Protein Modeling/Pluripotent Stem Cells

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This page refers to the 2011 topic of Protein Modeling.

The 2011 pre-build protein is Klf4, a protein used to turn adult somatic cells (i.e., normal body cells) into induced pluripotent stem cells (iPSCs), and found under the Protein Data Bank ID 2WBU.

At Regional competitions, the on-site model will be a selected region of Oct4 (PDB ID 1GTO). At States, it will be a section of Nanog (PDB ID 2KT0). At Nationals, it will be a part of c-Myc (PDB ID 1NKP). All four of these have been used in the process of creating iPSCs. If you go to an Invitational tournament, according to the CBM site, the on-site model will be Sox2 (possibly under PDB ID 1O4X, although neither the rules nor the CBM site specify a file).

The written test will, as usual, be about the relationship between protein structure and function, but will have an emphasis on iPSCs.



Klf4 is a DNA transcriptional factor characterized by its three Cys2 His2 zinc fingers. It can promote or repress the expression of other protein-coding genes, notably that of Nanog, another factor involved in pluripotency. It can also up-regulate its own expression, forming a positive feedback loop. It binds to the gene sequence CACCC.


Molecule of the Month article


Nanog is a transcriptional factor essential to maintaining pluripotency in stem cells. Its expression is promoted by Klf4 and Oct4.


Because c-Myc is oncogenic (promotes the development of cancer), researchers have been working to create iPSCs without the use of c-Myc. It is possible to create iPSCs without c-Myc, although the process is much less efficient (in human fibroblasts– one type of connective tissue cell- removing c-Myc decreased iPSC production by 90%; in epithelial– or membrane– cells, removing c-Myc decreased iPSC production by 40%). However, the risk of tumor formation outweighs this inefficiency when creating iPSCs for therapeutic use (which is not yet available, except experimentally).

More information about c-Myc can be found here.


Induced Pluripotent Stem Cells are ordinary body cells that have been turned back into undifferentiated stem cells with the ability to become any kind of body tissue. Pluripotent stem cells, including iPSCs, are characterized by their ability to become any type of cell from any of the three germ layers (although they can't become placental/extraembryonic tissue; only totipotent stem cells can do that), and to reproduce more or less indefinitely while maintaining their undifferentiated state. Scientists such as Shinya Yamanaka have done this by introducing the genes for different transcriptional factors involved in maintaining pluripotency in embryonic stem cells into somatic cells (originally mouse cells, but it has now been done with human cells as well) through retroviral transfection. Yamanaka used the four factors involved in the event this year. Other factors that have been used include Lin-28 and Esrrb.

Retroviral transfection (or transduction) is a method of introducing genes into cells by taking advantage of viruses' ability to insert genes into a host cell's chromosomes. Viruses do this in order to make the host cell produce the proteins they need in order to reproduce, but if they are instead loaded with the RNA that codes for a desired factor, the host cell will begin to produce that instead. The problem with this method is that it is nearly impossible to control where the virus will insert the gene it carries, so it can disturb necessary existing genes in the cell by inserting in the middle of them. Also, the virus often inserts multiple copies of the same gene, which– particularly in the case of transcription factors that promote cell reproduction and inhibit differentiation, like those involved in the creation of iPSCs– can carry a higher risk of tumor formation. Scientists are currently working on other methods of inserting the genes to lower these risks (for example, adenoviruses, which do not integrate their genes into the host cell genome, removing the risk of insertional mutagenesis).

The human cells initially used by Yamanaka and others were fibroblasts, a type of connective tissue cell that makes collagen. These don't divide a lot, so it's difficult to make them into iPSCs; more recently, epithelial cells have been used. Epithelial cells are found covering various tissue surfaces, and divide much more frequently than fibroblasts. They have therefore been more efficient at turning into iPSCs. Particularly, c-Myc (which is oncogenic) is less important in epithelial cell iPSCs, which decreases the likelihood of tumor formation.