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Membrane Fluidity

Membrane Fluidity

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.

Amino acids

Amino acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...

Membrane Fluidity

Membrane Fluidity

Membrane fluidity is explained by the fluid mosaic model of the cell membrane, which describes the plasma membrane structure as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character.
Mosaic nature of the membrane
The mosaic characteristic of the membrane helps the plasma membrane remain fluid. The integral proteins and lipids exist as separate but loosely-attached molecules in the membrane. The membrane is...

Multi-pass Transmembrane Proteins and β-barrels

Multi-pass Transmembrane Proteins and β-barrels

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...

Single-pass Transmembrane Proteins

Single-pass Transmembrane Proteins

Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...

Mechanisms of Membrane-bending

Mechanisms of Membrane-bending

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...

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

A knowledge-based scale for amino acid membrane propensity.

Marco Punta¹, Amos Maritan

¹International School for Advanced Studies (SISSA), and Istituto Nazionale di Fisica della Materia, Via Beirut 2-4, 34014 Trieste, Italy.

|December 10, 2002

Summary

This summary is machine-generated.

Researchers developed a new amino acid scale to predict transmembrane helices. This knowledge-based scale, derived from protein structures, shows performance comparable to existing hydropathy scales for membrane protein analysis.

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Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Predicting transmembrane helices is crucial for understanding membrane protein function.
Existing hydropathy scales are widely used but can be improved.
Knowledge-based approaches offer potential for more accurate predictions.

Purpose of the Study:

To derive a novel membrane-propensity scale for amino acids.
To evaluate the predictive power of the new scale for transmembrane helices.

Main Methods:

Utilized transmembrane helix segments from crystal structures.
Employed an optimization procedure to derive an optimal amino acid scale.
Tested the scale's predictive performance on various protein databases.

Main Results:

A knowledge-based membrane-propensity scale was successfully derived.
The new scale demonstrated robust performance, comparable to established hydropathy scales.
The scale showed significant predictive power across membrane proteins, soluble proteins, and signal peptides.

Conclusions:

The derived knowledge-based scale is effective for predicting transmembrane helices.
This method provides a robust alternative for analyzing membrane protein structures.
Accurate sequence databases are key for deriving reliable, knowledge-based scales.