Homology Modeling of Hemagglutinin/Protease [HA/P (vibriolysin)] from Vibrio Cholerae: Sequence Comparision, Residue Interactions and Molecular Mechanism Ghosia Lutfullah Æ Farhat Amin Æ Zahid Khan Æ Noreen Azhar Æ M. Kamran Azim Æ Sajid Noor Æ Khalida Shoukat Published online: 12 December 2007 Ó Springer Science+Business Media, LLC 2007 Abstract Vibrio cholerae produces a zinc-containing and calcium-stabilized soluble hemagglutinin/protease, which has been earlier shown to have the ability to cleave several physiologically important substrates including mucin, fibronectin and lactoferin. This study presents homology modeling of hemagglutinin/protease (vibriolysin) from Vibrio cholerae in the presence of inhibitor HPI [N-(1- carboxy-3-phenylpropyl)-phenylalanyl-alpha-aspargine]. The 3D structure was predicted based on its sequence homology with Pseudomonas aeruginosa elastase (PAE). Comparison of the 3D structures of PAE and HA/P reveals a remarkable similarity having a conserved a + b domain. The inhibitor shows similar binding features as seen in other metalloproteases of M4 peptidase family. The study also highlights the key catalytic residues as well as the residues at the S 1 and S 0 1 binding sub-sites. The similarities between the two proteins provide support for the hypoth- esis that the two enzymes have similar three-dimensional structures and a common mechanism of action. The fact that both enzymes are secreted as zinc-containing prote- ases, led us to further hypothesize that they may play similar role in pathogenesis. Keywords Vibrio cholerae Á Vibriolysin Á Hemagglutinin Á Homology modeling Á Pathogenesis Á Enzyme substrate interactions Abbreviations CT Cholera toxin Ace Accessory cholera enterotoxin Zot Zonula occludens toxin HA/P Hemagglutinin/protease PAE Pseudomonas aeruginosa elastase TLPs Thermolysin-like proteases HPI N-(1-Carboxy-3-phenylpropyl)- phenylalanyl-alpha-aspargine TLN Thermolysin 1 Introduction Vibrio cholerae of serogroups O1 and O139, the causative agent of water borne diarrheal disease cholera [1, 2] is a highly motile, non-invasive gram-negative bacterium, which colonizes the small intestine [3, 4]. Cholera is an imperative worldwide problem especially in developing countries [4]. It is characterized by the loss of significant fluid and dehydration and leads to death if left untreated [5]. Vibrio cholerae is a marine micro-organism [6] that can cause disease by its oral ingestion along with con- taminated sea food and drinking water [2, 6]. To cause disease, V. cholerae need to pass the protective gastric acid barrier, colonize the human small bowel, and secrete potent enterotoxin [7, 8]. The customary factors that are involved in the transmission of cholera are contaminated water supply, poor sanitation, indiscriminate defaecation and poor personal hygiene [9]. At the molecular level, the pathogenesis of cholera is a multifactorial process and involves several genes encoding virulence factors that aid the pathogen in its colonization, coordinated expression of virulence factors, and toxin action [4] In addition to potent CT, other putative toxic G. Lutfullah Á F. Amin (&) Á Z. Khan Á N. Azhar Center of Biotechnology, University of Peshawar, Peshawar, Pakistan e-mail: farhatamin.farhat@gmail.com M. K. Azim Á S. Noor Á K. Shoukat H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan 123 Protein J (2008) 27:105–114 DOI 10.1007/s10930-007-9113-0