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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...
Single-pass Transmembrane Proteins01:25

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...
Insertion of Single-pass Transmembrane Proteins in the RER01:26

Insertion of Single-pass Transmembrane Proteins in the RER

Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral proteins that span the lipid bilayer and monotopic proteins that are attached to either side of the membrane but do not pass through it.
Integral transmembrane proteins possess transmembrane and extra membrane domains. The transmembrane domains are primarily made of 20-25 hydrophobic amino acids arranged in a helical secondary confirmation. These...
Insertion of Multi-pass Transmembrane Proteins in the RER01:29

Insertion of Multi-pass Transmembrane Proteins in the RER

The rough ER membrane synthesizes, assembles, and embeds transmembrane proteins in diverse topologies. These proteins function as transporters or channels and can remain in the ER membrane or are sent to the Golgi complex, lysosome, and cell membrane.
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
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...

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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

ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability.

Masafumi Arai1, Hironori Mitsuke, Masami Ikeda

  • 1Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan.

Nucleic Acids Research
|June 25, 2004
PubMed
Summary

ConPred II predicts transmembrane protein topology using a two-step consensus approach. This method combines high-accuracy predictions with broader coverage for improved transmembrane segment analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Transmembrane (TM) proteins play crucial roles in cellular functions.
  • Accurate prediction of TM topology is essential for understanding protein function and structure.
  • Existing methods for TM topology prediction have limitations in accuracy or coverage.

Purpose of the Study:

  • To develop an improved computational tool for predicting transmembrane protein topology.
  • To combine the strengths of different prediction methods for enhanced accuracy and coverage.
  • To provide a user-friendly server for automated TM topology prediction.

Main Methods:

  • The ConPred II system integrates two previously developed prediction programs: ConPred_elite and ConPred_all.
  • ConPred_elite offers near-perfect accuracy but limited coverage (20-30%).
  • ConPred_all provides broader coverage for all sequences, with improved accuracy over individual methods.

Main Results:

  • ConPred II employs a two-step process: first, ConPred_elite is used for high-confidence predictions.
  • Sequences not predicted by ConPred_elite are then processed by ConPred_all.
  • The server returns predicted TM topology models, including graphical representations.

Conclusions:

  • ConPred II offers a robust and automated approach for TM topology prediction.
  • The combined strategy balances high accuracy with comprehensive coverage.
  • The tool facilitates research in transmembrane protein structure and function.