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Protein Interaction Domains and Motifs (4):
Recent article
Protein Interaction Domains and Motifs
Abstract
We found that the core ER-lumenal domain (cLD) of yeast Ire1 binds to unfolded proteins in yeast cells and to peptides primarily composed of basic and hydrophobic residues in vitro. Mutation of amino acid side chains exposed in a putative peptide-binding groove of Ire1 cLD impaired peptide binding....
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PMID: 21852455
PDF is available here.
PDF is available here.
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Abstract
We show that Rrn7, a subunit of the yeast Pol I core factor, and its human ortholog TAF1B are TFIIB-like factors. Although distantly related, Rrn7 shares many activities associated with TFIIB-like factors. Domain swaps between TFIIB-related factors show that Rrn7 is most closely related to the Pol I...
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PMID: 21921198
PDF is available here.
PDF is available here.
Abstract
CCL5 (RANTES) is a proinflammatory chemokine known to activate leukocytes through its receptor, CCR5. Although the monomeric form of CCL5 is sufficient to cause cell migration in vitro, CCL5's propensity for aggregation is essential for migration in vivo, T cell activation and apo...
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PMID: 21827949
PDF is available here.
PDF is available here.
Abstract
We test this hypothesis by comparing vulva induction in two genetically tractable nematodes, Caenorhabditis elegans and Pristionchus pacificus. Previous work indicated that the vulva is induced by epidermal growth factor (EGF)/RAS and WNT signaling in Caenorhabditis and Pristionchus, respectively. H...
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PMID: 21814488
PDF is available here.
PDF is available here.
Abstract
We have performed fluorescence polarisation assays to indirectly measure relative binding affinity, and applied computational simulations to interrogate the behaviour of the eight human BRC-RAD51 complexes, as well as a suite of BRC cancer-associated mutations. Our computational approaches encompass...
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PMID: 21789034
PDF is available here.
PDF is available here.
Abstract
We discuss the various modes of intramembrane protein-lipid interactions in cellular membranes, including examples for both annular and nonannular bound lipids. Furthermore, we will discuss possible functional roles of such specific protein-lipid interactions as well as roles of lipids as chaperones...
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PMID: 21536707
PDF is available here.
PDF is available here.
Abstract
We focus on Tyr223(5.58) as part of the Y(5.58)X(7)K(R)(5.66) motif. Mutation to Ala, Phe, or Glu results in specific impairments of G(t)-activation measured by intrinsic G(t) fluorescence. UV-vis/FTIR spectroscopy of rhodopsin and its complex with a C-terminal G(t)α peptide allows the assignment o...
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PMID: 21506561
PDF is available here.
PDF is available here.
Cell Cycle (10)8 2011
Abstract
We report that BMI1 contains a functional recognition motif for the F box protein βTrCP, which regulates ubiquitination and proteasome-mediated degradation of various proteins. We show that overexpression of wild-type βTrCP but not the ΔF mutant of it promotes BMI1 ubiquitination and degradation,...
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PMID: 21430439
PDF is available here.
PDF is available here.
Journal of Proteomics (74)4 2011
Abstract
We use a large, plasma based, proteome-derived peptide library as substrates along with mass spectrometry to explore the peptide bond specificity of three PI SVMPs and one PIII SVMP to determine their individual peptide cleavage consensus sequences. All of the proteinases assayed displayed a clear p...
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PMID: 21156218
PDF is available here.
PDF is available here.
Cell Host & Microbe (9)3 2011
Abstract
We determine the crystal structure of the L6 TIR domain and show that, although dispensable for pathogenic effector protein recognition, the TIR domain alone is both necessary and sufficient for L6 immune signaling. We demonstrate that the L6 TIR domain self-associates, most likely forming a homodi...
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PMID: 21402359
PDF is available here.
PDF is available here.
Abstract
We discuss the prospects for the realization of this idea....
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PMID: 21358629
PDF is available here.
PDF is available here.
Abstract
We show that helicase loading by ORC is inhibited by two distinct CDK-dependent mechanisms. Independent of phosphorylation, binding of CDK to an "RXL" cyclin-binding motif in Orc6 sterically reduces the initial recruitment of the Cdt1/Mcm2-7 complex to ORC. CDK phosphorylation of Orc2 and Orc6 inhib...
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PMID: 21289063
PDF is available here.
PDF is available here.
Virology Journal (8)1 2011
Abstract
We analyse the effect of these differences upon the binding of Influenza A virus NS1 protein to a range of cellular proteins involved in polarity and signal transduction....
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PMID: 21247458
PDF is available here.
PDF is available here.
EMBO Journal (29)23 2010
Abstract
We show that an N-terminal region of Spt6 (Spt6N) is responsible for interaction with Iws1. The crystallographic structures of Encephalitozoon cuniculi Iws1 and the Iws1/Spt6N complex reveal two conserved binding subdomains in Iws1. The first subdomain (one HEAT repeat; HEAT subdomain) is a putative...
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PMID: 21057455
PDF is available here.
PDF is available here.
Abstract
We present direct biochemical evidence that Tudor-Aubergine interaction surface is composed of different Tudor domains including those that have not been previously implicated in Aubergine recognition. Furthermore, we show that specific single Tudor domains determine localization of Tudor complex to...
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PMID: 20946872
PDF is available here.
PDF is available here.
Macromolecular Bioscience (10)11 2010
Abstract
I collagen (COL1A1) transcription, but is functionally limited as a free molecule. Using a matrix-binding domain (MBD) from microfibril-associated glycoprotein-1, the fusion protein MBD-CTGF was targeted to the ECM and tested for COL1A1 transcriptional activation. MBD-CTGF produced by the ECM-synthe...
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PMID: 20799254
PDF is available here.
PDF is available here.
Thrombosis and Haemostasis (104)5 2010
Abstract
We review here published information on these topics and touch upon ongoing studies aimed at finding definitive answers to outstanding questions relevant for a better understanding of thrombosis and haemostasis....
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PMID: 20941453
PDF is available here.
PDF is available here.
Abstract
Tumors are invariably less well-oxygenated than the normal tissues from which they arose. Hypoxia-inducible factor-1 (HIF-1), a key transcriptional regulator, plays a central role in the adaptation of tumor cells to hypoxia by activating the transcription of genes, which regulate sev...
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PMID: 20578983
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1813)9 2011
Abstract
We consolidate information about cargos that are directly recognized by import-Karyopherinβs and review common characteristics or lack thereof among cargos of different import pathways. Knowledge of Karyopherinβ-cargo interactions is also critical for the development of nuclear import inhibitors a...
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PMID: 21029754
PDF is available here.
PDF is available here.
Abstract
We report here the solution NMR structure of the full-length MinE dimer from Neisseria gonorrhoeae, with two parts of the N-terminal domain forming an integral part of the dimerization interface. Unexpectedly, solvent accessibility is highly restricted for residues that were previously hypothesized...
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PMID: 20937912
PDF is available here.
PDF is available here.
Abstract
β-Turns are secondary structure elements not only exposed on protein surfaces, but also frequently found to be buried in protein-protein interfaces. Protein engineering so far considered mainly the backbone-constraining properties of synthetic β-turn mimics as parts of surface-exposed loops. A β-...
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PMID: 20937907
PDF is available here.
PDF is available here.
Abstract
We previously demonstrated that the isolated WW3 domain of Smurf2, but not the WW2 domain, can directly bind to a Smad7 PY motif. We show here that the WW2 augments this interaction by binding to the WW3 and making auxiliary contacts with the PY motif and a novel E/D-S/T-P motif, which is N-terminal...
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PMID: 20937913
PDF is available here.
PDF is available here.
Abstract
We establish that, like other germ-line Tudor proteins, the ancestral staphylococcal nuclease domain-containing 1 (SND1) polypeptide is expressed and associates with PIWIL1/Miwi in germ cells. We find that human SND1 binds PIWIL1 in an arginine methylation-dependent manner with a preference for symm...
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PMID: 20937909
PDF is available here.
PDF is available here.
Current Genetics (56)5 2010
Abstract
We suggest that decreased stability of Tra1-L3733A accounts for the phenotypes since intragenic suppressors of tra1-L3733A restored Tra1 levels, and reducing wild-type Tra1 led to comparable growth defects. Also supporting a key role for the FATC domain in the structure/function of Tra1, addition of...
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PMID: 20635087
PDF is available here.
PDF is available here.
Abstract
We found that VPA0450 is an inositol polyphosphate 5-phosphatase that hydrolyzed the D5 phosphate from the plasma membrane phospholipid phosphatidylinositol 4,5-bisphosphate. VPA0450 disrupted cytoskeletal binding sites on the inner surface of membranes of human cells and caused plasma membrane bleb...
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PMID: 20724587
PDF is available here.
PDF is available here.
Abstract
Coxsackie and adenovirus receptor (CAR) is the primary cellular receptor for group B coxsackieviruses and most adenovirus serotypes and plays a crucial role in adenoviral gene therapy. Recent discovery of the interaction between junctional adhesion molecule-like protein (JAML) and CA...
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PMID: 20813955
PDF is available here.
PDF is available here.
Abstract
We describe a new approach for inferring the functional relationships between nonhomologous protein families by looking at statistical enrichment of alternative function predictions in classification hierarchies such as Gene Ontology (GO) and Structural Classification of Proteins (SCOP). Protein str...
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PMID: 20570776
PDF is available here.
PDF is available here.
Molecular Cell (39)4 2010
Abstract
We found a XPD protein complex containing MMS19 that was assumed to be a regulator of TFIIH. However, the MMS19-XPD complex did not contain any other subunits of TFIIH. Instead, it included FAM96B (now designated MIP18), Ciao1, and ANT2. MMS19, MIP18, and XPD localized to the mitotic spindle during...
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PMID: 20797633
PDF is available here.
PDF is available here.
Molecular Cell (39)4 2010
Abstract
We show that the Pol I-specific subunits A49 and A34.5 form a subcomplex that binds DNA and is related to TFIIF and TFIIE. The N-terminal regions of A49 and A34.5 form a dimerization module that stimulates polymerase-intrinsic RNA cleavage and has a fold that resembles the TFIIF core. The C-terminal...
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PMID: 20797630
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)34 2010
Abstract
We have used a modular approach to determine the crystal structures of the structured domains in the EBF family. The DNA binding domain reveals a striking resemblance to the DNA binding domains of the Rel homology superfamily of transcription factors but contains a unique zinc binding structure, ter...
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PMID: 20592035
PDF is available here.
PDF is available here.
Abstract
We report the crystal structure of the apo, oxidized C-MBD to 2.0 A resolution. In the structure, two C-MBD monomers form a domain-swapped dimer, which has not been observed previously for similar domains. In addition, the interaction of the C-MBD with the other cytoplasmic domains of CopA, the ATP...
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PMID: 20602459
PDF is available here.
PDF is available here.
Infection and Immunity (78)8 2010
Abstract
We provide new insight into the structure-function relationship of the SPATEs and the functional roles of their conserved residues....
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PMID: 20479079
PDF is available here.
PDF is available here.
Journal of General Virology (91)Pt 8 2010
Abstract
Bunyamwera virus NSs protein is involved in the inhibition of cellular transcription and the interferon (IFN) response, and it interacts with the Med8 component of Mediator. A spontaneous mutant of a recombinant NSs-deleted Bunyamwera virus (rBUNdelNSs2) was identified and characterized. This mutant...
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PMID: 20427562
PDF is available here.
PDF is available here.
Journal of Virology (84)16 2010
Abstract
We showed that SUMO binding by IE2 is necessary for its efficient transactivation function and for viral growth. IE2 bound physically to SUMO-1 through a SUMO-interacting motif (SIM). Mutations in SIM (mSIM) or in both SUMOylation sites and SIM (KR/mSIM), significantly reduced IE2 transactivation ef...
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PMID: 20519406
PDF is available here.
PDF is available here.
Abstract
In order to gain deeper insights into the functional sites of human placental alkaline phosphatase, the structures of the enzyme with the putative regulators L-Phe, pNPP and 5'-AMP [Llinas et al. (2005), J. Mol. Biol. 350, 441-451] were re-refined. Significant variations in ligand positioning and id...
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PMID: 20693656
PDF is available here.
PDF is available here.
Abstract
Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is essentially the same as that of the enzyme from ot...
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PMID: 20693660
PDF is available here.
PDF is available here.
Abstract
Hantaviral N and Gn proteins were shown to interact, thus providing the long-awaited evidence for one of the crucial steps in the virus replication at which RNPs are directed to the site of the virus assembly. Using pull-down assay and point mutagenesis it was demonstrated that intact, properly fold...
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PMID: 20566401
PDF is available here.
PDF is available here.
Abstract
Heat shock 70 kDa proteins (HSP70s) are ubiquitous molecular chaperones that function in a myriad of biological processes, modulating polypeptide folding, degradation and translocation across membranes, and protein-protein interactions. This multitude of roles is not easily reconciled with the unive...
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PMID: 20651708
PDF is available here.
PDF is available here.
Abstract
Tau is an abundant microtubule-associated protein which regulates the stability of the cytoskeleton. Tau binds microtubules directly through microtubule-binding domains in its C-terminus. However, tau is not only located in the cytosol of cells, but also associated with other intracellular domains,...
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PMID: 20658995
PDF is available here.
PDF is available here.
Abstract
The Sas10/C1D domain is found in a small group of eukaryotic proteins that have functions in RNA processing events, translational control and DNA repair mechanisms. The domain is predicted to be alpha-helical in nature and comprises approx. 80 amino acid residues. Whereas the Sas10/C1D domain has ye...
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PMID: 20659009
PDF is available here.
PDF is available here.
Genes & Development (24)14 2010
Abstract
We report that the major binding partners of the Connector Enhancer of KSR 1 (CNK1) scaffold are members of the cytohesin family of Arf guanine nucleotide exchange factors, and that the CNK1/cytohesin interaction is critical for activation of the PI3K/AKT cascade downstream from insulin and insulin-...
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PMID: 20634316
PDF is available here.
PDF is available here.
Abstract
The actin cytoskeleton consists of multiple actin binding proteins (ABPs) that participate cooperatively in different cellular functions such as the maintenance of polarity and cell motility as well as the invasion of target cells and regulation of gene expression, among others. Due to the important...
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PMID: 20338197
PDF is available here.
PDF is available here.
Abstract
Calmodulin directly binds and stabilizes ABCA1 in the presence of Ca(2+) and increases the generation of high-density lipoprotein....
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PMID: 20395597
PDF is available here.
PDF is available here.
Abstract
We searched for associating proteins and identified c-Jun activating binding protein 1 (JAB1) as a binding partner specifically for FcalphaRI. We found increased FcalphaRI surface expression after ectopic expression of JAB1 as well as diminished protein levels of total FcR gamma-chain levels after J...
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PMID: 20411563
PDF is available here.
PDF is available here.
Abstract
We confirm this link by finding that deletion of STI1 both suppresses Ssa1-21 impairment of [PSI(+)] and blocks Hsp104 curing of [PSI(+)]. Hsp104's tetratricopeptide repeat (TPR) interaction motif was dispensable for curing; however, cells expressing Sti1 defective in Hsp70 or Hsp90 interaction cure...
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PMID: 20479121
PDF is available here.
PDF is available here.
Abstract
We show here that Ror2 regulates Wnt5a-induced polymerization of Dishevelled (Dvl) and that this Ror2-mediated regulation of Dvl is independent of the cytoplasmic region of Ror2. Ror2 can associate with Frizzled7 (Fz7) via its extracellular cysteine-rich domain to form a receptor complex that is req...
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PMID: 20457807
PDF is available here.
PDF is available here.
Abstract
We describe a novel form of trans-tail regulation of histone modifications involving the N-terminal tail of histone H2A. Mutating or deleting residues in the N-terminal tail of H2A reduces H2B ubiquitylation and H3K4 methylation but does not affect the recruitment of the modifying enzymes, Rad6/Bre1...
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PMID: 20498280
PDF is available here.
PDF is available here.
Abstract
We utilized a polyarginine-rich, cell-permeable peptide that represents the portion of the SLP-76 PR region that interacts with the ITK SH3 domain as a competitive inhibitor to disrupt the association between ITK and SLP-76 in live cells. We demonstrate that treatment of cells with this peptide, by...
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PMID: 20457812
PDF is available here.
PDF is available here.
Abstract
Our results provide the first evidence of a role for KLF3 in muscle gene regulation and reveal an alternate mechanism for transcriptional regulation by SRF via its recruitment to KLF binding sites. Since both factors are expressed in all muscle lineages, SRF may regulate many striated- and smooth-mu...
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PMID: 20404088
PDF is available here.
PDF is available here.
Journal of Virology (84)13 2010
Abstract
We now show that one such L domain-independent HIV-1 Gag construct (termed Z(WT)) that has NC-p1-p6 replaced by a leucine zipper domain is resistant to dominant-negative inhibitors of the ESCRT pathway that block HIV-1 particle production. However, Z(WT) became dependent on the presence of an L doma...
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PMID: 20427536
PDF is available here.
PDF is available here.
Molecular Microbiology (77)1 2010
Abstract
We identify and characterize a member of this family (DipM) in Caulobacter crescentus. Unlike its E. coli counterparts, DipM is essential for viability under fast-growth conditions. Under slow-growth conditions, the DeltadipM mutant displays severe defects in cell division and FtsZ constriction. Con...
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PMID: 20497503
PDF is available here.
PDF is available here.
Abstract
We present the different streptococcal adhesin families categorized on the basis of their adhesive properties and structural characteristics, and, when available, we focus the attention on conserved functional domains.
© 2009 Novartis Vaccines and Diagnostics s.r.l. Journal compilat...
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PMID: 21255337
PDF is available here.
PDF is available here.
Molecular Immunology (47)14 2010
Abstract
We tested the ability of different combinations of NFATc2, NFATc1, cJun, and cFos to synergistically activate transcription from the IL-2 promoter. We found that NFATc2 and cJun are exclusive in their ability to synergistically activate human IL-2 transcription. Protein-protein interaction assays re...
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PMID: 20557936
PDF is available here.
PDF is available here.
Journal of Molecular Biology (399)4 2010
Abstract
We have studied the interaction between PFD and CPN using those from a hyperthermophilic archaeon, Thermococcus strain KS-1 (T. KS-1). In this study, we determined the crystal structure of the T. KS-1 PFDbeta2 subunit and characterized the interactions between T. KS-1 CPNs (CPNalpha and CPNbeta) and...
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PMID: 20434454
PDF is available here.
PDF is available here.
Abstract
We explore the range of applicability of such information by analyzing the extent to which the location of binding sites on protein surfaces is conserved among structural neighbors. We find, as expected, that interface conservation is most significant among proteins that have a clear evolutionary re...
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PMID: 20534496
PDF is available here.
PDF is available here.
Abstract
We used single particle cryoelectron microscopy to determine the quaternary arrangement of the phytochrome dimer as Pr, using the bacteriophytochrome (BphP) from Deinococcus radiodurans. Contrary to the long-standing view that the two monomers are held together solely via their C-terminal region, we...
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PMID: 20534495
PDF is available here.
PDF is available here.
EMBO Journal (29)12 2010
Abstract
We show that Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) binds directly and selectively to one of five mAChR subtypes, M4 receptors (M4Rs), at their C-terminal regions of second intracellular loops. This binding relies on Ca(2+) activation of the kinase and leads to the phosphorylation of...
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PMID: 20461055
PDF is available here.
PDF is available here.
Abstract
We tested the ability of alphaB-c to suppress the aggregation of a polyQ protein. We found that alphaB-c does not inhibit the formation of SDS-insoluble polyQ fibrils. We further tested the effect of alphaB-c on the aggregation of ataxin-3, a polyQ protein that aggregates via a two-stage aggregation...
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PMID: 20484674
PDF is available here.
PDF is available here.
Abstract
We have determined whether the C-terminal truncations of hPoleta that contain the PIP1 domain but lack the UBZ and PIP2 domains can still function in TLS in human cells. Our observations that such C-terminally truncated proteins promote efficient TLS opposite a cis-syn TT dimer and confer a high deg...
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PMID: 20498091
PDF is available here.
PDF is available here.
Abstract