Predicting protein transport mechanism and immune response using spatial protein motifs and epitopes

Abstract

Chlamydophila represents a distinct genus of gram negative bacteria associated with a spectrum of both human and animal disease and, as such, is an important health and economic concern. Central to the pathogenicity of Chlamydophila are antigenic proteins among which the Major Outer Membrane Proteins (MOMP) have received significant attention. MOMP from Chlamydophila pneumoniae and Chlamydia trachomatis, the human pathogens, to date, remain the best characterised. In addition, MOMP-derived peptides have been shown to potentiate anti-inflammatory and anti-atherogenecity, by a cell mediated system involving MHC class II proteins [2]. However, despite the importance of this protein as a vaccine target against inflammation driven pathologies attributed to Chlamydia, tremendous challenges in the isolation of this membrane-bound, cysteine-rich protein make it difficult to experimentally isolate the protein for detailed structural and immunological studies. In an effort to reveal a plausible structure and function for Chlamydophila MOMP and aid in the rational design of potential lead candidates for future drug design, computational methods have been employed. Firstly, a knowledge-based approach was used to explore Chlamydia MOMP sequences to identify Asp-ProX (NPX) motifs, commonly found in long chain fatty acid transporters such as aquaporins and some aquaglyceroporins. In Chlamydial MOMPs, a variety of substitutions are found at the third 'X' position; NP-A/S/E/T/K, which may account for its potential to transport a variety of solutes, as a strategy for coping with the absence of essential metabolic enzymes. Earlier findings suggest that MOMP from Chlamydophila pneumoniae is permeable to sugars, amino acids, dicarboxylates and ATP. Subsequent homology modeling of MOMP from C. pneumoniae (using template-based methods) has provided insight into the orientation of these functional motifs in the 3-dimensional structures of MOMPs, from which a plausible novel transport model has been derived [1]. In our model the NPA motif is oriented toward the extracellular side while the two NPS motifs are juxtaposed inside the barrel posed to fulfil a transport role, via solute binding. Secondly, to understand how such MOMP-derived peptides could potentiate an immune response, via binding MHC II alleles, a flexible molecular docking protocol was employed [1]. The reliability of the docking protocol was tested by docking peptides extracted from the PDB coordinates of the MHCs of interest and compared to the original peptide-MHC complex, as seen in the crystal structure of the complex. We used the docking protocol to score four peptides of interest for their candidacy as potential new leads in a rational drug design strategy against chronic inflammation, which characterises Chlamydial involvement in atherosclerosis and respiratory diseases. Our computational work offers new insight into the structure and functional mechanism involved in solute transport via MOMP across Chlamydial cell membranes, which could be used in the design of inhibitors that could obstruct nutrient uptake and halt Chlamydial viability in their host. Also, this work supports the role of MOMP-derived peptides as vaccine candidates for immune-therapy in chronic inflammation that can result in cardiovascular events.