From Protein Structure to Function with Bioinformatics.pdf

124 P. TompaTable 5.2 Classification scheme of IDPs. Classification of IDPs encompassing seven functionalcategories based on their molecular modes of action. Two examples within each category are given,specifying the binding partner (if applicable) and the actual cellular function of the proteinProtein Partner FunctionEntropic chainsNup2p FG repeat region n.a. Gating in NPCK channel N-terminal region n.a. Timing of gate inactivationDisplay sitesCREB KID PKA Phosphorylation siteCyclin B N-terminal domain E3 ubiquitin ligase Ubiquitination siteChaperonesERD 10/14 (e.g.) Luciferase Prevention of aggregationhnRNP A1 (e.g.) DNA Strand re-annealingEffectorsp27Kip1 CycA-Cdk2 Inhibition of cell-cycleSecurin Separase Inhibition of anaphaseAssemblersRNAP II CTD mRNA maturation factors Regulation of mRNA maturationCREB p300/CBP Initiation of transcriptionScavengersCasein Calcium phosphate Stabilization of calciumphosphate in milkSalivary PRPs Tannin Neutralization of plant tanninsPrionsUre2pUtilization of urea undernitrogenSup35p NusA, mRNA Suppression of stop codon,translation readthroughbristles/spacers, linkers, and clocks, and the underlying mechanisms can be bestdescribed as either influencing the localization of attached domains, or generatingforce against movements/structural changes (Dunker et al. 2002). The best characterizedexamples in this category are entropic gating in nuclear pore complex bydisordered regions of NUPs (Elbaum 2006), the entropic spacer/bristle function ofprojection domains of microtubule-associated proteins in the cytoskeleton(Mukhopadhyay and Hoh 2001), and the entropic spring action of the PEVK regionof titin, ensuring passive tension in resting muscle due to its elasticity (Trombitaset al. 1998).5.4.2.2 Function by Transient BindingIn the other six categories, IDPs function via molecular recognition, i.e. they bindother macromolecule(s) or small ligand(s) either transiently or permanently.Display sites are primarily targeted for post-translational modifications. For example,