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Related Concept Videos

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...
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.
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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.
Protein Organization01:13

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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.
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Protein Organization01:13

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Related Experiment Video

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Structural constraints on the covariance matrix derived from multiple aligned protein sequences.

William R Taylor1, Michael I Sadowski

  • 1Division of Mathematical Biology, MRC National Institute for Medical Research, London, United Kingdom. wtaylor@nimr.mrc.ac.uk

Plos One
|December 24, 2011
PubMed
Summary

Protein structure prediction accuracy improved by incorporating 3D structural constraints into contact predictions. This enhanced method increases the number of correct protein folds identified in top predictions.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Residue contact predictions traditionally rely on mutual information from protein sequence alignments.
  • Previous methods primarily considered statistical properties, often neglecting 3D structural consistency.

Purpose of the Study:

  • To introduce novel constraints for residue contact predictions to improve 3D structural consistency.
  • To enhance protein structure prediction accuracy and efficiency.

Main Methods:

  • Developed new measures to impose global and local secondary structure constraints on contact maps.
  • Integrated these constraints into the PLATO structure prediction server for efficient implementation.
  • Filtered contact pairs based on secondary structure properties.

Main Results:

  • The new constraints significantly improve the consistency of contact maps with 3D protein structures.
  • The enhanced implementation in PLATO shows a marked improvement in prediction success.
  • On average, over 50% of correct protein folds are now identified within the top 10 ranked models.

Conclusions:

  • Incorporating 3D structural properties into contact prediction is crucial for accurate protein structure modeling.
  • The improved method offers a more efficient and effective approach to protein structure prediction.
  • This advancement has direct implications for understanding protein function and design.