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2022 Video Challenge for High School Students

Molecular Mechanisms
of Cancer

 

Learn about the Molecular Mechanisms of Cancer

This page will be updated through December.

In order to understand the information below, you should be familiar with the biomolecular concepts listed below:

Below you will find the overview of the challenge topics with links to related resources and examples of relevant PDB structures to be visualized in the video entry.

Topic 1 overview:

Failure of cell-cycle arrest via p21 protein due to mutations in the TP53 tumor suppressor gene

Notice: This topic overview specifically highlights the proteins and their functions that are relevant to the p53/p21 pathway. Most of the proteins described here are essential components in other pathways.

Understanding the cell division cycle

The cell division cycle is a series of sequential events that lead to a cell splitting into 2 daughter cells. This process follows distinct phases: G1, S, G2, and M. In the G1 phase, the cell is increasing its supply of proteins relevant for DNA replication and copying its organelles. In the S phase, the cell replicates its DNA. In the G2 phase, the cell continues to grow, preparing itself for mitosis by reorganizing its microtubules to complete the division in the M phase (see Figure 1, outer ring).

Cell cycle with phase-specific CDKs/Cyclins highlighted

Figure 1. Cell division cycle with phase-specific cyclins and CDKs and their main functions highlighted.

CDK-Cyclin complex in active form and inactivated by p21

Figure 2. Active CDK (green)/cyclin (orange) complex is shown on the left. The same complex is shown on the right inactivated by the p21 protein (yellow). PDB structure 6p8h.

The cell cycle progression is mediated through various cyclins and cyclin-dependent kinases (CDKs). Kinases are a large family of proteins that can phosphorylate other proteins. Phosphorylation is a process of adding phosphoryl groups to certain amino acids (see Figure 4A). This process can activate or deactivate the protein. CDKs have to create a complex with another protein – cyclin – to be able to phosphorylate other proteins. The levels of various phase-specific CDKs are relatively stable throughout the cell cycle while the concentrations of phase-specific cyclins rise and fall. Figure 1 shows the phase-specific cyclins and CDKs and their key functions in the progression of the cell cycle.

The protein p53 is activated when DNA damage is detected. p53 triggers expression of the p21 protein. p21 inhibits CDK/cyclin complexes (see Figure 2) pausing the cell cycle progression and giving the cell time to repair its DNA or start pathways leading to its death.


Learn More:

Molecule of the Month articles:

Cyclin and Cyclin-dependent Kinase


Other Resources:

L. Ding et al. (2020) The Roles of Cyclin-Dependent Kinases in Cell-Cycle Progression and Therapeutic Strategies in Human Breast Cancer. Int J Mol Sci. 21(6): 1960.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7139603/

L. Wang et al. (2020) Function of p21 and its therapeutic effects in esophageal cancer (Review). Oncology Letters 21:2.
https://www.spandidos-publications.com/10.3892/ol.2020.12397

The p53 Tumor Suppressor

p53 is a transcription factor that responds to cell stress events that can result in DNA damage. p53 initiates and stimulates the production of proteins that assist in DNA repair, arrest the cell-division cycle, or initiate apoptosis. p53 is composed of four identical chains. At the center of p53 is a tetramerization domain that ties the four chains together. Each of the chains features a DNA-binding domain and a transactivation domain (see Figure 3 A).

The protein receives positive and negative stimulation through post-translational modifications (e.g. phosphorylation, acetylation, methylation and ubiquitination).

Negative control of p53

When there are no signals about DNA damage, MDM2 is bound to the transactivation domain of p53, preventing the protein from becoming activated (see Figure 3B).

p53: protein structure and inactivated form

Figure 3. A) the structure of p53 with the main domains highlighted. The illustration was created by overlaying PDB structures (1ycq-transactivation domain, 1sae-tetramerization domain, 3q01-DNA-binding domain) on the AlphaFold21computational model. B) p53 is expressed at steady levels. If DNA damage is not detected, MDM2 (PDB structure 1ycq) binds to the transactivation domain, marking the protein for destruction.

Positive stimulation of p53 resulting in production of p21

Cellular stresses such as UV light, ionizing radiation, and other factors can cause breaks in DNA strands. The DNA damage activates complex molecular pathways. One of the proteins activated through such pathways is the CHK2 kinase. The protein can phosphorylate the p53 transactivation domain at the Serine 20 site (see Figure 4A). This activates p53 causing it to bind to DNA. p53 typically binds to special sequences in the target genes called p53 response elements.

p53: phosphorylation and DNA binding

Figure 4. A) DNA damage activates complex molecular pathways. One component of them is CHK2 kinase (green, PDB structure 2cn5). The kinase phosphorylates p53 at the Serine 20 site. B) Phosphorylation activates p53 causing it to bind to a special segment of DNA called the p53 response element (PDB structure 3ts8).

One of the target genes for p53 is the CDKN1A gene encoding the p21 protein. After binding to the DNA, p53 engages the RNA Polymerase II (see Figure 5). The polymerase then transcribes the p21 gene into mRNA, starting the process leading to production of the p21 inhibitor. p21 then inhibits the CDK/cyclin complexes (see Figure 2) thus halting the progression of the cell cycle in the face of DNA damage present.

p53: phosphorylation and DNA binding

Figure 5. p53 engaging RNA Polymerase II (illustration created based on PDB structures 3ts8, 5iy6, and 6xre).

If a mutation is present at the DNA binding site, p53 can’t bind to DNA and initiate the p21 production. As a result, the cell will divide with errors in the DNA code.

Table 1: Examples of relevant PDB structures for Topic 1

PDB Structure ID

Structure Description

Visualization Resources

1w98

CyclinA-CDK2 complex

1w98 3D view from Mol*a

Chimera session (preview below)b

The Chimera session preview for the PDB structure 1w98 shows the CDK2 (green, chain A)/cyclin E (orange, chain B) complex. More examples of 3D structures of phase-specific cyclin and CDKs from the PDB can be found in Figure 1.

6p8h

Crystal structure of CDK4 in complex with Cyclin D and p21

6p8h 3D view from Mol*a

Chimera session (preview below)b

The Chimera session preview for the PDB structure 6p8h shows the CDK (green, chain B)/cyclin (orange, chain A) complex inactivated by the p21 protein (yellow, chain C).

3ts8

Crystal structure of a multidomain human p53 tetramer bound to the natural CDKN1A(p21) p53-response element

3ts8 3D view from Mol*a

Chimera session (preview below)b

The Chimera session preview for the PDB structure 3ts8 shows the DNA-binding domains of p53 in cyan (chains A, B, C, and D) and the CDKN1A(p21) p53-response element in orange.

6xre

Structure of the p53/RNA polymerase II assembly

6xre 3D view from Mol*a

Chimera session (preview below)b

The Chimera session preview for the PDB structure 6xre shows the RNA Polymerase II in dark red and one p53 DNA binding domain in cyan with the transactivation domain highlighted in green (chain M).


Topic 2 overview:

Continuous cell proliferation due to mutations in the RAS oncogene in the EGFR/Ras pathway

EGF and its receptor

Growth factors are required to initiate the G1 phase of the cell cycle. One such ligand is Epidermal Growth Factor (EGF). The small peptide can bind to the extracellular portion of the EGF receptor (EGFR). Ligand binding induces the dimerization of the EGFR. In this state the receptor phosphorylates itself and generates binding sites for SHC, GRB2, and SOS proteins.


Learn more:

Molecule of the Month article:

Epidermal Growth Factor

Ras Protein

Ras is a small, globular protein that can be switched on or off by binding GTP and GDP respectively. The EGFR-SHC-GRB2-SOS complex can bind inactive Ras which allows the GDP to GTP switch. Upon activation, Ras is free to activate other proteins, which ultimately turn on genes involved in cell growth and division.

Inactivation of Ras

Ras is inactivated by Ras-specific GTPase-activating proteins (RasGAPs) which hydrolyze the GTP to GDP. Mutated Ras can’t bind RasGAP and stays in the ‘on’ state promoting gene expression and cell growth.

Learn more:

Molecule of the Month article:
Ras Protein


Other Resources:

Intracellular Ras activation explained Video


Table 2: Examples of relevant PDB structures for Topic 2

PDB Structure ID

Structure Description

Visualization Resources

3njp

The Extracellular and Transmembrane Domain Interfaces in Epidermal Growth Factor

TBA

1m14

Tyrosine Kinase Domain from Epidermal Growth Factor Receptor

TBA

1n3h

Coupling of Folding and Binding in the PTB Domain of the Signaling Protein Shc

TBA

1gri

Structure of a ternary KRas(G13D)-SOS complex adaptor

TBA

7kfz

Structure of a ternary KRas(G13D)-SOS complex

TBA

5p21

4q21

Ras with GTP and GDP

TBA

1wq1

RasGAP Complex

TBA

References

  1. Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).

Visualization Resources References:

  1. You can download and open these sessions using UCSF Chimera. Use the tutorials available here and here to learn how to edit the sessions, create animations, or save pictures.
  2. Mol* is a web-based molecular viewer. Use the video tutorial Exploring PDB Structures in 3D with Mol*: Introductory Guide to get started with this molecular viewer. Access the full documentation learn about more advanced features. Mol* is accessible from each structure summary page, from the tab “3D View”.
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