2010 Biochemistry Protein Projects

Biochemistry I (CHM 340) or Foundations of Biochemistry (CHM 345)
Spring Semester
MAC Building Room 359
MWF, 1:20p.m.–2:30p.m.
Contact: Dr. Matthew Saderholm
CPO 2191
Berea College
Berea KY 40404

Amyloid Precursor Protein


Adam L. Meador

Protein Review Paper

CHM 345

Dr. Saderholm



Amyloid Precursor Protein: Alzheimer's Development and Propagation



In the ever-expanding realm of scientific research, great headway has been made in determining causation and pathogenesis of many diseases, infections, and other illnesses that humans are susceptible to. In order to understand the causation of these types of diseases, research must be conducted to better understand the organism(s) or biological properties that are involved. In many cases, abnormalities within the body are the causative agent, such as the case with amyloid precursor protein.

Amyloid precursor protein, abbreviated as APP, is a protein that is linked with the development of Alzheimer's disease in humans. It is estimated that over 20 million people are affected by this disease worldwide and this number is expected to keep growing (1). In this review, Alzheimer's disease and propagation will be discussed, followed by a breakdown of the basic components of amyloid precursor protein. Functions, direct and indirect, of APP and its subsequent processing will also be discussed. A review of the amyloid beta peptide, which seems to be the link between Alzheimer's disease and amyloid precursor protein, will also be given to better understand its importance to the disease.







Alzheimer's Disease and Propagation

Alzheimer's disease (AD) affects cognitive function in adults and the elderly. Alzheimer's is commonly defined as a disease that results in a decline in cognitive function as well as a degeneration of the brain (2). The problem with diagnosing a patient as having Alzheimer's disease is that the normal-aging process leads to some cognitive function degeneration and memory loss (3). Also, Alzheimer's has incompletely specified neuropsychological characteristics, which means that diagnosis is difficult due to the inconsistency in each individual patient's characteristics (4). Another difficulty is that confirmation can only be determined post-mortem (3). Amyloid precursor protein has been identified as one of few genetic links to Alzheimer's. Additionally, APP undergoes extensive post-translational modification which includes cleavage resulting in the amyloid beta fragment (5). Amyloid beta (Aβ) is the primary constituent of amyloid plaques in the brains of Alzheimer's patients; however it can only be quantified via post-mortem identification. The pathology of AD can be characterized as depositions of amyloid beta plaques in the brain, which leads to reactive Gliosis and neuronal dysfunction. Gliosis is the healing or repair of damaged cells within the central nervous system. These Aβ peptides are formed from cleavage of part of the amyloid precursor protein through proteolysis (6).








APP Structure

Amyloid precursor protein, also known as 3dxc, is a transmembrane protein and is found to be expressed throughout the human body (Figure 1) (7). The protein is composed of a massive Text Box: Figure 1. Proposed biological assembly image of 3dxc taken from the protein data bank (8).extracellular domain, a transmembrane region, and a cytoplasmic tail, which is the C-terminal region. The extracellular component comprises approximately 88% of the total mass of APP (9). APP is constructed of three highly conserved regions to form its complex structural domain. The regions are known as the E1, E2, and C regions (7, 10). Between the E1 and E2 regions lies a highly acidic region, while a protease-inhibitor domain lies in other isoforms of APP in this region. The E1 domain has two binding regions, one for Cu(II) binding and another that has a low-affinity for HSPG (heparan sulfate proteoglycans) binding. The E2 region, which is also the Text Box: Figure 2. Monomeric E2 domain/central APP domain (A) The position of the RERMS sequence is marked in blue, colored in green are amino-acid residues forming the two hydrophobic regions, and the conserved amino-acid residues of the HSPG-binding site are in red. (B) Surface representation of (A). The N- and C-termini as well as the underlined amino-acid residues of the RERMS sequence are labeled (11).largest of the three domains, also contains an HSPG binding site as well

as a pentapeptide sequence known as RERMS, which has been hypothesized to be the APP active site (Figure 2). This active site is thought to promote growth and differentiation for cells (7). The C region contains a binding site for Fe65, which is brain-enriched adaptor protein. Bound Fe65 is crucial for brain development. The C terminus region is structured so that up to eight phosphate groups can be bound. This distinction has proven to be connected to Alzheimer's disease-affected brains in that seven of these phosphorylation sites contain bound phosphate groups (2).


APP Function


The normal biological function of amyloid precursor protein in neurons has yet to be elucidated, but the protein has been shown to play important roles in the regulation of many important cellular functions (6, 9). In the central nervous system, APP is involved in synaptogenesis and synaptic plasticity (9). Synaptogenesis is the formation of new synapses between neurons, while synaptic plasticity refers to the ability of the synapse between two neurons to be able to change in strength. APP has also been shown to be a significant player as a contact receptor. Contact receptors can be thought of as adhesion proteins in that they are capable of binding specific cells or other components (9, 12). According to Gralle et al, studies utilizing cells in culture consistently showed APP in a role of cell adhesion to extracellular components or to other cells. APP was shown to increase adhesion to substrates, glial cells, and other cells in the nervous system. Within the central nervous system, APP seems to be an integral factor in the maturation of neurons (9).

Probably the most important aspect of amyloid precursor protein is its potential cleavage by three different enzymes known as α-, β-, and γ- secretases. Proteolytic cleavage by α- or β- secretase, which is carried out in a close range to the plasma membrane, expels the soluble extracellular domain of APP from the cell surface (7). This expelled component, known as secreted amyloid precursor protein (sAPPα), is hypothesized to be used by many cell types as a growth factor and has also been shown to promote neuronal repair (Figure 3) (9). Text Box: Figure 3. (A) Schematic representation of APP including the relative positions of α-, β- and γ-secretases cleavage sites. (B) The proposed growth factor domain, sAPPα, expelled to the extracellular region can be seen, as well as the proposed RERMS APP active site (11).Growth factors are substances that are capable of stimulating cellular proliferation, differentiation, as well as growth. Another probable hypothesis is that the membrane-bound APP may be involved in cell signaling, which is the complex communication system used by cells to govern basic cellular activities and actions. Molecules of APP that are not cleaved by α-secretase are capable of forming internalized endocytic compartments, which in turn are subsequently cleaved by β- and γ- secretases (6). γ- secretase carries out proteolytic modification further by processing the membrane-bound peptide into the amyloid beta (Aβ) peptide form (7). Generation of the Aβ peptide is borne solely from the cleavage of APP in which the amyloid precursor protein intracellular domain (AICD) is released and deposited in aggregated fibrils in senile plaques. Other APP protein family members do not form the Aβ peptide deposits on cleavage (6). It is important to restate that the physiological function of amyloid precursor protein and its relation to Alzheimer's disease propagation remain unclear, although other factors, such as identifying the secretases involved in proteolytic cleavage as well as other cellular factors involved in Aβ peptide deposits have been resolved (7).


Amyloid Beta Implications


Aβ peptide is responsible for forming senile plaques in the brain tissues of Alzheimer's disease patients (7). As stated earlier, Aβ is secreted from neurons through the cleavage of APP and seems to not play a major physiological role. Based on research conducted thus far, it seems that Aβ is nothing more than an expendable by-product of APP and its proteolytic cleavage by γ- secretase. According to Saido, no Aβ deposition takes place in healthy individuals even though APP processing occurs in the brains of both young and old. Based on these observations, Saido concurs that Aβ must be "constantly anabolized and rapidly catalyzed" under normal cellular conditions so that concentrations of the unwanted peptide are restrained. While it is certain that deposits of the Aβ peptide cause degeneration of neurons as well as dysfunction, the exact mechanism still remains to be resolved (1).




After reviewing the importance of Alzheimer's disease and the linked amyloid precursor protein, a better understanding can be gained into the importance of understanding this remarkably controversial protein and its structure as well as subsequent functions. Much research has been dedicated into discovering the actual function of APP, which would ultimately lend to the potential treatments for Alzheimer's patients. By understanding how Aβ deposits in the brain directly relate to the appearance of Alzheimer's as well as understanding the mechanism of the APP cleavage by the different secretases will be monumental in further developing possible treatment options for those suffering from Alzheimer's disease and its implications.


1. Saido, T. C. Aβ Metabolism and Alzheimer"s Disease; Landes Bioscience, Inc.: Georgetown, Texas, 2003.

2. Radzimanowski, J.; Simon, B.; Sattler, M.; Beyreuther, C.; Sinning, I.; Wild, K. Structure of the intracellular domain of the amyloid precursor protein in complex with Fe65-PTB2. EMBO Rep. 2008, 9 (11), 1134-1140.

3. Reischies, F. M. Dementia: Psychiatric Aspects. In International Encyclopedia of the Social and Behavioral Sciences; Elsevier Ltd., 2001; pp 3396-3401.

4. Almkvist, O. S2-04-05 What are neuropsychological criteria for differential diagnosis od dementia syndromes. Alzheimer"s and Dementia 2006, 2, S29.

5. Turner, P. R.; O"Connor, K.; Tate, W. P.; Abraham, W. C. Roles of amyloid precursor protein and its fragments in regulating neural activity, plasticity and memory. Progress in Neurobiology 2003, 70 (1), 1-32.

6. Priller, C.; Bauer, T.; Mitteregger, G.; Krebs, B.; Kretzschmar, H. A. Synapse Formation and Function Is Modulated by the Amyloid Precursor Protein. The Journal of Neuroscience 2006, 26 (27), 7212-7221.

7. Wang, Y.; Ha, Y. The X-Ray Structure of an Antiparallel Dimer of the Human Amyloid Precursor Protein E2 Domain. Molecular Cell 2004, 15, 343-353.

8. "Crystal structure of the intracellular domain of human APP in complex with Fe65-PTB2," http://www.rcsb.org/pdb/explore/explore.do?structureId=3DXC, accessed 2 December 2009.

9. Gralle, M.; Ferreira, S. T. Structure and functions of the human amyloid precursor protein: The whole is more than the sum of its parts. Progress in Neurobiology 2007, 82 (1), 11-32.

10. Beel, Andrew J.; Mobley, Charles K.; Kim, Hak J.; Tian, Fang; Hadziselimovic, Arina; Jap, Bing; Prestegard, James H.; Sanders, Charles R. Structural Studies of the Transmembrane C-Terminal Domain of the Amyloid Precursor Protein (APP): Does APP Function as a Cholesterol Sensor? Biochemistry 2008, 47, 9428-9446


11. Reinhard, Constanze.; Hebert, Sebastien S.; De Strooper, Bart. The amyloid-β precursor protein: integrating structure with biological function. The EMBO Journal, 2005, 24(23), 3996-4006.

12. Berg, J. M.; Tymoczko, J. L.; Stryer, L. Biochemistry, 6th ed.; W.H. Freeman and Company: New York, 2007.