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bioRxiv · 10.1101/2024.08.13.607716

Self-assembly of mycolic acid in water: monolayer or bilayer

Kumar, Y.·Basu, S.·Maiti, P. K.
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Abstract

The enduring pathogenicity of Mycobacterium tuberculosis can be attributed to its lipid-rich cell wall, with mycolic acids (MAs) being a significant constituent. Different MAs fluidity and structural adaptability within the bacterial cell envelope significantly influence their physicochemical properties, operational capabilities, and pathogenic potential. Therefore, an accurate conformational representation of various MAs in aqueous media can provide insights into their potential role within the intricate structure of the bacterial cell wall. We have carried out the MD simulations of MAs in an aqueous solution and shed light on the various structural properties such as thickness, order parameters, area-per-MAs, conformational changes, and principle component (PC) in the single component and mixed MAs monolayer. The different conformational populations in the monolayer have been estimated using the distance-based analysis between the function groups represented as W, U, and Z-conformations that lead to the fold of the MAs chain in the monolayer. Additionally, we have also simulated the mixture of alpha-MA (-MA or AMA), methoxy-MA (MMA), and keto-MA (KMA) with 56% AMA, 40 % MMA, and 14 % KMA composition. The thickness of the MAs monolayer was observed to range from 5 nm to 7 nm with an average 820 kg/m3 density for -MA, MMA, and KMA quantitative agreement with experimental results. The mero-chain (long chain), consisting of a functional group at the proximal and distal positions, tends to fold and exhibit a more disordered phase than the short chain. The keto-MA showed the greatest WUZ total conformations (35.32 %) with decreasing trend of eZ > eU > aU > aZ folds in both single component and mixture. Our results are in quantitative agreement with the experimental observations. The most minor population of sZ folds (0.75 % in a single component and 1.1 % in a mixture). However, eU and aU folds are most probable for the AMA and MMA. One striking observation is the abundance of MA conformers beyond the known WUZ convention because of the wide range distribution of intramolecular distances and change in dihedral angles. From the thermodynamic viewpoint, all monolayers were found to be stable in nature. The results from enhanced simulation revealed that changes in the magnitude of minimum free energy of the MAs are in order of KMA > AMA > MMA, and keto-MA exhibits more resistance (based on free energy values) for the drug molecules to permeate through the monolayer.

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Kumar, Y., Basu, S., Maiti, P. K.. 2024-08-16. Self-assembly of mycolic acid in water: monolayer or bilayer. https://doi.org/10.1101/2024.08.13.607716

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