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== Structural highlights == | == Structural highlights == | ||
The three-dimensional structure of WO2 was obtained thanks to X-ray crystallography. | 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 (antigen binding fragment) in the space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> (Form A) (the Form B, not discussed here, corresponds to the WO2 Fab crystallized in the space group P2<sub>1</sub>). Thus, in what follows, the different features correspond to the Form A. | + | The structure of WO2 that is described here is that of '''WO2 murine anti-Aβ monoclonal Fab (antigen binding fragment) in the space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> (Form A)''' (the Form B, not discussed here, corresponds to the WO2 Fab crystallized in the space group P2<sub>1</sub>). 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 '''(Figure 1)'''. The heavy chain is made up of 252 amino acids while the light chain is made up of 224 amino acids.<ref>http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=63842</ref> [[Image:Fig. 1a.png|thumb|'''Figure 1 :''' WO2 Fab variable domain structures after superimposition of their Cα atoms. Form A is in yellow and Form B is in green<ref>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</ref>]] | This structure appears to be that of a typical immunoglobulin (Ig) Fab heavy-chain/light-chain heterodimer '''(Figure 1)'''. The heavy chain is made up of 252 amino acids while the light chain is made up of 224 amino acids.<ref>http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=63842</ref> [[Image:Fig. 1a.png|thumb|'''Figure 1 :''' WO2 Fab variable domain structures after superimposition of their Cα atoms. Form A is in yellow and Form B is in green<ref>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</ref>]] | ||
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Ser62H is a non-CDR loop involved in symmetry-related close contacts. | 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 φ/Ψ 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.<ref>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</ref> | + | Val51 of the light chain is the only residue to fall outside allowed regions of the Ramachandran plot. The unfavorable φ / Ψ 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.<ref>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</ref> |
In the WO2 Form A structure, 2 sodium ions were found, involved in crystal contacts, and 1 zinc ion bound to Asp1L of WO2. | In the WO2 Form A structure, 2 sodium ions were found, involved in crystal contacts, and 1 zinc ion bound to Asp1L of WO2. | ||
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Aβ<sub>1-16</sub> 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. | Aβ<sub>1-16</sub> 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 '''(Figure 2)'''.[[Image:Fig. 2.png|left|frame|'''Figure 2 :''' Surface representation of the WO2 antibody CDRs in complex with Aβ<sub>1-16</sub><ref>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</ref>]] | + | 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 '''(Figure 2)'''.[[Image:Fig. 2.png|left|frame|'''Figure 2 :''' Surface representation of the WO2 antibody CDRs in complex with Aβ<sub>1-16</sub><ref>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</ref>]] |
The surface area of the Aβ<sub>2-8</sub> 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 '''(Table 1)''' that residues in the middle of the Aβ<sub>1-16</sub> structure exhibit lower B-factors than atoms at the N- and C- termini of the Aβ<sub>1-16</sub> 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[http://en.wikipedia.org/wiki/Debye%E2%80%93Waller_factor]).[[Image:Table 2.png|frame|center|'''Table 1 :''' Buried Surface Areas (BSAs) and B-factors of Aβ residues contacting WO2<ref>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</ref>]] Phe4 and His6 are completely buried in the Fab interface, each with about half of its surface area buried in the V<sub>H</sub> interface and about half buried in the V<sub>L</sub> interface. All other residues are located exclusively at the interface with either the V<sub>H</sub> or the V<sub>L</sub> domains. | The surface area of the Aβ<sub>2-8</sub> 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 '''(Table 1)''' that residues in the middle of the Aβ<sub>1-16</sub> structure exhibit lower B-factors than atoms at the N- and C- termini of the Aβ<sub>1-16</sub> 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[http://en.wikipedia.org/wiki/Debye%E2%80%93Waller_factor]).[[Image:Table 2.png|frame|center|'''Table 1 :''' Buried Surface Areas (BSAs) and B-factors of Aβ residues contacting WO2<ref>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</ref>]] Phe4 and His6 are completely buried in the Fab interface, each with about half of its surface area buried in the V<sub>H</sub> interface and about half buried in the V<sub>L</sub> interface. All other residues are located exclusively at the interface with either the V<sub>H</sub> or the V<sub>L</sub> domains. | ||
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===Comparison of unliganted and liganted WO2 Fab structures=== | ===Comparison of unliganted and liganted WO2 Fab structures=== | ||
| - | Unliganted and liganted structures '''(Figure 4)''' 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[http://en.wikipedia.org/wiki/Root-mean-square_deviation]). 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. | + | Unliganted and liganted structures '''(Figure 4)''' 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[http://en.wikipedia.org/wiki/Root-mean-square_deviation]). 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.<ref>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</ref> | Moreover, thanks to temperature-factors analysis, it appears that CDR H1 is much less flexible in the liganted structure.<ref>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</ref> | ||
[[Image:Fig. 1b.png|frame|'''Figure 4 :''' Representation of Aβ (shown as ball-and-stick) in the WO2 Fab variable domain CDRs after superimposition of their Cα atoms. The unliganted Form A is in yellow and the complex with Aβ<sub>1-16</sub> is in blue<ref>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</ref>]] | [[Image:Fig. 1b.png|frame|'''Figure 4 :''' Representation of Aβ (shown as ball-and-stick) in the WO2 Fab variable domain CDRs after superimposition of their Cα atoms. The unliganted Form A is in yellow and the complex with Aβ<sub>1-16</sub> is in blue<ref>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</ref>]] | ||
Revision as of 21:47, 3 January 2015
Anti-amyloid-beta Fab WO2 (Form A, P212121)
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