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. 2011 Feb 18;406(2):228-56.
doi: 10.1016/j.jmb.2010.10.030. Epub 2010 Oct 28.

A new clustering of antibody CDR loop conformations

Benjamin North  1 , Andreas Lehmann, Roland L Dunbrack Jr
Affiliations

A new clustering of antibody CDR loop conformations

Benjamin North et al. J Mol Biol. .

Abstract

Previous analyses of the complementarity-determining regions (CDRs) of antibodies have focused on a small number of "canonical" conformations for each loop. This is primarily the result of the work of Chothia and coworkers, most recently in 1997. Because of the widespread utility of antibodies, we have revisited the clustering of conformations of the six CDR loops with the much larger amount of structural information currently available. In this work, we were careful to use a high-quality data set by eliminating low-resolution structures and CDRs with high B-factors or high conformational energies. We used a distance function based on directional statistics and an effective clustering algorithm with affinity propagation. With this data set of over 300 nonredundant antibody structures, we were able to cover 28 CDR-length combinations (e.g., L1 length 11, or "L1-11" in our CDR-length nomenclature) for L1, L2, L3, H1, and H2. The Chothia analysis covered only 20 CDR-lengths. Only four of these had more than one conformational cluster, of which two could easily be distinguished by gene source (mouse/human; κ/λ) and one could easily be distinguished purely by the presence and the positions of Pro residues (L3-9). Thus, using the Chothia analysis does not require the complicated set of "structure-determining residues" that is often assumed. Of our 28 CDR-lengths, 15 have multiple conformational clusters, including 10 for which the Chothia analysis had only one canonical class. We have a total of 72 clusters for non-H3 CDRs; approximately 85% of the non-H3 sequences can be assigned to a conformational cluster based on gene source and/or sequence. We found that earlier predictions of "bulged" versus "nonbulged" conformations based on the presence or the absence of anchor residues Arg/Lys94 and Asp101 of H3 have not held up, since all four combinations lead to a majority of conformations that are bulged. Thus, the earlier analyses have been significantly enhanced by the increased data. We believe that the new classification will lead to improved methods for antibody structure prediction and design.

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Figures

Figure 1
Figure 1
CDR definitions used in this work. The sequence logos of each loop are shown with the first three and last three residues of the CDR in red and the flanking framework residues in black.
Figure 2
Figure 2
CDRs based on our definitions. a. L1 and H1; b. L2 and H2; c. L1 and H3. L1, L2, and L3 in dark blue; H1, H2, and H3 in magenta. Disulfides in yellow. The structure is PDB entry 1Q9R.
Figure 3
Figure 3
Ramachandran maps of clustering of L1-12. The median loop of cluster 1 (blue dots) has conformation BPABPBPAADBB, cluster 2 (magenta dots) has conformation BPABPPPLLPBB, and cluster 3 (green dots) has conformation BPPAADAAPPBB (see Figure 4 for definitions of Ramachandran regions).
Figure 4
Figure 4
Regions of the Ramachandran map.
Figure 5
Figure 5
Sequence logos for the three clusters of L1-11-1, L1-11-2, and L1-11-3 from top to bottom. The logos were drawn with the program Weblogo.
Figure 6
Figure 6
The median structures of clusters L1-11-1 (yellow) and L1-11-2 (magenta). The hydrogen bond of Tyr71 to the NH of residue 8 in cluster 2 is shown. The sequence and residue numbering given are from the L1-11-1 median structure, PDB-chain 1P7KL.
Figure 7
Figure 7
The median structures of the largest clusters of L3-9. a. L3-9-cis7-1 (yellow) + L3-9-cis7-2 (magenta). b. L3-9-cis7-1 (yellow) + L3-9-1 (blue) c. L3-9-cis7-1 (yellow) + L3-9-2 (green). The sequence of L3-9-cis7-1 from PDB entry-chain 1J1PL is marked.
Figure 8
Figure 8
Sequence logos for clusters H2-10-1, H2-10-2, H2-10-3, and H2-10-4 (top to bottom respectively).
Figure 9
Figure 9
The median structures of the largest clusters of H2-10. a. Cluster H2-10-1 (yellow) and H2-10-2 (magenta), b. H2-10-1 (yellow) and H2-10-3 (blue) and c. H2-10-1 (yellow) and H2-10-4 (green). The side chain of Arg71 of Clusters H2-10-2 and H2-10-4 are shown. This residue is Ala in both clusters 1 and 3 (not shown).
Figure 10
Figure 10
The median structures of the H3-anchor regions. a. Clusters H3-anchor-1 (yellow) and H3-anchor-2 (magenta); b. Clusters H3-anchor-1 (yellow) and H3-anchor-3 (blue/green). Clusters H3-anchor-1 and H3-anchor-3 are bulged and H3-anchor-2 is non-bulged.
Figure 11
Figure 11
Comparison of our CDR definitions with those of Al-Lazikani et al. and Martin-Thornton with the numbering scheme proposed by Honegger and Plückthun.
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References

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