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NMPdb: Database of Nuclear Matrix Proteins

¹ CUBIC and ² North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA, ³ Institute of Physical Biochemistry, University Witten/Herdecke, Stockumer Strasse 10, 58448 Witten, Germany and ⁴ Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 St Nicholas Avenue, New York, NY 10032, USA

^* To whom correspondence should be addressed. Tel: +1 212 305 4018; Fax: +1 212 305 7932; Email: mika@cubic.bioc.columbia.edu

Received July 23, 2004; Revised and Accepted October 27, 2004

The nuclear matrix (NM) is a structure resulting from the aggregation of proteins and RNA in the nucleus of eukaryotic cells; it is the ‘sticky bit’ that remains after aggressive DNAse digestion and salt extraction protocols. Owing to the important role of the NM in DNA replication, DNA transcription and RNA splicing, the expression pattern of NM proteins has become an important early indicator for numerous cancers/tumors. Recent descriptions of the NM structure distinguish between a network-like ‘internal nuclear matrix’ (INM) and a ‘nuclear shell’ that connects the INM to the inner and outer nuclear membranes. A cautious NM preparation protocol reveals a coat of proteins on top of the INM; these proteins are usually referred to as the ‘nuclear matrix-associated proteins’. Here, we describe a new database (NMPdb at http://www.rostlab.org/db/NMPdb/) that currently contains details of 398 NM proteins. We collected these data through a semi-automated analysis of over 3000 scientific articles in PubMed. We could match these 398 proteins to 302 protein sequences in UniProt or GenBank. Our NMPdb repository annotates these links along with the following annotations: organism, cell type, PubMed identifier, sequence-based predictions of structural and functional features and for some entries the explicit sequence segment that is responsible for localization (nuclear matrix targeting signal).