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  • structural
  • Sox5 and Sox18 show some cooperation on both elements, whereas Sox8 and Sox9 compete on both elements.Testing rationally mutated Sox proteins combined with structural modeling highlights critical amino acids for differential Sox-Oct4 partnerships and demonstrates that the cooperativity correlates with the efficiency in producing induced pluripotent stem cells.Our results suggest selective Sox-Oct partnerships in genome regulation and provide a toolset to study protein cooperation on DNA. (nih.gov)
  • Testing rationally mutated Sox proteins combined with structural modeling highlights critical amino acids for differential Sox-Oct4 partnerships and demonstrates that the cooperativity correlates with the efficiency in producing induced pluripotent stem cells. (nih.gov)
  • A structural alignment of DMC1 with the Methanococcus voltae RadA protein, a homolog of DMC1 in the helical filament form, indicated that these RAD54B-binding sites are located near the ATP-binding site at the monomer-monomer interface in the DMC1 helical filament. (nih.gov)
  • fusion proteins
  • As will become clear in this chapter, these fusion proteins, while they lack classic transforming activity, nevertheless have the capacity to disrupt hematopoiesis and effectively inactivate the molecular switch that governs promyelocytic maturation. (springer.com)
  • In several cell models, the resulting PML/RARα and PLZF/RARα fusion proteins recapitulate the leukemic phenotype by inducing a state of refractoriness to various inducers of myeloid differentiation and an increased potential for self-renewal ( 1 , 2 ). (aacrjournals.org)
  • Both fusion proteins bind the N-CoR-related as well as the SMRT-related HD-NCR through the CoR box region of RARα in a ligand-dependent manner, and binding can be released by pharmacologic doses of t-RA. (aacrjournals.org)
  • Putative
  • Diverse Combinatorial Patterns of RNA-Binding Protein Interactions with a Choice Sample of mRNAs(A-K) Putative binding sites of RBPs in target mRNAs. (nih.gov)
  • By expressing various NS5 mutants, we found that the SUMO acceptor sites are located in the N-terminal domain of NS5 and that a putative SUMO-interacting motif (SIM) of this domain is crucial for its SUMOylation.SUMOylation-defective mutants also failed to suppress the induction of STAT2-mediated host antiviral interferon signaling.Here, we found that the replicase of DENV, nonstructural protein 5 (NS5), can be SUMOylated. (nih.gov)
  • This suggests that computationally derived physical contacts might complement binary protein interaction assays and guide large-scale interactome mapping projects by prioritizing putative physical contacts for further experimental screens. (nih.gov)
  • All contain a poorly conserved putative bipartite kinase domain designated as FAST1_FAST2. (nih.gov)
  • Molecular
  • Despite characterization of the host factors that rely on SUMOylation to exert their antiviral effects, the enzymes that mediate these SUMOylation events remain to be defined.Moreover, in the absence of ICP0, high-molecular-weight SUMO-conjugated proteins do not accumulate if HSV-1 DNA does not replicate.The protein inhibitor of activated STAT (PIAS) family of SUMO ligases is predominantly associated with the suppression of innate immune signaling. (nih.gov)
  • B, Assessment of inferred and experimentally obtained physical contacts involving molecular chaperones against the Chaperone reference set of experimentally confirmed binary chaperone interactions. (nih.gov)
  • known or predicted
  • At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. (nih.gov)
  • inhibitory
  • NF-κB is a dimeric transcription factor composed of members of the Rel family that is kept in the cytoplasm of nonstimulated cells through interaction with inhibitory proteins, the IκBs ( 30 , 31 ). (pnas.org)
  • bind
  • Drugs bind in the vestibule formed by the S6 transmembrane domain, which also contains the activation gate that traps drugs in the vestibule and contributes to their efficacy of block. (nih.gov)
  • As SH2 domains only bind tyrosine-phosphorylated peptides, RGS binding to Gα depends on the Gα functional state. (aspetjournals.org)
  • Some LIM domains bind protein partners via tyrosine-containing motifs. (embl-heidelberg.de)
  • They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. (embl-heidelberg.de)
  • Sumoylation
  • Recent evidence indicated that the cellular SUMO conjugase Ubc9, a key component for protein SUMOylation, interacts with several dengue viral proteins (32, 34, 38). (nih.gov)
  • Overexpression of eYFP.PIAS4 drastically affected SUMO signaling homeostasis, increasing HMW SUMO-conjugated protein levels at least 4-fold and decreasing free SUMO levels 5-fold following 24 h of induction (Fig. 4A and B). Consequently, dynamic SUMO modification was affected, which resulted in a loss of constitutive PML and Sp100 SUMOylation and disrupted PML-NBs (Fig. 4C to E), a phenotype similar to that in Ubc9-depleted cells (18). (nih.gov)
  • amino acid
  • Although FASTKD2 is an inner mitochondrial membrane protein, it does not require mitochondrial localization to initiate apoptosis.We found that the pathway leads to apoptosis in LNCaP cells, including the two androgen-independent LNCaP cell lines that are generally resistant to apoptosis.Lastly, we identified that FASTKD2-mediated apoptosis is initiated by the 81 amino acid FAST2 region. (nih.gov)
  • Inhibitors
  • Two peptide fragments from another subunit, Phe505'‑Leu508' and Pro572'‑Thr577', played a critical role in the interactions with the inhibitors. (nih.gov)
  • Expression of the TPR domain in a wild-type background produces phenotypes similar to those caused by loss-of-function spy mutants including resistance to GA biosynthesis inhibitors, short hypocotyl length, and early flowering. (plantphysiol.org)
  • Intracellular
  • Intracellular protein expression levels and infectious DENV titer in the culture supernatant were measured by Western blotting (WB) (A) and by plaque forming assay (B), respectively. (nih.gov)
  • At the most intracellular extreme of the S6 region, Q664, Y667, and S668 were especially sensitive and together formed a ringed domain that occludes the pore in the closed state model. (nih.gov)
  • cytoplasmic
  • pAbl T735 interacted with 14-3-3 proteins, which caused cytoplasmic retention of c-Abl, where it potentiated Hp -mediated cell elongation and migration. (springer.com)
  • Major
  • Protein Kinase A (PKA) is the major receptor for the cyclic adenosine monophosphate (cAMP) secondary messenger in eukaryotes. (nih.gov)
  • Mutation
  • Probing CBD-A/B interactions in RIα (91-379) through the W260A mutation.Evaluation of the effect of the W260A mutation on the CBD-A/B interface through CCS differences in the apo and cAMP-bound states. (nih.gov)
  • Mutation of His 61 produces an inactive enzyme, whereas the H19A protein variant retains substantial activity, suggesting that His 61 serves as the catalytic base. (nih.gov)
  • The dwarfing of the floral shoot internodes caused by the gai mutation was suppressed by expression of the TRP domain. (plantphysiol.org)
  • GAPs
  • Sequences of ARF-GAP domains show no recognizable similarity to those of other GAPs, and contain a characteristic Cys-X(2)-Cys-X(16-17)-Cys-X(2)-Cys motif. (embl-heidelberg.de)
  • chromatin
  • How combinatorial chromatin modification states are recognized by epigenetic reader proteins and how this is linked to their biological function is largely unknown. (zfin.org)
  • Dimerization
  • This BCCL2 protein formed dimers and higher-order oligomers in solution.Approximately 40% of the BCCL2 secondary structure consisted of alpha helices.These results indicate that the B-box 2, coiled-coil and linker 2 regions of TRIM5α form a core dimerization motif that exhibits a high level of alpha-helical content. (nih.gov)
  • These results indicate that the B-box 2, coiled-coil and linker 2 regions of TRIM5α form a core dimerization motif that exhibits a high level of alpha-helical content. (nih.gov)
  • This way, we clustered Sox proteins according to their dimerization preferences illustrating that Sox HMG domains evolved different propensities to cooperate with Oct4. (nih.gov)
  • antagonists
  • Drugs targeting RGS proteins can be divided into five groups: 1) potentiators of endogenous agonist function, 2) potentiators/desensitization blockers of exogenous GPCR agonists, 3) specificity enhancers of exogenous agonists, 4) antagonists of effector signaling by an RGS protein, and 5) RGS agonists. (aspetjournals.org)
  • restriction
  • Like all tripartite motif (TRIM) proteins, the retroviral restriction factor TRIM5α consists of RING, B-box 2 and coiled-coil domains, with a C-terminal B30.2(SPRY) domain. (nih.gov)
  • Novel Role for Protein Inhibitor of Activated STAT 4 (PIAS4) in the Restriction of Herpes Simplex Virus 1 by the Cellular Intrinsic Antiviral Immune Response. (nih.gov)
  • purification
  • In particular, our new method outperforms competing approaches at discovering physical contacts involving proteins that have been screened multiple times in purification experiments. (nih.gov)
  • Interaction partners were identified by tandem-affinity purification. (springer.com)
  • receptor
  • Just as our understanding of receptor, G protein, and effector function seemed nearly complete, a new kid appeared on the scene injecting fresh life into the field. (aspetjournals.org)
  • and 6) enhance receptor-G protein coupling (see below). (aspetjournals.org)
  • Transition of the GH receptor TMDsThe interaction of the GH receptor TMDs in the inactive parallel State 1 and active crossover State 2 are shown. (nih.gov)
  • a protein required for the differentiation of the set of six touch receptor neurons in this nematode. (embl-heidelberg.de)
  • NK cell development takes place in the bone marrow (BM) after birth and is supported by stromal cells through receptor-ligand interactions and the production of cytokines and growth factors ( 2 , 3 ). (frontiersin.org)
  • superfamily
  • ADP ribosylation factors (ARFs), which are members of the Ras superfamily of GTP-binding proteins, are critical components of vesicular trafficking pathways in eukaryotes. (embl-heidelberg.de)
  • bound
  • To test this hypothesis, here we investigate by Nuclear Magnetic Resonance (NMR) the two-domain construct RIα (91-379) in its apo, cAMP2, and C-bound forms. (nih.gov)
  • The proteins bound to the RAD54B26-225-conjugated beads were eluted by SDS-PAGE sample buffer, and fractionated on a 12% SDS-PAGE gel. (nih.gov)
  • The proteins bound to the RAD54B26-225 beads were detected by SDS-PAGE. (nih.gov)
  • In contrast, RAD54B26-225 weakly bound to RecA, the bacterial homolog of RAD51 and DMC1, suggesting that the interactions between RAD54B26-225 and RAD51 or DMC1 were specific (Figure 3C). (nih.gov)
  • patterns
  • These scientific approaches focus no longer on individual units, such as nerve cells or genes, but rather on the emerging dynamic patterns of interactions between them. (nhbs.com)
  • effector
  • We report a novel mechanism and identified strong c-Abl threonine 735 phosphorylation (pAbl T735 ) mediated by the type-IV secretion system (T4SS) effector D-glycero-β-D-manno-heptose-1,7-bisphosphate (βHBP) and protein kinase C (PKC) as a new c-Abl kinase. (springer.com)
  • high throughput
  • Although the predicted PPIs may contain some false positives due to limited data resource and poor research background in non-model species, the computational method still provide reasonable amount of interactions, which can be further validated by high throughput experiments. (biomedcentral.com)
  • inhibition
  • Mapping the Free Energy Landscape of PKA Inhibition and Activation: A Double-Conformational Selection Model for the Tandem cAMP-Binding Domains of PKA RIα. (nih.gov)
  • The GAP activity explains RGS-mediated inhibition of G protein signaling. (aspetjournals.org)