How many trimers? Modeling influenza virus fusion yields a minimum aggregate size of six trimers, three of which are fusogenic

Abstract

PAPER Maria Pamela Dobay et al.How many trimers? Modeling infl uenza virus fusion yields a minimum aggregate size of six trimers, three of which are fusogenic Conflicting reports in leading journals have indicated the minimum number of influenza hemagglutinin (HA) trimers required for fusion to be between one and eight. Interestingly, the data in these reports are either almost identical, or can be transformed to be directly comparable. Different statistical or phenomenological models, however, were used to analyze these data, resulting in the varied interpretations. In an attempt to resolve this contradiction, we use PABM, a brane calculus we recently introduced, enabling an algorithmic systems biology approach that allows the problem to be modeled in a manner following a biological logic. Since a scalable PABM executor is still under development, we sufficiently simplified the fusion model and analyzed it using the model checker, PRISM. We validated the model against older HA-expressing cell-to-cell fusion data using the same parameters with the exception of three, namely HA and sialic acid (SA) surface densities and the aggregation rate, which were expected to be different as a result of the difference in the experimental setup. Results are consistent with the interpretation that a minimum aggregate size of six HA trimers, of which three undergo a conformational change to become fusogenic, is required for fusion. Of these three, two are free, while one is bound. Finally, we determined the effects of varying the SA surface density and showed that only a limited range of densities permit fusion. Our results demonstrate the potential of modeling in providing more precise interpretations of data. I n d e x e d i n M E D L I N E !

Mechanisms of influenza viral membrane fusion

“…However, whether this necessarily involves inter-HA interactions is hard to conclude from these types of experiments. A large number of studies have established that multiple HAs are needed for fusion, yet there is no consensus on the number of HAs involved [88][89][90][91][92][93]. The number found depends on the experimental technique used and the model applied.…”

“…Single-particle experiments on influenza viral fusion showed that the waiting times between decrease of the pH and the cessation of rolling, and hemifusion and pore formation events showed rise-and-decay behavior, suggesting that these processes involve multiple steps [61,88,96,97,100]. The powerful combination of single-particle experiments and analytical [101] and numerical [61] modeling has resulted in a picture in which fusion is the result of a number of HAs acting in a parallel, stochastic fashion, whose proximity allows their stochastic activity to result in a level of coordination needed to overcome the large energetic barriers associated with fusion.…”

Heterosubtypic Antibodies to Influenza A Virus Have Limited Activity against Cell-Bound Virus but Are Not Impaired by Strain-Specific Serum Antibodies

“…Based on the postulated aggregation of an estimated six HA molecules required for fusion (three of which have to undergo a conformational change [33]), we concluded that a cluster of HA molecules is formed whose center is not accessible to hMAbs. Accordingly, three or more HA spikes can still undergo The attached viruses were then incubated with titrated amounts of HA stem-reactive (3.1, 1.12, and FI6) or hemagglutinationinhibiting (30D1 and H36-4) MAbs, and residual infectivity was detected.…”

“…the confirmation change required for infection (33). We believe that the lower impact of prior cell attachment on the neutralizing activity of hemagglutination-inhibiting antibodies originates in the poor affinity of the HA protein for its receptor: apically binding antibodies should have no problem with displacing dissociated receptors if they are sufficiently affine and concentrated.…”

Computational Approaches to Enhance Nanosafety and Advance Nanomedicine

“…Further analysis showed that the discrepancy was rooted in their use and interpretation of different statistical inference methods. This led us to develop a stochastic model 9 inspired by an Algorithmic/Executable Systems Biology approach and implemented in the model checker PRISM. The model not only verified the conclusion of the Harvard group about the number of fusogenic trimers, it also provided more details about related quantities such as the aggregation size and the number of membrane-bound trimers in the minimal configuration.…”