Sandbox Reserved 963

Alzheimer's disease (AD), is the most common form of dementia. It is a chronic neurodegenerative disease that usually develops slowly and get worse over time, becoming severe enough to interfere with daily tasks. The most common early symptom of Alzheimer's disease is the difficulty in remembering recently learned information. As the patient with Alzheimer’s disease ages, symptoms such as speaking problems, language problems, mood swings, disorientation, behavioural issues, and loss of motivation, can appear.

Acetylcholinesterase inhibitors such as rivastigmine, tacrine, donepezil and galantamine or, memantine, which is a NMDA receptor antagonist, are used to treat the patients suffering from AD but unfortunately, the benefit from their use is small. It is important to understand that none of these medications stops the disease itself.

However, many groups of researchers are seeking a solution to this problem and most of them are currently focused on the activity of a small peptide called Amyloid β (Aβ).

One of the hypothetical causes of this disease is depicted as the presence of the amyloid plaques (which are composed of Aβ) found in the brains of Alzheimer patients.

These are peptides of 36–43 amino acids, obtained via proteolysis of Amyloid Precursor Protein (APP) by β and γ secretases. An immunologic approach to the disease is made. Researchers have developped a monoclonal antibody, WO2, which can bind specifically to the Aβ’s epitope, thus leading the complex to be phagocyted.

Structural highlights

The three-dimensional structure of WO2 was obtained thanks to X-ray crystallography. The structure of WO2 that is described here is that of WO2 murine anti-Aβ monoclonal Fab in the space group P2₁2₁2₁ (Form A) (the Form B, not discussed here, corresponds to the WO2 Fab crystallized in the space group P2₁). Thus, in what follows, the different features correspond to the Form A.

This structure appears to be that of a typical immunoglobulin (Ig) Fab heavy-chain/light-chain heterodimer. The heavy chain is made up of 252 amino acids while the light chain is made up of 224 amino acids.^[1]

In Form A, we notice an elbow angle of 192°.

Constant (C) and variable (V) domains of both light (_L) and heavy (_H) chains include the following residues : V_L(1-107), C_L(108-212), V_H(2-113) and C_H(114-213).

V_H(Pro40 to Lys43) corresponds to a loop in the sequence between CDRs (Complementarity Determining Regions) heavy-chain 1 (H1) and H2, located in the hinge region of the Fab away from the ligand binding site. However, this loop is associated with poor electron density and, therefore, there is some uncertainty about the accuracy of the model in this region. Ser62H is a non-CDR loop involved in symmetry-related close contacts. Val51 of the light chain is the only residue to fall outside allowed regions of the Ramachandran plot. The unfavorable phi/psi torsion angles arise from the fact that this residue is in a γ-turn restrained by the (i to i+2) hydrogen bond between the Gln50L backbone carbonyl and the Ser52L amide.^[2]

In the WO2 Form A structure, 2 sodium ions were found, involved in crystal contacts, and 1 zinc ion bound to Asp1L of WO2.

Here are the on the complexe.

Interactions with the ligand Aβ(1-16)

Overview of the WO2:Aβ(1-16) complex

Aβ(1-16) represents the minimal zinc binding domain and contains the entire immunodominant B-cell epitope of Aβ, it is therefore interesting to see how this fragment of Aβ interacts with WO2.

First, the main residues which closely contact the CDRs of WO2 by sitting within the antigen binding site of WO2 are Ala2 to Ser8 and they stretch 20 Å from the N-terminus to the C-terminus.

The surface area of the Aβ(2-8) structure is 1118 Ų, of which 60% is buried (665 Ų) in the antibody interface. What’s more, we note two significant interfaces between Aβ and WO2 : a 367 Ų surface contacting the heavy chain and a 298 Ų surface contacting the light chain. We notice that residues in the middle of the Aβ(1-16) structure exhibit lower B-factors than atoms at the N- and C- termini of the Aβ(1-16) peptide, indicating they are more flexible (since the B-factor, also called the temperature factor, represents the relative vibrational motion of different parts of a structure and thus, atoms with low B-factors belong to a part of the structure quite rigid whereas atoms with high B-factors generally belong to part of a structure that is very flexible[1]). Phe4 and His6 are completely buried in the Fab interface, each with about half of its surface area buried in the V_H interface and about half buried in the V_L interface. All other residues are located exclusively at the interface with either the V_H or the V_L domains.

Residues of the light chain closely contacting Aβ residues include His27(D)L, Ser27(E)L and Tyr32L from light-chain CDR 1 (L1) and Ser92L, Leu93L, Val94L and Leu96L from L3.

All residues from Phe4 to Ser8, except Asp7, make close contact with the WO2 heavy-chain CDRs. Close contacting interface residues include His50H, Tyr52H, Asp54H and Asp56H from H2 and Tyr100(B)H and Asn100(E)H from H3.

Besides, we observe no contact between Aβ and the L2 or H1 CDRs of WO2 and there is no evidence in the structure of any water-mediated contacts between WO2 and Aβ.^[3]

Details of the close interactions between WO2 and Aβ(2-8)

As mentionned previously, the residues of Aβ closely interacting with the CDRs of WO2 extend from Ala2 to Ser8. Let's focus on the interactions of each of these residues with the antibody :

Interactions with Ala2

Ala2 of is recognized by WO2 through a hydrogen bond between its main chain carbonyl and the amide of Val94L.

Interactions with Glu3

There is a hydrogen bond between the side chain of Glu3 and the main-chain amide of Ser27(E)L. In addition, there are potential salt bridges between the side chain of Glu3 and Nδ1/Nε2 atoms of His27(D)L.

Interactions with Phe4

There is a hydrogen bond between the amide of Phe4 and the carbonyl of Ser92L.

Interactions with Arg5

Arg5 is a donor for 5 side chain-side chain hydrogen bonds and 1 main chain-side chain hydrogen bond, involving Asp54H, Asp56H and Tyr52H as follows :

• The side chain of Arg5 forms :
  • Two hydrogen bonds with the carboxylate of Asp54H
  • One hydrogen bond with the side chain of Asp56H
• The main chain of Arg5 interacts with the side-chain hydroxyle (OH) of Tyr52H

Interactions with His6

His6 contacts both heavy- and light-chain elements with 10 side chain-side chain hydrophobic contacts with Asn100(E)H. Van der Waals contacts have been detected between His6 and Tyr32L of WO2. With Phe4 and Arg5, His6 represents the core of the epitope of Aβ which sits at the heavy-chain/light-chain junction of the CDRs of WO2.

Interactions with Ser8

Ser8 makes a single Van der Waals contact with Tyr100(B)H of WO2.

The special case of Asp7

Asp7 sits above a large water-filled cavity in the Fab antigen binding site but makes no direct or water-mediated contacts with WO2.

Comparison of unliganted and liganted WO2 Fab structures

Unliganted and liganted structures superimpose very closely with an r.m.s.d. (root-mean-square deviation) of 0.3 Å on all Cα atoms (the r.m.s.d. is the measure of the average distance between the atoms of superimposed proteins[2]). Even the CDRs of liganted and unliganted states are barely distinguishable. Except some small variations (<1 Å) around Ser27(E)L (L1), Lys33H (H1), Asp54H (H2) and Glu100(C)H (H3), there is no substantial change in the CDRs when Aβ binds WO2. Moreover, thanks to temperature-factors analysis, it appears that CDR H1 is much less flexible in the liganted structure.^[4]

Biological Relevance

One of the most common isoforms of Aβ is the 42-mer Aβ (its sequence is 1-DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA-42), which is the most fibrillogenic isoforms and is therefore linked to disease states.

Aβ₄₂ damages and kills neurons by generating reactive oxygen species when it self-aggregates. Aβ self-aggregation is promoted by its binding with metal ions (such as Cu²⁺, Zn²⁺, etc) thanks to, among others, its His6, His13, His14, Tyr10, Asp1 and Glu11 residues. If this process occurs on the membrane of neurons, it causes lipid peroxidation and the generation of a toxic aldehyde called 4-hydroxynonenal which, in turn, impairs the function of ion-motive ATPases, glucose transporters and glutamate transporters. It also triggers depolarization of the synaptic membrane, excessive calcium influx and mitochondrial impairment, making neurons vulnerable to excitotoxicity and apoptosis : this is the beginning of the neurodegenerative process of AD.^[5]

The important role of metals in AD is highlighted by a metal chelator, the clioquinol, which reduces amyloid plaques in the brain of AD patients.

The mAb WO2 recognises the N-terminus of Aβ. This region of Aβ constitutes the immunodominant B-cell epitope of Aβ and lacks T-cell epitopes involved in the toxicity of previous clinical trials. Thanks to some experiments, it has been deduced that the great interest of WO2 lies in the fact that when it binds Aβ, it prevents Asp 1 and His6 of Aβ to participate in metal coordination, preventing Aβ from aggregating and thus, harmful effects of Aβ are neutralized.^[6]

Related Structures

• 1plg : Another IgG_2a κ murine mAb Fab
• PFA1, PFA2
• 3bkc : WO2 Fab Form B
• 3bkj : WO2 Fab:Aβ(1-16) complex
• 3bae : WO2 Fab:Aβ(1-28) complex

Contributors

Kerim Secener and Nicolas Pautrieux

References

1. ↑ http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=63842
2. ↑ Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.,Miles LA, Wun KS, Crespi GA, Fodero-Tavoletti MT, Galatis D, Bagley CJ, Beyreuther K, Masters CL, Cappai R, McKinstry WJ, Barnham KJ, Parker MW J Mol Biol. 2008 Mar 14;377(1):181-92. Epub 2008 Jan 30. PMID:18237744
3. ↑ Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.,Miles LA, Wun KS, Crespi GA, Fodero-Tavoletti MT, Galatis D, Bagley CJ, Beyreuther K, Masters CL, Cappai R, McKinstry WJ, Barnham KJ, Parker MW J Mol Biol. 2008 Mar 14;377(1):181-92. Epub 2008 Jan 30. PMID:18237744
4. ↑ Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.,Miles LA, Wun KS, Crespi GA, Fodero-Tavoletti MT, Galatis D, Bagley CJ, Beyreuther K, Masters CL, Cappai R, McKinstry WJ, Barnham KJ, Parker MW J Mol Biol. 2008 Mar 14;377(1):181-92. Epub 2008 Jan 30. PMID:18237744
5. ↑ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091392/
6. ↑ Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.,Miles LA, Wun KS, Crespi GA, Fodero-Tavoletti MT, Galatis D, Bagley CJ, Beyreuther K, Masters CL, Cappai R, McKinstry WJ, Barnham KJ, Parker MW J Mol Biol. 2008 Mar 14;377(1):181-92. Epub 2008 Jan 30. PMID:18237744