Biology subjects

Brown, T. P.

Publications and source records attributed to Brown, T. P..

3 recordsLinked to original sources

bioRxiv2026

Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments

The mycobacterial outer membrane (MOM) constitutes an asymmetric permeability barrier that influences lipid organization and transport in Mycobacterium tuberculosis. In this study, we have developed MARTINI 3 coarse-grained (CG) lipid models of the MOM, incorporating -mycolic acids, 5 different trehalose-based lipids, and PDIM (phthiocerol dimycocerosate). The CG models were parameterized and validated using all-atom simulations of symmetric inner- and outer-leaflet membranes, as well as fully asymmetric MOM models. Bonded parameters were optimized through an iterative refinement procedure targeting atomistic bonded distributions. The CG simulations show good agreement with the all-atom simulation data and available experimental measurements in terms of the membrane thickness, solvent accessible surface area, lipid density profiles, and the outer-leaflet-induced lipid disorder in -mycolic acids at the inner leaflet. The model reproduces the temperature-dependent phase behavior of all-atom -mycolic acid membranes. Using this model, we demonstrate that PDIM localization, diffusion, and aggregation are strongly modulated by membrane fluidity and lipid composition, with enhanced translocation and clustering in liquid disordered environments. Our CG MOM lipid models provide a validated platform for large-scale simulations of mycobacterial membranes and enable mechanistic studies of lipid organization, membrane dynamics, and protein-membrane and membrane-drug interactions.

biophysics↗

bioRxiv2025

Dynamic Architecture of Mycobacterial Outer Membranes Revealed by All-Atom Simulations

Tuberculosis remains a global health crisis due to the resilience of Mycobacterium tuberculosis (Mtb), largely attributed to its unique cell envelope. The impermeability and structural complexity of the outer membrane of this envelope, driven by mycolic acids and glycolipids, pose significant challenges for therapeutic intervention. Here, we present the first all-atom models of an Mtb outer membrane using molecular dynamics simulations. We demonstrate that -mycolic acids adopt extended conformations to stabilize bilayers, with a phase transition near 338 K that underscores their thermal resilience. Lipids in the outer leaflet such as PDIM and PAT induce membrane heterogeneity, migrating to the interleaflet space and reducing lipid order. The simulated mycobacterial outer membrane has ordered inner leaflets and disordered outer leaflets, which contrasts with the outer membrane of Gram-negative bacteria. These findings reveal that PDIM- and PAT-driven lipid redistribution, reduced lipid order, and asymmetric fluidity gradients enable Mtbs outer membrane to resist host-derived stresses and limit antibiotic penetration, thereby promoting bacterial survival. Our work provides a foundational framework for targeting the mycobacterial outer membrane in future drug development. TeaserMolecular dynamics simulations reveal the unique architecture of the mycobacterial outer membrane: a fluid outer leaflet and an ordered, tightly packed inner leaflet.

biophysics↗

bioRxiv2025

Identification of chemical features that influence mycomembrane permeation and antitubercular activity

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is the deadliest single-agent infection worldwide. Current antibiotic treatment for TB takes a minimum of four months, underscoring the need for better therapeutics. The unique mycobacterial cell envelope, particularly the outermost mycomembrane, has long been thought to promote intrinsic antibiotic resistance by limiting compound entry into Mtb. Understanding chemical features that influence permeation across the mycomembrane may enable more accurate predictions of whole cell anti-Mtb activity, leading to development of more effective antibacterials. Here we query the mycomembrane permeation of over 1500 azide-tagged compounds in live Mtb with the bioorthogonal click chemistry-based assay PAC-MAN. We use cheminformatics and machine learning to identify chemical features associated with mycomembrane permeation and show that they have predictive value via systematic modification of two small molecule series. Additionally, we find that chemical features that influence mycomembrane permeation correlate with anti-Mtb activity in large compound libraries. These findings suggest that the mycomembrane is indeed a significant barrier to whole cell activity in Mtb and provide a rational framework for designing or modifying compounds to overcome this barrier.

microbiology↗