Conformational diversity of CDR region during affinity maturation determines the affinity and stability of Sars-Cov-1 VHH-72 nanobody

  1. Suji George

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Abstract

The affinity maturation of Sars-Cov-1 VHH-72 nanobody from its germline predecessor has been studied at the molecular level. The effect of somatic mutations accumulated during affinity maturation process on flexibility, stability and affinity of the germline and affinity matured nanobody was studied. Affinity maturation results in loss of local flexibility in CDR of H3 and this resulted in a gain of affinity towards the antigen. Further affinity maturation was found to destabilize the nanobody. Mechanistically the loss of flexibility of the CDR H3 is due to the redistribution of hydrogen bond network due to somatic mutation A50T, also this contributes significantly to the destability of the nanobody. Unlike antibody, in nanobody the framework region is highly conserved and structural diversity in CDR is the determining factor in diverse antigen binding and also a factor contributing to the stability. This study provide insights into the interrelationship between flexibility, stability and affinity during affinity maturation in a nanobody.

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  1. ScreenIT

    SciScore for 10.1101/2020.12.08.416164: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Antibodies
    SentencesResources
    Nanobody Modeling: The X-ray crystal structure of the Sars-Cov-1 Receptor Binding Domain (RBD) bound by the single domain antibody SARS VHH-72 antibody (6waq was downloaded from the protein Data Bank (PDB; www.pdb.org (Wrapp et al., 2020)□.
    Sars-Cov-1 Receptor Binding Domain (RBD
    suggested: None
    Software and Algorithms
    SentencesResources
    Stability calculation for Germline and Mature Nanobody: The effects of somatic hyper mutation on the stability of Nbs were studied using FoldX.
    FoldX
    suggested: (FoldX, RRID:SCR_008522)
    Docking of nanobody to RBD: We used the web interface of RosettaDOCK to dock 6waqG and 6waqM to RBD (Chaudhury et al., 2011; Lyskov and Gray, 2008)□□.
    RosettaDOCK
    suggested: (RosettaDock, RRID:SCR_013393)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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  2. Version published to 10.1101/2020.12.08.416164v1 on bioRxiv