CalcAGene, Inc.

1219 Broad St.

Durham, NC 27705
February 2, 2015
To: Chief Scientist, Center for Genome Dynamics, Jackson Lab
Subject: Apolipoprotein-E Case Study

Scope of Work
In this work, we analyze the apolipoprotein E protein that has been linkd with Alzheimers disease. We
characterize it in terms of its composition and features. We then create a rooted phylogenetic tree to
visualize the evolutionary changes in this protein. Lastly, we provide analysis of a biochemical pathway
to help understand the behavior of the APOE protein.

Methodology
Our methods are as follows:

1. Profile the APOE protein and its important alleles.

1.1. Import the proteins secondary structure from the Protein Data Bank.

2. Create a rooted phylogenetic tree to understand how it has changed over evolution.
2.1. For this part, we use the Student Biology Workbench.

3. Analyze a biochemical pathway from PharmGKB to better understand the behavior of APOE.

Results
Profile of the APOE protein
1. Apolipoptoein-E (APOE) is a protein produced by the liver that forms lipoproteins by combining
with lipids in the body. This is essential for the transport of cholestrol and fats through the
bloodstream. In particular, APOE helps move excess cholestrol to the liver for handling. The
proper functioning of APOE is vital to preventing cardiovascular diseases (Genetics Home
Reference).
2. Secondary structure of APOE:

YangProteinCaseStudy.nb

Import[
"http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&
structureId=2L7B", "PDB"]

3. In humans, the APOE gene is located on chromosome 19 from base pair 45,409,122 to base
pair 45,412,650. In mice, it is located on chromosome 17 from base pair 19,696,109 to base
pair 19,699,166 (Wikipedia).
4. APOE contains 299 amino acids (Wikipedia).
5. APOE has three major isoforms (different forms of the same protein): APOE2, APOE3, and
APOE4. These three differ at a couple of sites in their primary structures (Wikipedia).
6. The allelic form of APOE that is responsible for Alzheimers disease is the E4 allele. It has an
allele frequency of 14 percent and it is suspected of interacting with amyloid, resulting in
aggregates of amyloid plaques (Wikipedia).
7. It is important to keep in mind that people who with APOE4 are only at a higher risk for
developing Alzheimers disease. The allele does not always lead to the disease, and people
with the disease do not always have the allele (Genetics Home Reference).

References
APOE Gene. Genetics Home Reference. US National Library of Medicine, 10 Dec. 2008. Web. 31
Jan. 2015.
Apolipoprotein E. Wikipedia. Wikimedia Foundation, 11 Mar. 2006. Web. 02 Feb. 2015.

YangProteinCaseStudy.nb

Rooted Phylogenetic Tree

Protein sequences were uploaded to the Biology Workbench. The CLUSTALW alignment tool was
used to create an alignment file. Results were then obtained by using the DRAWGRAM function. The
output is displayed below.

YangProteinCaseStudy.nb

Statin Pathway

In this chart, the violet rectangle represents a drug (in this case, statin), the green rectangles represent
biological intermediates, the blue ovals represent regular genes, the light blue ovals represent transporter genes, and the arrows represent routes along which the molecules react. In this particular pathway, the production of APOE is inhibited by the introduction of statin, which inhibits the metabolism of
the cholestrol ester, into the liver cell (Source: Introduction to Computational Biology). This in turn
affects the transport of APOE through the plasma of the cell, reducing cardiovascular disease risk.