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Title: A structure-based database of antibody variable domain diversity

Abstract

The diversity of natural antibodies is limited by the genetic mechanisms that engender diversity and the functional requirements of antigen binding. Using an in vitro-evolved autonomous heavy chain variable domain (V{sub H}H-RIG), we have investigated the limits of structurally-tolerated diversity in the three complementarity-determining regions and a fourth loop within the third framework region. We determined the X-ray crystal structure of the V{sub H}H-RIG domain at 1.9 {angstrom} resolution and used it to guide the design of phage-displayed libraries encompassing the four loops. The libraries were subjected to selections for structural stability, and a database of structurally-tolerated sequences was compiled from the sequences of approximately 1000 unique clones. The results reveal that all four loops accommodate significantly greater diversity than is observed in nature. Thus, it appears that most sequence biases in the natural immune repertoire arise from factors other than structural constraints and, consequently, it should be possible to enhance the functions of antibodies significantly through in vitro evolution.

Authors:
; ; ;  [1]
  1. (Genentech)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE
OSTI Identifier:
1008600
Resource Type:
Journal Article
Journal Name:
J. Mol. Biol.
Additional Journal Information:
Journal Volume: 348; Journal Issue: (3) ; 2005; Journal ID: ISSN 0022-2836
Country of Publication:
United States
Language:
ENGLISH
Subject:
36 MATERIALS SCIENCE; ANTIBODIES; ANTIGENS; CHAINS; CRYSTAL STRUCTURE; DESIGN; FUNCTIONALS; GENETICS; IN VITRO; MUTAGENESIS; PROTEIN ENGINEERING; RESOLUTION; STABILITY

Citation Formats

Bond, C.J., Wiesmann, C., Marsters, Jr., J.C., and Sidhu, S.S. A structure-based database of antibody variable domain diversity. United States: N. p., 2010. Web.
Bond, C.J., Wiesmann, C., Marsters, Jr., J.C., & Sidhu, S.S. A structure-based database of antibody variable domain diversity. United States.
Bond, C.J., Wiesmann, C., Marsters, Jr., J.C., and Sidhu, S.S. Tue . "A structure-based database of antibody variable domain diversity". United States.
@article{osti_1008600,
title = {A structure-based database of antibody variable domain diversity},
author = {Bond, C.J. and Wiesmann, C. and Marsters, Jr., J.C. and Sidhu, S.S.},
abstractNote = {The diversity of natural antibodies is limited by the genetic mechanisms that engender diversity and the functional requirements of antigen binding. Using an in vitro-evolved autonomous heavy chain variable domain (V{sub H}H-RIG), we have investigated the limits of structurally-tolerated diversity in the three complementarity-determining regions and a fourth loop within the third framework region. We determined the X-ray crystal structure of the V{sub H}H-RIG domain at 1.9 {angstrom} resolution and used it to guide the design of phage-displayed libraries encompassing the four loops. The libraries were subjected to selections for structural stability, and a database of structurally-tolerated sequences was compiled from the sequences of approximately 1000 unique clones. The results reveal that all four loops accommodate significantly greater diversity than is observed in nature. Thus, it appears that most sequence biases in the natural immune repertoire arise from factors other than structural constraints and, consequently, it should be possible to enhance the functions of antibodies significantly through in vitro evolution.},
doi = {},
journal = {J. Mol. Biol.},
issn = {0022-2836},
number = (3) ; 2005,
volume = 348,
place = {United States},
year = {2010},
month = {7}
}