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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 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 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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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Why are they missing? : Bioinformatics characterization of missing human proteins.

Amr Elguoshy1, Sameh Magdeldin2, Bo Xu3

  • 1Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan; Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt.

Journal of Proteomics
|August 19, 2016
PubMed
Summary

Researchers analyzed "missing proteins" lacking experimental evidence. Findings reveal challenges in identifying these proteins due to properties like hydrophobicity and lack of unique tryptic peptides, suggesting improved strategies for detection.

Keywords:
BioinformaticsMissing proteinSignal peptidomeTransmembrane domain

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Human protein research

Background:

  • NeXtProt database identifies 20,060 human proteins.
  • 16.8% of canonical proteins lack experimental evidence (PE2-PE5), termed 'missing proteins'.
  • A bioinformatics workflow is proposed for analyzing these missing proteins.

Purpose of the Study:

  • Analyze physicochemical properties of missing proteins.
  • Determine the existence and distribution of tryptic cleavage sites.
  • Identify signature peptides for missing proteins.

Main Methods:

  • Bioinformatic analysis of protein properties.
  • In silico prediction of tryptic cleavage sites and peptides.
  • Evaluation of different database and enzyme strategies for peptide identification.

Main Results:

  • 23.7% of missing proteins are hydrophobic with transmembrane domains.
  • 40 missing protein entries yield tryptic peptides outside mass detection range or mapping to other proteins.
  • 21% of missing entries lack unique tryptic peptides.
  • In silico endopeptidase combination and dual database strategies enhance identification potential.

Conclusions:

  • Identification of missing proteins requires tailored sample preparation, digestion, and data analysis.
  • Utilizing mature protein and signal peptidome databases can aid in identifying N-terminal and C-terminal peptides.
  • Further optimization of proteomic workflows is crucial for discovering missing human proteins.