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Canonical structures of short CDR-L3 in antibodies.

Teplyakov A, Gilliland GL - Proteins (2014)

Bottom Line: Their correct identification is essential for successful prediction of antibody structure.This in turn requires regular updates of the classification of canonical structures to match the expanding experimental database.We have analyzed all crystal structures of Fab and Fv with the eight-residue CDR-L3 and identified three major canonical structures covering 82% of a nonredundant set.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Center of Excellence, Janssen Research and Development, LLC, Spring House, Pennsylvania, 19477.

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Regions of the Ramachanran plot according to North et al.5 A for α-helix, B for β-sheet, P for polyproline II, L for the left-handed helix, D for the δ-region, G for the γ-region.
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fig02: Regions of the Ramachanran plot according to North et al.5 A for α-helix, B for β-sheet, P for polyproline II, L for the left-handed helix, D for the δ-region, G for the γ-region.

Mentions: The CDR conformations were described in terms of the backbone dihedral angles φ and ψ. For visual convenience, the CDR sequences were mapped onto the Ramachandran plot divided into six regions (Fig. 2) following North et al.5 Canonical structures were assigned manually on the basis of φ/ψ patterns only. Spatial orientation with respect to other CDRs was not taken into account. All crystallographic calculations were performed with the CCP4 suite of programs.9 Protein structures were inspected using Coot.10 Figures were created with PyMOL, version 0.98 (DeLano Scientific, LLC).


Canonical structures of short CDR-L3 in antibodies.

Teplyakov A, Gilliland GL - Proteins (2014)

Regions of the Ramachanran plot according to North et al.5 A for α-helix, B for β-sheet, P for polyproline II, L for the left-handed helix, D for the δ-region, G for the γ-region.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4260120&req=5

fig02: Regions of the Ramachanran plot according to North et al.5 A for α-helix, B for β-sheet, P for polyproline II, L for the left-handed helix, D for the δ-region, G for the γ-region.
Mentions: The CDR conformations were described in terms of the backbone dihedral angles φ and ψ. For visual convenience, the CDR sequences were mapped onto the Ramachandran plot divided into six regions (Fig. 2) following North et al.5 Canonical structures were assigned manually on the basis of φ/ψ patterns only. Spatial orientation with respect to other CDRs was not taken into account. All crystallographic calculations were performed with the CCP4 suite of programs.9 Protein structures were inspected using Coot.10 Figures were created with PyMOL, version 0.98 (DeLano Scientific, LLC).

Bottom Line: Their correct identification is essential for successful prediction of antibody structure.This in turn requires regular updates of the classification of canonical structures to match the expanding experimental database.We have analyzed all crystal structures of Fab and Fv with the eight-residue CDR-L3 and identified three major canonical structures covering 82% of a nonredundant set.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Center of Excellence, Janssen Research and Development, LLC, Spring House, Pennsylvania, 19477.

Show MeSH
Related in: MedlinePlus