5ADO

Crystal structure of the paraoxon-modified A.17 antibody FAB fragment - Light chain S35R mutant

Summary for 5ADO

• Entry DOI: 10.2210/pdb5ado/pdb
• Related: 5ADP
• Descriptor: FAB A.17, DIETHYL PHOSPHONATE, ... (4 entities in total)
• Functional Keywords: immune system, enzyme reprogramming, antibodies, ig superfamily, in silico antibody maturation
• Biological source: Homo sapiens (HUMAN); More
• Total number of polymer chains: 2
• Total formula weight: 54215.72

Authors

Chatziefthimiou, S.D.,Smirnov, I.V.,Golovin, A.V.,Stepanova, A.V.,Peng, Y.,Zolotareva, O.I.,Belogurov, A.A.,Ponomarenko, N.A.,Blackburn, G.M.,Gabibov, A.A.,Lerner, R.,Wilmanns, M. (deposition date: 2015-08-21, release date: 2016-11-09, Last modification date: 2024-10-23)

Primary citation

Smirnov, I.V.,Golovin, A.V.,Chatziefthimiou, S.D.,Stepanova, A.V.,Peng, Y.,Zolotareva, O.I.,Belogurov, A.A.,Kurkova, I.N.,Ponomarenko, N.A.,Wilmanns, M.,Blackburn, G.M.,Gabibov, A.G.,Lerner, R.A.
Robotic Qm/Mm-Driven Maturation of Antibody Combining Sites.
Sci.Adv., 2:01695-, 2016

PubMed Abstract: In vitro selection of antibodies from large repertoires of immunoglobulin (Ig) combining sites using combinatorial libraries is a powerful tool, with great potential for generating in vivo scavengers for toxins. However, addition of a maturation function is necessary to enable these selected antibodies to more closely mimic the full mammalian immune response. We approached this goal using quantum mechanics/molecular mechanics (QM/MM) calculations to achieve maturation in silico. We preselected A17, an Ig template, from a naïve library for its ability to disarm a toxic pesticide related to organophosphorus nerve agents. Virtual screening of 167,538 robotically generated mutants identified an optimum single point mutation, which experimentally boosted wild-type Ig scavenger performance by 170-fold. We validated the QM/MM predictions via kinetic analysis and crystal structures of mutant apo-A17 and covalently modified Ig, thereby identifying the displacement of one water molecule by an arginine as delivering this catalysis.

PubMed: 27774510
DOI: 10.1126/SCIADV.1501695

Experimental method

X-RAY DIFFRACTION (1.55 Å)