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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...
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Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Intrinsically Disordered Proteins02:18

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Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

Globally, unrelated protein sequences appear random.

Daniel T Lavelle1, William R Pearson

  • 1Department of Biochemistry and Molecular Genetics, University of Virginia, Jordan Hall Box 800733, Charlottesville, VA 22908, USA.

Bioinformatics (Oxford, England)
|December 2, 2009
PubMed
Summary

Protein sequences show few constraints on amino acid word usage. Most word patterns appear random, with minimal impact from folding or secondary structure preferences, especially in non-redundant protein sets.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Investigating constraints on amino acid word frequencies in proteins.
  • Comparing observed word frequencies against random sequence models.

Purpose of the Study:

  • To determine if protein folding constraints and secondary structure preferences limit amino acid word diversity.
  • To assess the randomness of amino acid word usage in protein sequences.

Main Methods:

  • Analyzed frequencies of four- and five-amino acid word clumps in proteins.
  • Compared protein word frequencies to four different random sequence models.
  • Utilized false discovery rate (q-value) analysis to identify significant overrepresentation.
  • Examined enrichment of words in conserved regions and secondary structures (alpha-helix, beta-strand).

Main Results:

  • In non-redundant protein sets, very few amino acid word clumps are significantly overrepresented compared to random models.
  • The number of exceptional words in real proteins is comparable to that between random models.
  • Consensus overrepresented words are not enriched in conserved regions.
  • Four- and five-amino acid words show a slight enrichment in alpha-helical structures but not beta-strands.
  • Overall, protein sequences exhibit minimal constraints on word usage, appearing largely random.

Conclusions:

  • Protein folding constraints and secondary structure preferences do not significantly restrict the space of amino acid words.
  • While some biases exist for alpha-helical structures, global word usage in proteins is predominantly random.
  • The findings suggest that the majority of amino acid word combinations in proteins occur by chance.