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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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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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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Protein Folding01:25

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Protein Function Prediction: Problems and Pitfalls.

William R Pearson1

  • 1University of Virginia School of Medicine, Charlottesville, Virginia.

Current Protocols in Bioinformatics
|September 4, 2015
PubMed
Summary
This summary is machine-generated.

Assigning biological functions to new proteins is challenging. Improving protein function prediction requires careful consideration of evolutionary distance, functional similarity, and database annotation limitations.

Keywords:
EC numbersfunction predictiongene ontologyhomologyorthologyparalogy

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • New sequencing technologies have revolutionized genome characterization.
  • Accurate functional assignment of newly identified proteins remains a significant challenge for biologists.

Purpose of the Study:

  • To highlight challenges in inferring protein function from sequence similarity.
  • To provide strategies for improving the accuracy of protein function prediction.

Main Methods:

  • Analysis of challenges in functional inference from sequence similarity.
  • Review of strategies for enhancing protein function prediction accuracy.

Main Results:

  • Functional inference from sequence similarity presents several difficulties.
  • Accuracy can be improved by being conservative about evolutionary distance, clarifying 'functional similarity', and understanding annotation limitations.

Conclusions:

  • Protein function prediction is not a one-size-fits-all process.
  • Understanding the nuances of protein function and annotation is crucial for effective prediction strategies.