Molecular dynamics simulations of lectin domain of FimH and immunoinformatics for the design of potential vaccine candidates

• MD simulations were carried out for the FimH lectin domain from UPEC J96.
• The high affinity state lectin domain was found to be largely rigid and stable.
• Two sequence motifs were designed around a functionally important region.
• Immunoinformatics was used to predict epitopes for the FimH lectin domain of UPEC J96.
• MD simulation data was used to assess the accessibility of the epitopes.

Adhesion of uropathogenic E. coli (UPEC) to uroepithelial cell receptors is facilitated through the lectin domain of FimH adhesin. In the current study, Molecular Dynamics (MD) simulations were performed for the lectin domain of FimH from UPEC J96. The high affinity state lectin domain was found to be stable and rigid during the simulations. Further, based on conserved subsequences around one of the disulfide forming cysteines, two sequence motifs were designed. An immunoinformatics approach was utilized to identify linear and discontinuous epitopes for the lectin domain of FimH. We propose that the accessibility of predicted epitopes should also be assessed in a dynamic aqueous environment to evaluate the potential of vaccine candidates. Since MD simulation data enables assessing the accessibility in a dynamic environment, we evaluated the accessibility of the top ranked discontinuous and linear epitopes using structures obtained at every nanosecond (ns) in the 1–20 ns MD simulation timeframe. Knowledge gained in this study has a potential utility in the design of vaccine candidates for Urinary Tract Infection (UTI).

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