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Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic...
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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...
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Lipids are an essential component of all biological membranes. The average lipid content in mammalian membranes is 50%, though it can be as low as 20% in the inner mitochondrial membrane or as high as 80% in the myelin sheath present around the nerve cells.
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Crystallizing Membrane Proteins for Structure Determination using Lipidic Mesophases
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The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions.

Thomas D Newport1, Mark S P Sansom1, Phillip J Stansfeld1

  • 1Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.

Nucleic Acids Research
|November 13, 2018
PubMed
Summary

The MemProtMD database provides automated lipid bilayer assembly for membrane protein structures. This resource enables visualization and analysis of protein-lipid interactions for the scientific community.

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Integral membrane proteins are vital for cellular functions.
  • High-resolution structures are increasingly available but rarely include lipids.
  • Understanding protein-lipid interactions is crucial for membrane protein function.

Purpose of the Study:

  • To present the MemProtMD database and web server.
  • To provide automated lipid bilayer assembly for PDB membrane protein structures.
  • To facilitate the study of membrane protein-lipid interactions.

Main Methods:

  • Automated lipid bilayer assembly using the MemProtMD pipeline.
  • Development of a web database for data accessibility.
  • Interactive 3D and 2D visualizations of simulation results.
  • Ensemble analyses for conserved lipid interaction patterns.

Main Results:

  • A database of 3506 PDB entries with assembled lipid bilayers.
  • Web-based visualization tools for protein-lipid interactions and topology.
  • Identification of conserved lipid interaction motifs across protein families.
  • Provision of simulation-ready files for further research.

Conclusions:

  • MemProtMD offers a valuable resource for studying membrane proteins in a lipid environment.
  • The database enhances the understanding of protein-lipid interactions.
  • It supports further computational and experimental investigations of membrane proteins.