Aroop Sircar - Analysis and Modeling of the Variable Region of Camelid Single Domain Antibodies

Version 1

      Publication Details (including relevant citation   information):

      Aroop Sircar, Kayode A. Sanni, Jiye Shi & Jeffrey J. Gray

      The Journal of Immunology, 2011

      Abstract:

      Camelids have a special type of antibodies, known as heavy chain   antibodies (HCAbs), that are devoid of classical antibody light   chains. Relative to classical antibodies, camelid HCAbs (cAbs)   have comparable immunogenicity, antigen recognition diversity and   binding affinities, higher stability and solubility, and better   manufacturability, making them promising candidates for alternate   therapeutic scaffolds. Rational engineering of cAbs to improve   therapeutic function requires knowledge of the differences of   sequence and structural features between cAbs and classical   antibodies. Here, amino acid sequences of 27 cAb variable regions   (VHH) were aligned with the respective regions of 54 classical   antibodies to detect amino acid differences, enabling automatic   identification of cAb VHH complementarity determining regions   (CDRs). CDR analysis revealed that the H1 often (and sometimes   the H2) adopts diverse conformations not classifiable by   established canonical rules. Also, while the cAb H3 is much   longer than classical H3 loops, it often contains common   structural motifs and sometimes a disulfide bond to the H1.   Leveraging these observations, we created a Monte Carlo based cAb   VHH structural modeling tool, where the CDR H1 and H2 loops   exhibited a median root-mean-square-deviation (rmsd) to native of   3.1 and 1.5 Å respectively. The protocol generated 8-12, 14-16   and 16-24 residue H3 loops with a median rmsd to native of 5.7,   4.5 and 6.8 Å respectively. The large deviation of the predicted   loops underscores the challenge in modeling such long loops. cAb   VHH homology models can provide structural insights into   interaction mechanisms to enable development of novel antibodies   for therapeutic and biotechnological use.

      Address (URL): http://dx.doi.org/10.4049/jimmunol.1100116