AltPDB


Immersive Demo Here


An immersive VR environment for viewing and discussing complex biological proteins


Version 0.1 - Proteins of the Immune System (demo environment)



Developed by Tom Skillman and Steven Vergenz

We have created a room-size immersive VR environment for the study of the atomic structure of complex proteins. It significantly increases your ability to understand the form and function of inter-molecular interactions.

This AltspaceVR application brings this VR environment into a shared VR-space where multiple people can enter to view and discuss proteins, sharing a common view of the protein, walking around (and through) the protein, while discussing it with audio connectivity. All interactively and in real-time. While many viewing platforms are supported, our experience is that the immersive goggle systems such as Vive and Oculus provide a significantly richer immersive environment and highly recommend using those types of devices when using this application.

Researchers, scientists, educators, and students can now collaboratively develop an understanding of molecular structure and interactions.

This demo was designed to specifically look at protein components of the immune system. Your immune system is a complex set of molecular components that work together to identify viruses and bacteria that are invading your body. It is what takes a few days to figure out what's attacking you and how to kill it. It is also what can cause you severe problems if your immune system gets confused and starts attacking your own cells instead of foreign cells. When this happens you see diseases such as Type I Diabetes (pancreas attacked), Multiple Sclerosis (brain attacked), or Rheumatoid Arthritis (joints attacked). Research centers, such as Benaroya Autoimmune Research Institute in Seattle, are working to find a cure for these diseases by understanding autoimmune dysfunction, and finding a way to repair it, that is, a cure.

The virtual space is pre-loaded with several key protein structures that work together in a cell to present peptide fragments (e.g., virus fragments) from the interior of the host cell onto its exterior cell surface. It does this at a very well defined location and orientation. The peptide is held in place by a molecular "groove". The specific shape of this groove and the way it holds the peptide is key to the proper operation of the immune system. Once on the cell surface, another component of the immune system, a Killer T-cell, can "inspect" the peptide in the groove and if it is recognized as a "normal" part of the host cell biology (self) no action is taken. If however the peptide is recognized as not part of the normal cell (not-self) the Kill T-cell attacks the host cell and destroys it, thereby halting that cell from producing and spreading additional virus.

If this is all new to you, you might want to view this 6 minute video (https://www.youtube.com/watch?v=VPvCekgPwRI) that shows the details of the immune recognition process.

You can schedule time to run this demo yourself and explore your proteins, or you can sign up for full interactive demos where you can join others, and a moderator, to literally walk through (e.g., Vive) an example: A piece of virus bound it the groove awaiting inspection by the Killer T-cell. You can view the "atomic" structure to see binding details, or the approximating "ribbon" model that will help you get oriented to the overall molecular structure, with helices and sheets, or amino acids, creating the structure that is the "groove".