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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Mechanisms of Membrane-bending01:15

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...
Membrane Fluidity01:26

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 a relatively...
Membrane Fluidity01:23

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.
Multi-pass Transmembrane Proteins and β-barrels01:09

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 G-protein-linked receptors (GPCRs) and...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: May 7, 2026

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)
08:14

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)

Published on: April 20, 2015

Membrane protein orientation and refinement using a knowledge-based statistical potential.

Timothy Nugent1, David T Jones

  • 1Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK. d.jones@cs.ucl.ac.uk.

BMC Bioinformatics
|September 20, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a new computational method for accurately orienting membrane proteins within lipid bilayers. The approach enhances the study of protein structure-lipid interactions and improves protein model refinement.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Related Experiment Videos

Last Updated: May 7, 2026

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)
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Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)

Published on: April 20, 2015

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Increasing numbers of membrane protein crystal structures require automated computational tools for placement within lipid bilayers.
  • Accurate orientation is crucial for studying sequence-structure-lipid relationships, which are difficult to probe experimentally.
  • Experimental techniques face challenges in crystallizing membrane proteins within intact membranes.

Purpose of the Study:

  • To develop an automated computational method for orienting membrane proteins in lipid bilayers.
  • To refine membrane protein models and discriminate between native and decoy structures.
  • To facilitate the study of membrane protein structure and function.

Main Methods:

  • Developed a knowledge-based membrane potential derived from statistical analysis of transmembrane protein structures.
  • Utilized a combination of genetic and direct search algorithms for protein positioning.
  • Applied the method for protein placement, model refinement, and decoy discrimination.

Main Results:

  • Successfully positioned both alpha-helical and beta-barrel membrane proteins within the lipid bilayer.
  • Achieved orientations with closer agreement to experimental values compared to existing methods.
  • Demonstrated consistent and significant refinement of membrane protein models.
  • Effectively discriminated between native and decoy structures.

Conclusions:

  • The developed method offers rapid and accurate orientation of membrane proteins.
  • It provides improved accuracy over current approaches for membrane protein positioning.
  • The method effectively refines models and distinguishes correct structures, aiding structural biology research.