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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...
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...
Signal Sequences and Sorting Receptors01:41

Signal Sequences and Sorting Receptors

Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...
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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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: Jun 2, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Optimal mutation sites for PRE data collection and membrane protein structure prediction.

Huiling Chen1, Fei Ji, Victor Olman

  • 1Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602-4712, USA.

Structure (London, England : 1993)
|April 13, 2011
PubMed
Summary

This study introduces a computational method to optimize labeling for nuclear magnetic resonance paramagnetic relaxation enhancement (PRE) in protein structure prediction. This approach simplifies determining the topology of helical transmembrane proteins with fewer labels.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Nuclear magnetic resonance paramagnetic relaxation enhancement (PRE) is crucial for protein structure prediction, measuring long-range distances to labeled residues.
  • Traditional PRE methods involve time-consuming labeling of multiple protein sites individually.
  • Accurate prediction of transmembrane protein structures is essential for understanding their function.

Purpose of the Study:

  • To develop a computational strategy for optimal placement of a minimal number of labels for PRE experiments.
  • To facilitate the determination of helical transmembrane protein topology.
  • To reduce the labor involved in experimental structure prediction using PRE.

Main Methods:

  • A computational procedure utilizing protein sequence and secondary structure models was developed.
  • The method focuses on identifying optimal label positions for minimum labeling requirements.
  • The approach was tested on the DsbB protein and validated using simulated PRE data.

Main Results:

  • Predicting the topology of a four-helix protein (DsbB) using a single label was successful in 80% of cases, with structures within 6 Å of the native structure.
  • Simulated data indicated that two labels can predict the topology of five-helix proteins, and three labels for six-to-seven-helix proteins.
  • An average success rate of 76% was achieved for topology prediction with high structural precision.

Conclusions:

  • The developed computational method significantly streamlines the process of structure prediction using PRE.
  • This approach offers a promising strategy for experimentally constrained structure prediction of membrane proteins.
  • Optimal label placement reduces experimental effort while maintaining high accuracy in determining protein topology.