Dataset Information

Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities.

ABSTRACT: Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from human convalescent plasma, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.

SUBMITTER: Casalino L

PROVIDER: S-EPMC9387122 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities.

Casalino Lorenzo L Seitz Christian C Lederhofer Julia J Tsybovsky Yaroslav Y Wilson Ian A IA Kanekiyo Masaru M Amaro Rommie E RE

bioRxiv : the preprint server for biology 20220807

Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investi ...[more]

PMID: 35982676

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Project description:The hemagglutination inhibition assay (HAI) is widely used to evaluate vaccine-induced antibody responses as well as to antigenically characterize influenza viruses. The results of an HAI assay are based on an endpoint titration where the titers are generally manually interpreted and recorded by a well-trained expert. For serological applications, the lack of standardization in endpoint interpretation and interference from non-specific inhibitors in clinical samples can translate into a high degree of variability in the results. For example, tilting HAI plates at 45-60 degrees to look for a "tear drop pattern" with avian red blood cells is a common practice by many, but not all, research laboratories. In this work, we tested the hypothesis that an automated image analysis algorithm can be used to achieve an accurate and non-subjective interpretation of HAI assays-specifically without the need to tilt plates. In a side-by-side comparison study performed during FDA's biannual serological screening process for influenza viruses, titer calls for more than 2200 serum samples were made by the Cypher One automated hemagglutination analyzer without tilting and by an expert human with tilting. The comparison yielded 95.6% agreement between the expert reader and automated interpretation method (within ± 1 dilution) for the complete dataset. Performance was also evaluated relative to the type of red blood cell (turkey and guinea pig) and influenza strain (12 different viruses). For the subset that utilized guinea pig red blood cells (~44% of the samples), for which no plate tilting was required, the agreement with an expert reader was 97.2%. For the subset that utilized turkey red blood cells (~56% of the samples), for which plate tilting was necessary by the expert reader, the agreement was 94.3%. Overall these results support the postulate that algorithm-based interpretation of a digital record with no plate tilting could replace manual reading for greater consistency in HAI assays.

Dataset Information

Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities.

Publications

Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities.

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