Structure of the apo anti-influenza CH65 Fab

Lee, Peter S.; Arnell, Ashley; Wilson, Ian A.

doi:10.1107/s2053230x14027599

Cited by 5 publications

(3 citation statements)

References 25 publications

(20 reference statements)

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“…The diffraction data sets were processed and scaled with the XDS (Kabsch, 2010) and scala (Winn et al, 2011) program software packages. The crystal structure of Fabs was determined by molecular replacement with Phaser (McCoy et al, 2007) using the variable and constant domains of Fabs in the PDB (4WUK, 4HKB) (Lee et al 2015, Schmidt et al, 2013 as search models for CH65:1203d4/CH65:7969d2 and CH67:1203d4, respectively. The model was rebuilt iteratively using Coot (Emsley and Cowtan, 2004) and refined in Phenix (Adams et al, 2010).…”

Section: Methods Detailsmentioning

confidence: 99%

Identification of Structurally Related Antibodies in Antibody Sequence Databases Using Rosetta-Derived Position-Specific Scoring

et al. 2020

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The amount of antibody (Ab) variable gene sequence information is expanding rapidly, but our ability to predict the function of Abs from sequence alone is limited. Here, we describe a sequence-to-function prediction method that couples structural data for a single Ab/Antigen (Ag) complex with repertoire data. We used a position-specific structure-scoring matrix (P3SM) incorporating structure-prediction scores from Rosetta to identify Ab variable loops that have predicted structural similarity to the influenza virus-specific human Ab CH65. The P3SM approach identified new members of this Ab class. Recombinant Ab expression, crystallography, and virus inhibition assays showed that the HCDR3 loops of the newly identified Abs possessed similar structure and antiviral activity as the comparator CH65.

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Section: Methods Detailsmentioning

confidence: 99%

Identification of Structurally Related Antibodies in Antibody Sequence Databases Using Rosetta-Derived Position-Specific Scoring

et al. 2020

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“…rim of influenza RBD) and adding or removing glycans. These immune evasion mechanisms can therefore require long CDR loops to reach sites of vulnerability (9, 10) or short CDR loops to avoid clashes and allow closer proximity (6). Structure-based design must account for these immune-evasion mechanisms.…”

Section: Concepts Of Antibody Neutralization and B Cell Targetingmentioning

confidence: 99%

Structure-Based Vaccine Antigen Design

2019

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Enabled by new approaches for rapid identification and selection of human monoclonal antibodies, atomic-level structural information for viral surface proteins, and capacity for precision engineering of protein immunogens and self-assembling nanoparticles, a new era of antigen design and display options has evolved. While HIV-1 vaccine development has been a driving force behind these technologies and concepts, clinical proof-of-concept for structure-based vaccine design may first be achieved for respiratory syncytial virus (RSV), where conformation-dependent access to neutralization-sensitive epitopes on the fusion glycoprotein determines the capacity to induce potent neutralizing activity. Success with RSV has motivated structure-based stabilization of other class I viral fusion proteins for use as immunogens and demonstrated the importance of structural information for developing vaccines against other viral pathogens particularly difficult targets that have resisted prior vaccine development efforts. Solving viral surface structures also supports rapid vaccine antigen design and application of platform manufacturing approaches for emerging pathogens.

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“…Importantly, these epistatic interactions are essential for the acquisition of affinity to both MA90-G189E and SI06. To investigate the molecular details of this epistasis, we compared the crystal structures of the unbound UCA, I-2, and CH65 as well as CH65 bound to SI06 3,4,64 . Additionally, we produced several variants as recombinant IgG to assay the binding kinetics by biolayer interferometry.…”

Section: Resultsmentioning

confidence: 99%

Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody

Phillips

Maurer

Brooks

et al. 2022

Preprint

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Broadly neutralizing antibodies (bnAbs) that neutralize diverse variants of a particular virus are of considerable therapeutic interest. Recent advances have enabled us to isolate and engineer these antibodies as therapeutics, but eliciting them through vaccination remains challenging, in part due to our limited understanding of how antibodies evolve breadth. Here, we analyze the landscape by which an anti-influenza receptor binding site (RBS) bnAb, CH65, evolved broad affinity to diverse H1 influenza strains. We do this by generating an antibody library of all possible evolutionary intermediates between the unmutated common ancestor (UCA) and the affinity-matured CH65 antibody and measure the affinity of each intermediate to three distinct H1 antigens. We find that affinity to each antigen requires a specific set of mutations – distributed across the variable light and heavy chains – that interact non-additively (i.e., epistatically). These sets of mutations form a hierarchical pattern across the antigens, with increasingly divergent antigens requiring additional epistatic mutations beyond those required to bind less divergent antigens. We investigate the underlying biochemical and structural basis for these hierarchical sets of epistatic mutations and find that epistasis between heavy chain mutations and a mutation in the light chain at the VH-VL interface is essential for binding a divergent H1. Collectively, this work is the first to comprehensively characterize epistasis between heavy and light chain mutations and shows that such interactions are both strong and widespread. Together with our previous study analyzing a different class of anti-influenza antibodies, our results implicate epistasis as a general feature of antibody sequence-affinity landscapes that can potentiate and constrain the evolution of breadth.

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Structure of the apo anti-influenza CH65 Fab

Cited by 5 publications

References 25 publications

Identification of Structurally Related Antibodies in Antibody Sequence Databases Using Rosetta-Derived Position-Specific Scoring

Identification of Structurally Related Antibodies in Antibody Sequence Databases Using Rosetta-Derived Position-Specific Scoring

Structure-Based Vaccine Antigen Design

Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody

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