Chromosome conformation capture techniques (often abbreviated to 3C technologies or 3C-based methods) are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. (wikipedia.org)
This idea was the basis for his development of the chromosome conformation capture (3C) assay, published in 2002 by Job Dekker and colleagues in the Kleckner lab at Harvard University. (wikipedia.org)
1) Various complex formation of Histone methyltransferases for repressive chromatin and the molecular basis of their formation, 2) Relationship between heterochromatin formation and repressive histone modification on inactive X chromosome, 3) Involvement of an HP1 binding protein in pathway choice for repairing double-strand breaks. (nii.ac.jp)
Studies using a derivative of chromosome conformation capture (3C) known as 'Hi-C' have revealed that long-range genomic contacts segregate TADs into an active (A) and inactive (B) compartment [ 37 ]. (biomedcentral.com)
Ligands2
Our results reveal previously unappreciated diversity and dynamics in the inactive conformations of D 2 R. These findings are critical for rational drug discovery, as limiting a virtual screen to a single conformation will miss relevant ligands. (elifesciences.org)
An array of activating ligands participate in the conformation of GPCRs which leads to signaling via G-proteins and downstream effectors. (thermofisher.com)
Receptors5
By analyzing and simulating inactive conformations of the highly-homologous dopamine D 2 and D 3 receptors (D 2 R and D 3 R), we find that eticlopride binds D 2 R in a pose very similar to that in the D 3 R/eticlopride structure but incompatible with the D 2 R/risperidone structure. (elifesciences.org)
The active and inactive conformations of these receptors coexist in equilibrium. (hindawi.com)
Agonists of these receptors stabilize the active conformation, whereas antagonists stabilize the inactive conformation. (hindawi.com)
Ligand binding to G protein-coupled receptors (GPCRs) is thought to induce changes in receptor conformation that translate into activation of downstream effectors. (pasteur.fr)
Different conformations of active receptors were detected (for wild-type CXCR4, D133N, and N119S), suggesting that different receptor conformations are able to trigger G(alpha)(i) activity. (pasteur.fr)
Receptor conformations3
Based on these findings and our experimental results, we propose that the divergent receptor conformations stabilized by Na + -sensitive eticlopride and Na + -insensitive risperidone correspond to different degrees of inverse agonism. (elifesciences.org)
These data provide biophysical evidence for different receptor conformations being active with respect to a single readout. (pasteur.fr)
We show that Nb60 stabilizes a previously unappreciated low-affinity receptor state which corresponds to one of two inactive receptor conformations as delineated by X-ray crystallography and NMR spectroscopy. (nih.gov)
GPCRs1
All GPCRs share a structural motif consisting of seven membrane-spanning helices, and exist in both active and inactive forms. (thermofisher.com)
Residues4
The final family of calculated structures displays three well-defined beta- or gamma-turn regions, comprising residues 1-5, 7-10, and 24-27, but has otherwise a random conformation. (consensus.app)
These residues occur in an active-like conformation stabilized by lanthanum ions. (rcsb.org)
Specifically, we tested the hypothesis that some OCRL1VAR are stabilized in a non-functional conformation by focusing on missense mutations affecting the phosphatase domain, but not changing residues involved in binding/catalysis. (bvsalud.org)
About 70% of the iodide in thyroglobulin exists in the inactive precursors monoiodotyrosine (MIT) and diiodotyrosine (DIT), while 30% is in the iodothyronyl residues thyroxine (T4) and triiodothyronine (T3). (medscape.com)
Transitions2
Moreover, our simulations reveal that the extracellular loops are highly dynamic, with spontaneous transitions of extracellular loop 2 from the helical conformation in the D 2 R/risperidone structure to an extended conformation similar to that in the D 3 R/eticlopride structure. (elifesciences.org)
Another key result is the critical role of rare, transient, high-energy conformations in biological function: proteins spontaneously undergo transitions between multiple structural states that are either active or inactive. (lu.se)
Catalytically1
One cluster includes kinases in catalytically active conformations. (rcsb.org)
Furthermore, increasing biophysical evidence, primarily using the β2-adrenergic receptor (β2AR) as a model system, supports the existence of multiple active and inactive conformational states. (nih.gov)
Distinct3
Each of the other clusters contains a distinct inactive conformation. (rcsb.org)
We report the X-ray structure of the lck/imatinib complex, confirming that the conformation adopted by lck is distinct from other structurally-characterized src-family kinases and instead resembles kinases abl1 and kit in complex with imatinib. (rcsb.org)
Here we report stabilization of two distinct β2AR conformations using single domain camelid antibodies (nanobodies)-a previously described positive allosteric nanobody (Nb80) and a newly identified negative allosteric nanobody (Nb60). (nih.gov)
Reveals1
Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation. (cathdb.info)
Efficacy1
Activity of these inhibitors depends on their mechanism of receptor binding (active vs inactive conformation) and efficacy against the FLT3-ITD and -TKD mutations (type 1 inhibitors are active both on FLT3 -ITD and TKD, whereas type 2 inhibitors are active only on FLT3 -ITD). (dovepress.com)
Bent1
As explained below, this binding stabilizes a kinked ("bent") DNA double helix conformation. (proteopedia.org)
Molecular1
We analyzed substitutions in the arginine cage DRY motif and in the conserved asparagine N(3.35)119, which are pivotal molecular switches for receptor conformation and activation. (pasteur.fr)
Agonists1
In contrast, for a number of partial agonists, both stabilization of R80 and destabilization of the inactive, Nb60-bound state (R60) contribute to their ability to modulate receptor activation. (nih.gov)
Typically2
Typically, kinases adopt at most one of the inactive conformations in available X-ray structures, implying that one of the conformations is preferred for many kinases. (rcsb.org)
Changes in temperature are typically sensed as a result of conformation changes of protein structure as well as misfolded proteins. (springer.com)
Active conformations1
To that end, cells have an arsenal of signaling molecules linked together in signaling pathways, which switch between inactive and active conformations. (booksamillion.com)
Protein2
We report a clustering of public human protein kinase structures based on the conformations of two structural elements, the activation segment and the C-helix, revealing three discrete clusters. (rcsb.org)
Upon photon capture, 11- cis -retinal isomerizes to all-trans resulting in a shift in rhodopsin's conformation and binding to the G-protein transducin ( Ridge and Palczewski, 2007 ). (jneurosci.org)
Adopt1
Here, we review current insights into the trans-acting factors that enable the genome to flexibly adopt different functionally relevant conformations. (biomedcentral.com)
Spectroscopy1
By using two-dimensional proton NMR spectroscopy, complete relaxation matrix analysis, and simulated annealing, the conformation of porcine galanin was determined in a membrane-mimicking solvent containing sodium dodecyl sulfate (SDS) micelles. (consensus.app)
Activity1
The link between receptor conformation and activity is still insufficiently understood, as current models of GPCR activation fail to take an increasing amount of experimental data into account. (pasteur.fr)
Full-length1
The dimer in solution differs from the active form observed in the crystal, resembling instead the model of the inactive full-length response regulator PhoB. (rcsb.org)
Structures1
The AtAgo10-guide-target complex adopts slicing-competent and slicing-incompetent conformations that are unlike known prokaryotic AGO structures. (nature.com)
Complex1
Fig. 3: Catalytic-competent conformation of the AtAgo10-guide-target complex. (nature.com)
Structure1
To elucidate structure-function relationships in GPCR activation, we used bioluminescence resonance energy transfer to directly assess the conformation of mutants of the chemokine receptor CXCR4. (pasteur.fr)
Suggests2
For example, selective inhibition of lck among src-family kinases by imatinib (Gleevec) suggests that the relative stabilities of inactive conformations of lck are different from other src-family kinases. (rcsb.org)
Comparison of the active and inactive forms by circular dichroism and chromatographic analyses suggests that the active form, both the natural and the synthetic forms, is more structured, condensed, and rigid than the inactive form, which has a more nonstructured conformation. (nofima.no)
Domain1
All mutations resided in the N-SH2 domain name, destabilizing SHP-2s inactive conformation. (eprf.ca)
Synthetic2
An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. (ucsf.edu)
A synthetic peptide whose sequence was identical to that of the isolated fragment was initially inactive but could be activated by binding it to a cation-exchange column. (nofima.no)
Data1
Importantly, data support the inactive-conformation hypothesis. (bvsalud.org)
Comparison1
Comparison with an inactive analog and a galanin receptor antagonist. (consensus.app)
State1
Bax resides in an inactive state in the cytosol of many cells. (scienceopen.com)
Studies1
Additional NMR studies were carried out on an inactive analogue, Ala2-galanin, and an antagonist M40. (consensus.app)