Deciphering Aquaporin-1 Permeability Modulation by Membrane Lipid Composition and Bilayer Mechanical Stress via Atomistic Simulations
; Casal, Juan José
; Toriano, Roxana Mabel 
Otros responsables
Fecha
Publicador:
Consejo Nacional de Investigaciones Científicas y Técnicas
Fecha de depósito:
18/12/2025
Fecha de creación:
01/03/2024-05/06/2025
Clasificación temática
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Resumen
Aquaporin-1 (AQP1) is a critical water channel whose functionality is inherently tied to its surrounding lipid environment. Using atomistic molecular dynamics (MD) simulations totaling several microseconds, we investigated the coupled influence of membrane composition and bilayer mechanical tension on AQP1 water permeability. Specifically, systems featuring varying concentrations of anionic lipids (e.g., POPG, Cardiolipin) and differential lateral pressures were analyzed. Our results reveal a non-linear modulation of water flux, quantified via single-channel permeability coefficients and potential of mean force (PMF) profiles, across the channel's selectivity filter. High mechanical tension, regardless of the lipid type, consistently induced a statistically significant decrease in water conductance, attributed to a subtle yet critical tilting of the pore-lining helices and a local increase in the energy barrier within the NPS region. Conversely, specific anionic lipid compositions attenuated this effect, suggesting a compensatory, charge-mediated stabilization of the channel structure under stress. These findings underscore the necessity of considering the membrane's chemomechanical state when modeling AQP1 function and provide essential insights for rational drug design targeting the ADMET properties of water-soluble compounds.
Métodos
The molecular dynamics simulations were performed using the GROMACS (Version ) software package.Force Field: The Charmm36m force field was employed for the protein (Aquaporin-1) and the lipid bilayer components.Water Model: The TIP3P water model was used to solvate the systems.Ions: Counterions Na+ y Cl- were added to neutralize the system and achieve a physiological concentration (e.g., 0.15 M).System Size: The total system size typically ranged from 120,000 to 150,000 atoms, depending on the specific lipid composition and box dimensions. Simulation Protocol: The protocol followed standard equilibration and production steps: Minimization: Energy minimization was performed using the steepest descent algorithm. Equilibration: Systems were equilibrated in the NVT (Isothermal-Isochoric) and NPT (Isothermal-Isobaric) ensembles for a total of 50-100 ns to relax the lipid bilayer around the protein. Production Runs: Final production runs were executed in the NPT ensemble, ensuring anisotropic pressure coupling for accurate membrane tension control (often set at 1 bar pressure and 310 K temperature). Integration Time Step: A 2 fs time step was used, coupled with the LINCS algorithm to constrain bond lengths involving hydrogen atoms.AnalysisTrajectory analysis utilized standard GROMACS tools and custom Python scripts leveraging MDAnalysis for detailed quantification of:Water Permeability: Calculated via water crossing events or potential of mean force (PMF) profiles. Membrane Properties: Bilayer thickness, area per lipid (APL), and mechanical tension profiles.Protein Dynamics: Conformational changes and helix tilting related to the applied mechanical stress.
Información de Series
The provided datasets comprise a comprehensive collection of time-series and structural profiles derived from Molecular Dynamics simulations of the Aquaporin-1 (AQP1) tetramer, focused on quantifying water transport mechanisms and pore stability. These series, primarily stored in tidy CSV format, capture the trajectory of water molecules and the conformational evolution of the protein over microsecond timescales. The data includes discrete water permeation events and collective displacement coordinates used to calculate osmotic and diffusive permeability coefficients, as well as the z-axis trajectories of individual molecules that characterize the single-file transport regime.
Geometrical analysis is represented through pore radius profiles and the structural stability of functional landmarks, such as the NPA motifs and the aromatic/arginine (ar/R) selectivity filter. These are complemented by time-resolved records of pore occupancy and water-residue coordination, which identify the hydrogen-bonding networks and dipole orientation shifts responsible for proton exclusion. Additionally, the datasets track the dynamics of the surrounding lipid bilayer and the global stability of the protein through root mean square deviation and radius of gyration metrics. Collectively, these series enable a multi-scale analysis of AQP1 function, correlating local atomic fluctuations with macroscopic transport properties and energetic barriers.
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