COGRIMEN: Coarse-Grained Method for Modeling of Membrane Proteins in Implicit Environments.
Przemysław Miszta1, Paweł Pasznik1, Szymon Niewieczerzał1
1Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland.
Journal of Chemical Theory and Computation
|August 23, 2022
Summary
A new coarse-grained method (COGRIMEN) enables efficient molecular dynamics simulations for large membrane protein complexes in implicit environments. This approach accelerates the study of vital cellular proteins and their interactions.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Membrane proteins are crucial cellular components involved in various biological processes.
- These proteins often form large, complex structures within cellular membranes and organelles.
- Investigating these large complexes requires efficient simulation methodologies.
Purpose of the Study:
- To develop a novel computational methodology for simulating membrane protein complexes.
- To enable faster and more accessible molecular dynamics simulations of these systems.
- To provide a tool for studying the structure and dynamics of large membrane protein assemblies.
Main Methods:
- Utilized a coarse-grained representation of biomolecules in implicit environments.
- Combined the coarse-grained MARTINI model with an effective energy function (COGRIMEN) for water/membrane mimicry.
- Optimized force field solvation parameters using Genetic Algorithms based on the IMM1 method.
- Implemented the COGRIMEN method as a patch for the NAMD program.
Main Results:
- Successfully tested the COGRIMEN methodology on various membrane proteins, their complexes, and oligomers.
- Demonstrated the capability of the method for coarse-grained simulations in implicit environments.
- Validated the efficiency of the approach for large membrane protein systems.
Conclusions:
- The COGRIMEN method offers a valuable tool for rapid and efficient studies of large membrane protein complexes.
- This methodology facilitates the investigation of membrane protein function and interactions within cellular compartments.
- The NAMD implementation allows broader accessibility for researchers studying complex biological systems.
Related Concept Videos
01:19Fluid Mosaic Model
12.4K
Scientists identified the plasma membrane in the 1890s and its principal chemical components (lipids and proteins) by 1915. The model for plasma membrane structure, proposed in 1935 by Hugh Davson and James Danielli, was the first model to be widely accepted in the scientific community. The model was based on the plasma membrane's "railroad track" appearance in early electron micrographs. Davson and Danielli theorized that the plasma membrane's structure resembled a sandwich...
12.4K
01:24Protein Diffusion in the Membrane
4.5K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
4.5K
00:59Mechanisms of Membrane Domain Formation
3.1K
Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
Another mechanism for membrane domain formation involves membrane proteins interacting with...
Another mechanism for membrane domain formation involves membrane proteins interacting with...
3.1K
01:23Membrane Fluidity
155.0K
Cell membranes are composed of phospholipids, proteins, and carbohydrates loosely attached to one another through chemical interactions. Molecules are generally able to move about in the plane of the membrane, giving the membrane its flexible nature called fluidity. Two other features of the membrane contribute to membrane fluidity: the chemical structure of the phospholipids and the presence of cholesterol in the membrane.
155.0K
01:09Multi-pass Transmembrane Proteins and β-barrels
5.5K
In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
5.5K
01:16Introduction to Membrane Proteins
67.2K
The cell membrane, or plasma membrane, is an ever-changing landscape. It is described as a fluid mosaic where various macromolecules are embedded in the phospholipid bilayer. Among the macromolecules are proteins. The protein content varies across cell types. For example, mitochondrial inner membranes contain ~76% protein content, while myelin contains ~18% protein content. Individual cells contain many types of membrane proteins—red blood cells contain over 50—and different cell...
67.2K