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Conformational analysis of the first observed non-proline cis-peptide bond occurring within the complementarity determining region (CDR) of an antibody
- Source :
- Journal of Molecular Biology. 284:549-555
- Publication Year :
- 1998
- Publisher :
- Elsevier BV, 1998.
-
Abstract
- An analysis has been performed on the first example of a non-proline cis- peptide bond found within a complementarity determining region (CDR) of an antibody. The bond is located in CDR 3 of the heavy chain (H3) and makes substantial interactions to a peptide from a breast tumour-associated antigen. The antibody-peptide complex is compared, both in H3 length (six residues) and peptide conformation, to a number of other such complexes in the Brookhaven Data Bank (PDB). There is only one other H3 loop of the same length. Analysis of loop searches of the PDB, taken over the H3 framework of SM3, suggest that there is a limited repertoire of conformations for loops of length 6 compared to loops of length 5 and 7. It is argued that the cis-peptide bond is present because of the limited number of loop conformations of length 6, plus, the requirement of the H3 loop to contact the bound peptide. Modelling suggests that an all-trans-peptide loop conformation can replace the H3 loop and this raises the question of whether there is a trans- to cis-peptide bond isomerization upon peptide binding.
- Subjects :
- Models, Molecular
chemistry.chemical_classification
Databases, Factual
Proline
Protein Conformation
Stereochemistry
Immunoglobulin Variable Region
Protein Data Bank (RCSB PDB)
Peptide
Peptide binding
Complementarity determining region
Crystallography, X-Ray
Antibodies
Peptide Conformation
Loop (topology)
Crystallography
Protein structure
chemistry
Structural Biology
Peptide bond
Peptides
Molecular Biology
Subjects
Details
- ISSN :
- 00222836
- Volume :
- 284
- Database :
- OpenAIRE
- Journal :
- Journal of Molecular Biology
- Accession number :
- edsair.doi.dedup.....db6a5ff7d98a6f383b767e7b7f0a8077