همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

Biomechanical Characterization of Realistic Bacterial Membranes Across Different Biofilm Ages: A Molecular Dynamics Study

نویسندگان :

Fatemeh Ebrahimi Tarki¹ Mahboobeh Zarrabi² Mahkame Sharbatdar³

1- Alzahra University 2- Alzahra University 3- K. N. Toosi University of Technology

کلمات کلیدی :

Biomechanical Properties،Biofilm Aging،Lipid Bilayers،Membrane،Molecular Dynamics

چکیده :

The cell membrane plays a crucial role in cellular activities, making understanding its biophysical and biomechanical characteristics essential. Bacterial biofilms, resist antibiotics, posing challenges in clinical settings (Flemming et al., 2016). A comprehensive understanding of mechanical properties can lead to novel treatment methods to overcome antimicrobial resistance. Pseudomonas aeruginosa, an opportunistic pathogen, excels at biofilm formation, causing chronic infections in immunocompromised patients and complicating conditions like cystic fibrosis (Linnane et al., 2015). As biofilm age increases, the biofilm's matrix thickness and the fatty acid profile of the inner membrane significantly change (Pericolini et al., 2018; Wagner and Iglewski, 2008). In this study, membrane constructs representing planktonic, 24-hour (BF1), 48-hour (BF2), and 6-day biofilms (BF6) were modeled using lipidomic analysis from Benmara et al. and the online CHARMM-GUI tool (Benamara et al., 2014; Wu et al., 2014). The lipid bilayers were fully hydrated and neutralized with sodium and chloride ions at a concentration of 0.15 M. Following standard equilibration in CHARMM-GUI, input files for the simulations were created. Energy minimization addressed excessive forces from structural deviations to achieve stability. Simulations were conducted under NPT ensemble conditions (constant pressure of 1 bar) using the Parrinello-Rahman algorithm with a two-femtosecond time step (Parrinello and Rahman, 1981). A fixed temperature of 310.15 K was maintained with a Nosé-Hoover thermostat (Hoover, 1985; Nosé, 1984). Bond constraints were applied using the LINCS algorithm, while non-bonded interactions, including electrostatics and van der Waals forces, were calculated with the PME method and a cutoff of 1.2 nm (Darden et al., 1993; Hess, 2008). The CHARMM36m force field was utilized for 500-nanosecond simulations in Gromacs 2018.1. For each lipid bilayer, the head-to-head thickness (DHH), hydrophobic thickness (DC), area per lipid (APL), bilayers' interdigitation, and compressibility moduli (KA and KC) were calculated over the 500-nanosecond simulation. Order parameters and lateral diffusion coefficients were computed to evaluate the microscopic fluidity of the lipid bilayers. The BF1 showed the lowest APL, indicating tighter molecular packing when transitioning from planktonic to biofilm states, which decreased as the biofilm aged. This change led to a 1.78-fold increase in the lateral diffusion coefficient, linked to reduced packing. Increased interdigitation may also influence lateral diffusion due to higher membrane viscosity (Frewein et al., 2022). The packing variations of lipid bilayers significantly impact microscopic fluidity during the transition from planktonic to biofilm states and biofilm aging. As this transition occurs, lipid bilayers become more ordered, decreasing APL. This increased order is followed by a gradual decline as the biofilm ages from one to six days, approaching a state similar to planktonic. Microscopic fluidity and lipid bilayer interdigitation changes were noted with biofilm aging. As biofilms mature, lateral diffusion coefficients and lipid interdigitation decrease, gradually resembling planktonic conditions, as Benamara et al. pointed out (Benamara et al., 2014). This suggests that the membrane composition prepares bacteria for potential detachment. Understanding biomechanical features is vital for developing strategies to disrupt biofilm formation and enhance treatment efficacy, paving the way for future research into targeted therapies against biofilm-associated infections.