Sharmila Acharya Dave Hjulberg William Schuetz Richard Sprague Govindan Subramani
December 6, 2002
Overall approach SAGE map Protein structure Organism comparisons Implications
What¶s special about APOE?
³Polymorphic´: like eye color, each of us has one of three common kinds. Differs by ancestral origin Affects likelihood of disease
± If you have the ³bad´ kind, then your odds of Alzheimers are significantly higher. ± If you have the ³good´ kind, then enjoy a high-fat diet with low risk of heart disease.
Accession #: M12529
Protein ID: AAB59518.1
Literature PubMed OMIM
OMIM #: 107741
What drugs are used?
Protein Cn3D Structure Protein Explorer Analysis
Three types of human apolipoprotein E (alleles)
± E2, E3, and E4, encoded by epsilon2, 3, and 4, respectively.
Epsilon3 is the most common allele (³wildtype´).
E3 NH2 ---- Cys112 -----Arg158 ---- COOH
Epsilon4 differs from epsilon3 by a cys-to-arg change at position 112 (cys112arg).
E4 NH2 ---- Arg112 ------Arg158 -----COOH
Epsilon 2 differs from epsilon3 by a arg-to-cys change at position 158
E2 NH2 ---- Cys112 -----Cys158 -----COOH
What is Apolipoprotein?
Combine with cholesterol and triglycerols Apolipoproteins, including APOE,
± Help maintain lipoprotein structures ± Co-factor in lipid metabolism ± Act as ligands for lipoprotein receptors
The protein part of fatty proteins. Critical to formation of VLDL and chylomicrons.
Apoe3 ³most common´ version Generally characterized by low incidence of heart disease 2 major domains
Mutations in the first domain result in APOE2 and APOE4
2 Common Mutations
Both are in the Receptor Binding Domain with the "Receptor" being a binding region on the Low Density Lipoprotein (LDL). The literature suggests that the difference in the disease-producing ability of the changed proteins lies in their relative binding abilities to the Chylomicrons that clear cholesterol from the blood.
Apoe2 homozygotes (having 2 Apoe2 alleles) are more likely to develop a disease called Type III Hyperlipoproteinemia, characterized by high blood plasma cholesterol and triglycerides and an increased risk of atherosclerosis. But this Apoe2 homozygosity occurs in only about 1% of the population, and it seems that additional genetic and environmental factors are required to develop the disease. An extremely low-fat and low-cholesterol diet does not seem to affect the disease, once established.
APOE4 amino acid substitution at amino acid 112
± Arginine (positively charged, hydrophillic) instead of cysteine (uncharged, hydrophobic). ± Similar to APOE2, a lot-fat diet does not help.
188 mRNA sequences²158 of them clustered in 1 UniGene cluster (Hs. 169401, apoE), and 30 of them unclustered # Libraries
26 20 16 12 5
Brain mammary gland prostate or ovary colon, pancreas, or intestine kidney, vascular, or thalamus
Collaboration of SAGE Results
³Apolipoprotein is synthesized in various organs including liver, brain, spleen, and kidney.´
Science 1988 Apr 29;244:4852 (622-30)
³APOE is expressed at highest levels in liver, with almost no intestinal expression. Brain levels of expression were second only to liver. Adrenal, testis, and ovary also express APOE at lower levels. Treatment with exogenous estradiol caused significant increases in brain APOE mRNA´
Expression in Tissues
Expression in Tissues
± PDB data viewed through Protein Explorer ± Made 3 images of each structure (Helices, SpaceFill, and SaltBridges), except for the fragment (which has no salt bridges) ± Rotate each image into similar position ± Compare
Lipid Binding and Hydrophobic Clusters
Protein Structure: APOE3
Protein Structure: APOE2
Protein Structure: APOE4
APOE is the primary ligand for 2 receptors
± Low density lipoprotein (LDL) receptor found in the liver. ± An APOE-specific receptor found in blood plasma.
In the mutations, the binding capability may be compromised.
Tandem repeats in coding regions suggest the gene evolved through duplications of a primordial gene. J Mol Biol 1986; 187:325-40
M.musculus: (mouse) R.norvegicus: (rat)
ref:NP_033826.1 apolipoprotein E [Mus musculus] sp:P02650 - APE_RAT APOLIPOPROTEIN E PRECURSOR (APO-E)
% identity and length
71 % / 315 aa (see ProtEST ) 69 % / 315 aa (see ProtEST )
ref:NP_196392.1 putative protein [Arabidopsis thaliana]
28 % / 303 aa (see ProtEST
D.melanogas ref:NP_524658.1 30 % / 305 aa ter: pericardine [Drosophila (see ProtEST ) melanogaster] (fruit fly)
APOE2 Mediterranean Lapps Khoi San Pygmies Aborigines (Australia) Native Americans 0.00 0.04 0.20 APOE3 APOE4 0.89 0.07 0.31 0.37 0.41 0.26 0.28
Source: OMIM # 107741: Corbo and Scacchi (1999)
Craig Ventor of Celera has APOE4
± Associated with Alzheimers and Mad Cow
± http://www.bioheartinc.com/biogeno_pricelist_ 0700a.html
Will test your APOE e4 alleles for $295.
Complete list of labs that test for APOE.