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PDBsum entry 1seq
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Immune system
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PDB id
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1seq
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References listed in PDB file
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Key reference
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Title
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Neutralization of ngf-Trka receptor interaction by the novel antagonistic anti-Trka monoclonal antibody mnac13: a structural insight.
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Authors
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S.Covaceuszach,
A.Cattaneo,
D.Lamba.
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Ref.
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Proteins, 2005,
58,
717-727.
[DOI no: ]
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PubMed id
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Abstract
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MNAC13, a mouse monoclonal antibody, recognizes with high affinity and
specificity the neurotrophin receptor TrkA and displays a neutralizing activity
toward the NGF/TrkA interaction. Detailed knowledge of the molecular basis
determining the specificity of this antibody is of importance because of its
potential use as a modulator of the TrkA-mediated NGF activity. Here, we report
a full biochemical and structural characterization of the MNAC13 antibody.
Epitope mapping studies, by serial deletion mutants and by phage display, reveal
a conformational epitope that is localized on the carboxy-terminal region of the
first immunoglobulin-like domain (d4) of TrkA. The X-ray crystal structure of
the MNAC13 Fab fragment has been determined and refined to 1.8 A resolution. The
antigen-binding site is characterized by a crevice, surrounded by
hydrophilic-charged residues on either side, dipping deep toward three mainly
hydrophobic subsites. Remarkably an isopropanol molecule has been found to bind
in one of the hydrophobic crevices. Overall, the surface topology (shape and
electrostatic potential) of the combining site is consistent with the binding
data on TrkA ECD serial deletions mutants. The structure of the MNAC13 Fab
fragment may assist in the rational structure-based design of high affinity
humanized forms of MNAC13, appropriate for therapeutic approaches in neuropathy
and inflammatory pain states.
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Figure 2.
Figure 2. Perspective view of FabMNAC13 binding site: A:
Hydrophobic and hydrophilic characteristics of the
antigen-bindingsite of MNAC13 Fab fragment: (hydrophilic
residues are colored in cyan, hydrophobic residues in green,
basic residues in blue and acidic residues in red): molecular
surface representation of FabMNAC13 P1 pocket with bound
isopropanol colored in yellow (right) and empty (left). Figures
produced by GRASP.[56] B: Stereo view of the cleft with the
final  [a]
weighted 2Fo-Fc map contoured at 1.5 ;
showing an isopropanol molecule (green density) and a water
molecule trapped at the bottom of the P1 subsite encompassing
Tyr L32, Trp L91 and His L34 (blue density).
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Figure 3.
Figure 3. Homology structure-based TrkA d4 domain model to
telokin[35] (PDBID 1FHG) template produced with the 3D-PSSm
server,[34] MNAC13 epitope is shown in red: (A) Sequence
alignment of TrkA_d4 with the two templates, (B) Ribbon
representation of TrkA d4 model.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2005,
58,
717-727)
copyright 2005.
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Secondary reference #1
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Title
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Purification, Crystallization and preliminary X-Ray analysis of the FAB fragment from mnac13, A novel antagonistic anti-Tyrosine kinase a receptor monoclonal antibody.
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Authors
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S.Covaceuszach,
A.Cattaneo,
D.Lamba.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
1307-1309.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 A typical prismatic bundle-like crystal of FabMNAC13,
approximate dimensions are 0.8 × 0.3 × 0.2 mm.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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