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Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics
 

Summary: Soft docking an L and a D peptide to an anticholera toxin
antibody using internal coordinate mechanics
Rolf-Dietrich Stigler1*, Berit Hoffmann1, Ruben Abagyan2 and
Jens Schneider-Mergener1
Background: The tremendous increase in sequential and structural information
is a challenge for computer-assisted modelling to predict the binding modes of
interacting biomolecules. One important area is the structural understanding of
protein­peptide interactions, information that is increasingly important for the
design of biologically active compounds.
Results: We predicted the three-dimensional structure of a complex between
the monoclonal antibody TE33 and its cholera-toxin-derived peptide epitope
VPGSQHID. Using the internal coordinate mechanics (ICM) method of flexible
docking, the bound conformation of the initially extended peptide epitope to
the antibody crystal or modelled structure reproduced the known binding
conformation to a root mean square deviation of between 1.9 Ĺ and 3.1 Ĺ.
The predicted complexes are in good agreement with binding data obtained
from substitutional analyses in which each epitope residue is replaced by all
other amino acids. Furthermore, a de novo prediction of the recently
discovered TE33-binding D peptide dwGsqhydp (single-letter amino acid
code where D amino acids are represented by lower-case letters) explains

  

Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego

 

Collections: Biology and Medicine