Nowak, Wieslaw
Prof. dr hab. Wieslaw Nowak is currently a head of Chair of Biophysics at the Institute of Physics, N Copernicus Univ. Torun, Poland. He got MSc in 1979 in chemistry, PhD in 1989 in theoretical physics, habilitation in 2000 in Biophysics, after spending several years as a postdoc at UIC Chicago, Ecole Polytechnique (Paris) and Kyoto University. His current interest are computational studies of medically important proteins, optogenetics and single molecule AFM force spectroscopy
Abstract:
Nanomechanics of nanobodies-protein S SARS-CoV-2 virus complexes revealed by a Virtual Atomic Force Microscope
Topic:
World population is to a large extent saved by development of antibodies against pathogens such as SARS-CoV-2. Despite natural antibodies induced by a viral infection or vaccination, application of nanobodies is extremely promising technology in fight with the current pandemic. Nanobodies are single-domain antibodies that can be effectively produced in the lab. The main step in the research towards new tools against SARS-associated viruses is effective screening (or de novo design) of nanobodies. Here we propose a computational strategy called Virtual Atomic Force Microscopy to monitor the strength of a nanobody interaction with protein S from the SARS-CoV-2 virus. Starting from recently published cryo-EM structures of Nb6 nanobody bound to closed and open SpikeS2P protein, we use Steered Molecular Dynamics computational modeling method to assess unbinding forces and to determine molecular mechanisms of binding-unbinding processes. Our approach allows for efficient ranking of synthetic nanobodies affinities to protein S. The proposed computational pipeline may be particularly useful for initial checking of already developed nanobodies against new variants of SARS viruses. Acknowledgement: This project is funded by IDUB N. Copernicus ANTICO and #MEMOBIT grants. ICNT UMK computer facilities are acknowledged
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