title: Robotic QM/MM-driven maturation of antibody combining sites.
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.
authors: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ulitsa Miklukho-Maklaya 16/10, 117997 Moscow V-437, Russian Federation.
authors: Ivan V
authors: IV
authors: Smirnov
authors: Lomonosov Moscow State University, Moscow 119991, Russian Federation.
authors: Andrey V
authors: 0000-0002-8908-4268
authors: AV
authors: Golovin
authors: European Molecular Biology Laboratory, Hamburg Unit, c/o German Synchrotron Research Center, Notkestrasse 85, 22603 Hamburg, Germany.
authors: Spyros D
authors: 0000-0001-7569-5474
authors: SD
authors: Chatziefthimiou
authors: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ulitsa Miklukho-Maklaya 16/10, 117997 Moscow V-437, Russian Federation.
authors: Anastasiya V
authors: AV
authors: Stepanova
authors: Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road MB-10, La Jolla, CA 92037, USA.
authors: Yingjie
authors: Y
authors: Peng
authors: Lomonosov Moscow State University, Moscow 119991, Russian Federation.
authors: Olga I
authors: OI
authors: Zolotareva
authors: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ulitsa Miklukho-Maklaya 16/10, 117997 Moscow V-437, Russian Federation.
authors: Alexey A
authors: AA
authors: Belogurov
authors: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ulitsa Miklukho-Maklaya 16/10, 117997 Moscow V-437, Russian Federation.
authors: Inna N
authors: IN
authors: Kurkova
authors: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ulitsa Miklukho-Maklaya 16/10, 117997 Moscow V-437, Russian Federation.
authors: Natalie A
authors: NA
authors: Ponomarenko
authors: European Molecular Biology Laboratory, Hamburg Unit, c/o German Synchrotron Research Center, Notkestrasse 85, 22603 Hamburg, Germany.
authors: Matthias
authors: M
authors: Wilmanns
authors: Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
authors: G Michael
authors: 0000-0002-3941-0459
authors: GM
authors: Blackburn
authors: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ulitsa Miklukho-Maklaya 16/10, 117997 Moscow V-437, Russian Federation.; Lomonosov Moscow State University, Moscow 119991, Russian Federation.
authors: Alexander G
authors: AG
authors: Gabibov
authors: Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road MB-10, La Jolla, CA 92037, USA.
authors: Richard A
authors: RA
authors: Lerner
mesh_terms: D000911:Antibodies, Monoclonal / Q000737:chemistry / Q000235:genetics; D001666:Binding Sites, Antibody; D003198:Computer Simulation; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D012371:Robotics
chemical_list: D000911:Antibodies, Monoclonal
keywords: Immunology; antibodies