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

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

Mesh terms: Active Transport, Cell Nucleus | Amino Acid Sequence | Amino Acids | Animals | Binding Sites | Cell Nucleus | Databases, Protein | Electrophoresis, Polyacrylamide Gel | Humans | Hydrophobic and Hydrophilic Interactions | Internet | Karyopherins | Models, Molecular | Molecular Sequence Data | Nuclear Export Signals | Protein Binding | Protein Structure, Secondary | Protein Structure, Tertiary | Proteins | Receptors, Cytoplasmic and Nuclear | Saccharomyces cerevisiae Proteins | Schizosaccharomyces pombe Proteins

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Associated grants

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

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WEBLOGO

A web based application designed to make the generation of sequence logos as easy and painless as possible. Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.

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NCBI BLAST

A data analysis service to find regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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