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3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes

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journal contribution
posted on 29.12.2018, 06:39 by Maximilien Lopes-Rodrigues, David Zanuy, Carlos Alemán, Catherine Michaux, Eric A. Perpète

Brucella melitensis is a pathogenic bacterium responsible for brucellosis in mammals and humans. Its outer membrane proteins (Omp) control the diffusion of solutes through the membrane, and they consequently have a crucial role in the design of diagnostics and vaccines. Moreover, such proteins have recently revealed their potential for protein-based biomaterials. In the present contribution, the structure of the B. melitensis porin Omp2a is built using the RaptorX threading method. This is a 16-stranded β-barrel with an α-helix on the third loop folding inside the barrel and forming the constriction zone of the channel, a typical feature of general porins such as PhoE and OmpF. The preferential diffusion of cations over anions experimentally observed in anterior studies is evidenced by the presence of distinct clusters of charges in the extracellular loops and in the inner pore. Docking studies support the previously reported hypothesis of Omp2a ability to aid maltotetraose diffusion. The monomer model is then assembled into a homotrimer, stabilized by the L2 loop involved in most of the interface interactions. The stability of the trimer is evaluated in three bilayers: pure 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), pure 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and a mixture of 1:1 of POPC/POPE. All-atom molecular dynamics simulations demonstrate the β-barrel-structural stability over time even though a breathing-like motion is observed. Compared to the pure bilayers, the POPC/POPE better preserves the integrity of the protein and its channel. Overall, this work demonstrates the relevancy of the Omp2a model and will help to design new therapeutic agents and bioinspired nanomaterials.

Funding

M.L.-R., D.Z. and C.A. thank the support from MINECO [MAT2015-69367-R] and AGAUR [2017 SGR 359]. Support for the research of C.A. was received through the prize ‘ICREA Academia’ for excellence in research funded by the Generalitat de Catalunya. C.M. and E.A.P. thank the Belgian National Fund for Scientific Research for their research associate and senior research associate positions, respectively. This research used resources of the ‘Consortium des Équipements de Calcul Intensif (CÉCI)’, particularly those of the ‘Technological Platform of High Performance Computing (PTCI)’, located at the University of Namur, Belgium, and supported by the F.R.S.-FNRS.

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