 interaction allows for other essential interactions between collagen and surrounding ligands to take place.