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Review
. 2002 Mar 15;21(6):1248-54.
doi: 10.1093/emboj/21.6.1248.

Addressing protein localization within the nucleus

Wendy A Bickmore  1 , Heidi G E Sutherland
Affiliations
Review

Addressing protein localization within the nucleus

Wendy A Bickmore et al. EMBO J. .

Erratum in

  • EMBO J 2002 May 15;21(10):2507

Abstract

Bridging the gap between the number of gene sequences in databases and the number of gene products that have been functionally characterized in any way is a major challenge for biology. A key characteristic of proteins, which can begin to elucidate their possible functions, is their subcellular location. A number of experimental approaches can reveal the subcellular localization of proteins in mammalian cells. However, genome databases now contain predicted sequences for a large number of potentially novel proteins that have yet to be studied in any way, let alone have their subcellular localization determined. Here we ask whether using bioinformatics tools to analyse the sequence of proteins whose subnuclear localizations have been determined can reveal characteristics or signatures that might allow us to predict localization for novel protein sequences.

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Figures

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Fig. 1. Frequency histograms showing the pI values, estimated using the ProtParam tool (http://www.expasy.ch/tools/protparam.html) (at 0.25 unit intervals) of nuclear proteins that have been reported to concentrate in different nuclear compartments (splicing speckles, nucleolus, nuclear periphery, and chromatin-associated). A selection of proteins that appear to be diffusely localized through the nucleoplasm are included for comparison.
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Fig. 2. Scatter plots of pI versus molecular weight (kDa), estimated using the ProtParam tool (http://www.expasy.ch/tools/protparam.html), for proteins reported to concentrate in nuclear compartments. For considerations of scale, only proteins with molecular weights of <300 kDa are shown here, but these large proteins are included in the analyses summarized in Table I.
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Fig. 3. Average amino acid frequencies for proteins reported to concentrate in nuclear compartments. Amino acids are grouped into those with non-polar, and those with uncharged and charged polar R groups. The values for cytoplasmic proteins, taken from Schwartz et al. (2001), are shown (black) for comparison.
See this image and copyright information in PMC

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