Overview Edit

The Molecular Modeling Database is an online resource hosted by the National Center for Biotechnology Information (NCBI). It hosts experimentally determined 3-dimensional molecular structures, and connects these structures to related literature such as protein and nucleic acid sequences as well as chemical and molecular interactions. The database is especially useful for identifying homologues and determining the sequence-structure interactions that are crucial for the structural genomics field.

In another of my classes we briefly discussed the use of Interleukin-2 as method of preventing the spread of cancer, and its relatively low rates of success as a sole remedy. The protein when injected into the patient jump starts an immunological response by proliferating cytotoxic T-cells that destroy infected or diseased cells. Although the treatment wasn't incredibly effective in our case study I used the MMDB to learn more about IL-2.

Search Example Edit

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The basic search page of MMDB. This is the what is shown after I search for IL-2.

To begin I just had to search IL-2 and a list of different structures came up. All of them were either human IL-2, IL-2 mutants, or IL-2 in a bonded state with other macromolecules. There were 177 different structures that came up from the search for IL-2, most of them significantly more complex than just the single protein.

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Structure Summary Page, this is displayed when you click on one of the links from the search. From this page you can navigate and find similar structures.

I chose the second selection which was the IL-2 mutant D10. The search link brings you to a basic page where the structure is displayed, as well as the literature from which this specific structure was taken.This page is the basis for navigating the site, it is here where they show the source of the model, method by which is was made, and the link to similar structures. The vast majority of structures that I found on the database where created through x-ray crystallography.

This specific literature, found by following the citation link in the top left, was about the creation IL-2 mutant D10, which has a higher affinity for binding to cytotoxic T-cells receptors IL-2Rbeta and IL-2Rgamma, because it binds without the T-Cells having to activate CD25, which is normally needed before binding to IL-2. This new protein induced higher rates of T-cell expansions leading to increased antitumor immune responses making it a viable replacement for regular injections of IL-2 that failed to help the patient in the case study that initiated my search.

Link to mentioned case: