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Sequence and structural analyses of nuclear export signals in the NESdb database.

Molecular biology of the cell | 2012

We compiled >200 nuclear export signal (NES)-containing CRM1 cargoes in a database named NESdb. We analyzed the sequences and three-dimensional structures of natural, experimentally identified NESs and of false-positive NESs that were generated from the database in order to identify properties that might distinguish the two groups of sequences. Analyses of amino acid frequencies, sequence logos, and agreement with existing NES consensus sequences revealed strong preferences for the Φ1-X(3)-Φ2-X(2)-Φ3-X-Φ4 pattern and for negatively charged amino acids in the nonhydrophobic positions of experimentally identified NESs but not of false positives. Strong preferences against certain hydrophobic amino acids in the hydrophobic positions were also revealed. These findings led to a new and more precise NES consensus. More important, three-dimensional structures are now available for 68 NESs within 56 different cargo proteins. Analyses of these structures showed that experimentally identified NESs are more likely than the false positives to adopt α-helical conformations that transition to loops at their C-termini and more likely to be surface accessible within their protein domains or be present in disordered or unobserved parts of the structures. Such distinguishing features for real NESs might be useful in future NES prediction efforts. Finally, we also tested CRM1-binding of 40 NESs that were found in the 56 structures. We found that 16 of the NES peptides did not bind CRM1, hence illustrating how NESs are easily misidentified.

Pubmed ID: 22833565 RIS Download

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Associated grants

  • Agency: NIGMS NIH HHS, United States
    Id: R01-GM069909
  • Agency: Howard Hughes Medical Institute, United States
  • Agency: NIGMS NIH HHS, United States
    Id: F32GM093493
  • Agency: NIGMS NIH HHS, United States
    Id: F32 GM093493
  • Agency: NIGMS NIH HHS, United States
    Id: R01-GM094575
  • Agency: NIGMS NIH HHS, United States
    Id: R01 GM094575
  • Agency: NIGMS NIH HHS, United States
    Id: R01 GM069909

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This is a list of tools and resources that we have found mentioned in this publication.


WEBLOGO (tool)

RRID:SCR_010236

Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator.

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NCBI BLAST (tool)

RRID:SCR_004870

Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.

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