Literature DB >> 28864894

Evolution of catalytic centers of antibodies by virtual screening of broad repertoire of mutants using supercomputer.

A V Golovin1, I V Smirnov2, A V Stepanova2, A O Zalevskiy1, A S Zlobin1, N A Ponomarenko2, A A Belogurov2, V D Knorre3, E N Hurs4, S D Chatziefthimiou5, M Wilmanns5, G M Blackburn6, R M Khomutov4, A G Gabibov1,2.   

Abstract

It is proposed to perform quantum mechanical/molecular dynamics calculations of chemical reactions that are planned to be catalyzed by antibodies and then conduct a virtual screening of the library of potential antibody mutants to select an optimal biocatalyst. We tested the effectiveness of this approach by the example of hydrolysis of organophosphorus toxicant paraoxon using kinetic approaches and X-ray analysis of the antibody biocatalyst designed de novo.

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Year:  2017        PMID: 28864894     DOI: 10.1134/S1607672917040019

Source DB:  PubMed          Journal:  Dokl Biochem Biophys        ISSN: 1607-6729            Impact factor:   0.788


  8 in total

1.  At the crossroads of chemistry and immunology: catalytic antibodies.

Authors:  R A Lerner; S J Benkovic; P G Schultz
Journal:  Science       Date:  1991-05-03       Impact factor: 47.728

2.  PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.

Authors:  Sidhartha Chaudhury; Sergey Lyskov; Jeffrey J Gray
Journal:  Bioinformatics       Date:  2010-01-07       Impact factor: 6.937

3.  Reactibodies generated by kinetic selection couple chemical reactivity with favorable protein dynamics.

Authors:  Ivan Smirnov; Eugénie Carletti; Inna Kurkova; Florian Nachon; Yvain Nicolet; Vladimir A Mitkevich; Hélène Débat; Bérangère Avalle; Alexey A Belogurov; Nikita Kuznetsov; Andrey Reshetnyak; Patrick Masson; Alexander G Tonevitsky; Natalia Ponomarenko; Alexander A Makarov; Alain Friboulet; Alfonso Tramontano; Alexander Gabibov
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-06       Impact factor: 11.205

4.  DNA hydrolyzing autoantibodies.

Authors:  A M Shuster; G V Gololobov; O A Kvashuk; A E Bogomolova; I V Smirnov; A G Gabibov
Journal:  Science       Date:  1992-05-01       Impact factor: 47.728

5.  Toward antibody-catalyzed hydrolysis of organophosphorus poisons.

Authors:  P Vayron; P Y Renard; F Taran; C Créminon; Y Frobert; J Grassi; C Mioskowski
Journal:  Proc Natl Acad Sci U S A       Date:  2000-06-20       Impact factor: 11.205

6.  Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods.

Authors:  Jan Řezáč; Pavel Hobza
Journal:  J Chem Theory Comput       Date:  2011-12-22       Impact factor: 6.006

Review 7.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Proteins       Date:  2010-05-01

8.  [Expression Of DNA-Encoded Antidote to Organophosphorus Toxins in the Methylotrophic Yeast Pichia Pastoris].

Authors:  S S Terekhov; T V Bobik; Yu A Mokrushina; A V Stepanova; N M Aleksandrova; I V Smirnov; A A Belogurov; N A Ponomarenko; A G Gabibov
Journal:  Prikl Biokhim Mikrobiol       Date:  2016 Mar-Apr
  8 in total
  1 in total

1.  Structural and Functional Mise en Abyme.

Authors:  Bérangère Avalle; Séverine Padiolleau-Lefevre; Alain Friboulet
Journal:  Front Mol Biosci       Date:  2019-11-28
  1 in total

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