Thu, 21 Aug 2008 15:25:15 BST CiteULike: barry's Garcia http://www.citeulike.org/user/barry/author/Garcia CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/barry/article/2707595 <i>PLoS Biology, Vol. 6, No. 4. (1 April 2008), e98.</i><br /><br />The microtubule (MT) cytoskeleton is required for many aspects of cell function, including the transport of intracellular materials, the maintenance of cell polarity, and the regulation of mitosis. These functions are coordinated by MT-associated proteins (MAPs), which work in concert with each other, binding MTs and altering their properties. We have used a MT cosedimentation assay, combined with 1D and 2D PAGE and mass spectrometry, to identify over 250 MAPs from early Drosophila embryos. We have taken two complementary approaches to analyse the cellular function of novel MAPs isolated using this approach. First, we have carried out an RNA interference (RNAi) screen, identifying 21 previously uncharacterised genes involved in MT organisation. Second, we have undertaken a bioinformatics analysis based on binary protein interaction data to produce putative interaction networks of MAPs. By combining both approaches, we have identified and validated MAP complexes with potentially important roles in cell cycle regulation and mitosis. This study therefore demonstrates that biologically relevant data can be harvested using such a multidisciplinary approach, and identifies new MAPs, many of which appear to be important in cell division. A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis Julian Hughes Ana Meireles Katherine Fisher Angel Garcia Philip Antrobus Alan Wainman Nicole Zitzmann Charlotte Deane Hiroyuki Ohkura James Wakefield doi:10.1371/journal.pbio.0060098 PLoS Biology, Vol. 6, No. 4. (1 April 2008), e98. 2008-04-23T13:18:47-00:00 2008 PLoS Biology 6 4 e98 mts protein_protein tubulin http://www.citeulike.org/user/barry/article/161152 <i>Nucleic Acids Research, Vol. 32, No. 16. (2004), pp. 4732-4741.</i><br /><br />Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix-turn-helix (HTH), helix-hairpin-helix (HhH) and helix-loop-helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif. [Journal Article; In English; England] Identifying DNA-binding proteins using structural motifs and the electrostatic potential Hugh Shanahan Mario Garcia Susan Jones Janet Thornton Nucleic Acids Research, Vol. 32, No. 16. (2004), pp. 4732-4741. 2005-04-14T18:42:08-00:00 2004 Nucleic Acids Research 32 16 4732 4741 bioinf_methods protein_protein protein_structure structural_bioinformatics