Related Experiment Video
Updated: Jan 4, 2026
06:32
Reconstitution of Septin Assembly at Membranes to Study Biophysical Properties and Functions
Published on: July 28, 2022
2.6K
Curvature as a Collective Coordinate in Enhanced Sampling Membrane Simulations
1Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources , CNRS UMR7378/Université de Picardie Jules Verne , 10, rue Baudelocque , 80039 Amiens Cedex, France.
Journal of Chemical Theory and Computation
|October 31, 2019
Summary
This study introduces a new computational method to simulate membrane bending, crucial for cell functions. The approach enables efficient analysis of membrane free energy landscapes and deformations, aiding in understanding cellular processes.
Area of Science:
- Biophysics
- Computational Biology
- Membrane Biophysics
Background:
- Membrane plasticity, including bending and budding, is vital for cellular functions like recognition and communication.
- Existing molecular simulation methods for characterizing membrane deformations are limited in scope and computational efficiency.
Purpose of the Study:
- To develop a novel, computationally efficient collective coordinate for simulating membrane bending.
- To enable quantitative characterization of membrane bending free energy landscapes.
- To apply the new method to key biological problems involving membrane remodeling.
Main Methods:
- Definition of a new collective coordinate based on local atomic curvatures for membrane bending.
- Utilizing enhanced sampling simulations along this coordinate to explore the free energy landscape.
- Application to simulate a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) bilayer, POPE liposome formation, and bacterial outer membrane budding.
Main Results:
- The novel collective coordinate provides realistic yet computationally inexpensive evaluation of membrane bending.
- Enhanced sampling simulations successfully mapped the bending free energy landscape for a POPE bilayer.
- The method was applied to study liposome formation and the influence of Pseudomonas quinolone signal on bacterial membrane budding.
Conclusions:
- The developed collective coordinate offers a powerful tool for studying membrane mechanics and dynamics.
- This method significantly enhances the accessibility and efficiency of simulating membrane deformations.
- The findings provide insights into fundamental cellular processes and potential targets for therapeutic intervention.
Related Concept Videos
01:15Mechanisms of Membrane-bending
3.2K
The living membranes are flexible due to their fluid mosaic nature; however, their bending into different shapes is an active process regulated by specific lipids and proteins. The membrane bending can be transient as seen in vesicles or stable for a long time as in microvilli. Cells regulate the size, location, and duration of the membrane curvature.
Membrane bending can happen due to intrinsic changes in lipid composition or extrinsic association with different proteins. The proteins involved...
Membrane bending can happen due to intrinsic changes in lipid composition or extrinsic association with different proteins. The proteins involved...
3.2K
01:23Curvilinear Motion: Rectangular Components
1.0K
Curvilinear motion characterizes the movement of a particle or object along a curved path, notably evident when envisioning a car navigating a winding road. If the car starts at point A, its position vector is established within a fixed frame of reference, where the ratio of the position vector to its magnitude signifies the unit vector pointing in the position vector's direction.
As the car advances, its position evolves over time. Quantifying the car's velocity involves computing the...
As the car advances, its position evolves over time. Quantifying the car's velocity involves computing the...
1.0K
01:14Bending of Curved Members - Strain Analysis
461
The mechanics of deformation in curved members, such as beams or arches, under bending moments, involve complex responses. When such a member, symmetric about the y-axis and shaped like a segment of a circle centered at point C, is subjected to equal and opposite forces, its curvature and surface lengths change significantly. This alteration results in the shift of the curvature's center from C to C', indicating a tighter curve.
The important part of bending analysis for such a member...
The important part of bending analysis for such a member...
461
01:16Bending of Curved Members - Neutral Surface
449
In curved beams, unlike straight beams, the stress distribution across the cross-section is not uniform due to the beam's curvature. This non-uniformity arises because the neutral axis, where stress is zero, does not align with the centroid of the section. In a curved beam, the strain varies along the section as a function of the distance from the neutral axis.
Consider the curved member described in the previous lesson. According to Hooke's law, which relates stress to strain within the...
Consider the curved member described in the previous lesson. According to Hooke's law, which relates stress to strain within the...
449
01:27Curvilinear Motion: Normal and Tangential Components
756
When a car traverses a curved road, its motion can be elucidated by breaking it down into tangential and normal components. The car-centric coordinates attached to the vehicle move with it.
The positive direction of the t-axis aligns with the increasing position of the car along the curved path, denoted by the unit vector ut. Simultaneously, the n-axis, perpendicular to the t-axis, dissects the curved path into differential arc segments, each forming the arc of a circle with a radius of...
The positive direction of the t-axis aligns with the increasing position of the car along the curved path, denoted by the unit vector ut. Simultaneously, the n-axis, perpendicular to the t-axis, dissects the curved path into differential arc segments, each forming the arc of a circle with a radius of...
756
01:27Curvilinear Motion: Polar Coordinates
770
In polar coordinates, the motion of a particle follows a curvilinear path. The radial coordinate symbolized as 'r,' extends outward from a fixed origin to the particle, while the angular coordinate, 'θ,' measured in radians, represents the counterclockwise angle between a fixed reference line and the radial line connecting the origin to the particle.
The particle's location is described using a unit vector along the radial direction. Deriving the particle's position...
The particle's location is described using a unit vector along the radial direction. Deriving the particle's position...
770