Molecular dynamics simulations of lectin domain of FimH and immunoinformatics for the design of potential vaccine candidates Muthukumar Singaravelu a, b , Anitha Selvan a , Sharmila Anishetty a, * a Centre for Biotechnology, Anna University, Chennai 600 025, India b National Institute of Ocean Technology, Chennai 600 100, India A R T I C L E I N F O Article history: Received 2 April 2014 Received in revised form 11 August 2014 Accepted 11 August 2014 Available online xxx Keywords: FimH adhesin Molecular dynamics simulation Rigidity Motif Immunoinformatics Vaccine A B S T R A C T 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). ã 2014 Elsevier Ltd. All rights reserved. 1. Introduction Bacterial adhesins are virulence factors important for patho- genesis. Urinary Tract Infection (UTI) is a disease more commonly seen in women. They have a 50% chance of an infection during their lifetime (Bouckaert et al., 2006). Uropathogenic Escherichia coli (UPEC) are implicated in 90% of UTI. 95% of UTI causing E. coli possess type1 fimbriae (Tchesnokova et al., 2011). Adhesion of UPEC to the high mannose glycoprotein uroplakin Ia receptor in the bladder epithelium is mediated by FimH of the filamentous type I pilus system (Zhou et al., 2001). The type I pilus of UPEC has four structural subunits FimA, FimF, FimG and FimH. Each structural subunit of the pilus has a single pilin domain while FimH has an additional lectin domain through which it attaches to the mannose based receptors of the host. The pilus rod is able to stretch and unwind under mechanical stress without dissociating from the host cell receptors (Puorger et al., 2011). UPEC has to withstand the shear stress while establishing an infection. Although UTI can be treated with antibiotics, recurrence is a major problem. This is compounded with the emergence of multidrug resistant UTI causing strains. Invasion of bladder epithelial cells by E. coli is also mediated by FimH (Martinez et al., 2000). When UPEC gets into the host cytosol, it can grow and form intracellular bacterial communities (IBC) (Anderson et al., 2003). The FimH lectin domain is an elongated 11 stranded beta barrel with an immunoglobulin fold (Bouckaert et al., 2005). FimH forms mechanical force enhanced catch bonds due to an interdomain allosteric regulation wherein it switches over to a high affinity state which shows stronger binding to mannose (Yakovenko et al., 2008). Experimental and Molecular Dynamics (MD) simulation studies have addressed FimH adhesin (Thomas et al., 2002; Nilsson et al., 2007; Aprikian et al., 2011). Steered Molecular Dynamics (SMD) simulation of the lectin domain of FimH was performed wherein shear induced force was simulated (Thomas et al., 2002). The importance of cysteine bond of FimH in the adaptation to bind surfaces under increased shear stress was also evaluated through experiments and MD simulations (Nilsson et al., 2007). Single molecule force spectroscopy experiments show that the fimbrial tip mediates shear dependent adhesion of bacteria to uroepithelial cells and the force enhances interaction with mannose (Aprikian et al., 2011). Further, MD simulations of the quaternary structure of the fimbrial tip was used to evaluate inter domain flexibility in the presence and absence of force and a hook chain model was proposed for the fimbrial tip complex (Aprikian et al., 2011). * Corresponding author. Tel.: +91 44 2235 0772; fax: +91 44 2235 0299. E-mail addresses: s_anishetty@yahoo.co.uk, s_anishetty@annauniv.edu (S. Anishetty). http://dx.doi.org/10.1016/j.compbiolchem.2014.08.002 1476-9271/ ã 2014 Elsevier Ltd. All rights reserved. Computational Biology and Chemistry xxx (2014) 18–24 Contents lists available at ScienceDirect Computational Biology and Chemistry journal homepa ge: www.elsev ier.com/locate/compbiolchem