1gpo
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(New page: 200px<br /> <applet load="1gpo" size="450" color="white" frame="true" align="right" spinBox="true" caption="1gpo, resolution 1.95Å" /> '''CRYSTAL STRUCTURE O...)
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Revision as of 07:24, 18 November 2007
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CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT
Overview
In a protein design study the artificial antibody M41 was modelled with, its binding site complementary to the protease inhibitor cystatin, which, was chosen as a structurally well-characterized "antigen". The modelling, of M41 took advantage of the crystal structure of the anti-lysozyme, antibody HyHEL-10 as a structural template. Its combining site was, reshaped by replacing 19 amino acid side-chains in the hypervariable, loops. In addition, ten amino acid residues were substituted in the, framework regions. The crystal structure of the corresponding antibody, model M41, which was produced as an F(ab) fragment in Escherichia coli, was determined at a resolution of 1.95 A. The crystals exhibited symmetry, of the space group P2(1)2(1)2(1) (a = 96.5 A; b = 103.5 A; c = 113.6 A), with two F(ab) fragments in the asymmetric unit, which were independently, refined (final R-factor 21.7%). The resulting coordinates were used for a, detailed comparison with the modelled protein structure. It was found that, the mutual arrangement of the six complementarity-determining regions as, well as most of their backbone conformation had been correctly predicted., One major difference that was detected for the conformation of a five, residue insertion in complementarity-determining region L1 could be, explained by an erroneously defined segment in the structure of the, antibody 4-4-20, which had been used as a template for this loop. In the, light of more recent crystallographic data it appears that this segment, adopts a new canonical structure. Apart from this region, most of the, side-chains in the antigen-binding site had been properly placed in the, M41 model. There was however one important exception concerning Trp H98, whose side-chain conformation had been kept as it appeared in HyHEL-10., The differing orientation of this residue in the model compared with the, crystal structure of the artificial F(ab) fragment M41 explains why an, antigen affinity could not be detected so far. The detailed analysis of, this and other, more subtle deviations suggests how to make this F(ab), fragment function by introducing a few additional amino acid changes into, M41.
About this Structure
1GPO is a Protein complex structure of sequences from Mus musculus and Synthetic construct with SO4 as ligand. Full crystallographic information is available from OCA.
Reference
The rational construction of an antibody against cystatin: lessons from the crystal structure of an artificial Fab fragment., Schiweck W, Skerra A, J Mol Biol. 1997 May 23;268(5):934-51. PMID:9180382
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