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Exploring distinct binding site regions of β2-adrenergic receptor via coarse-grained molecular dynamics simulations

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Despite these helical deformations, the 3-dimensional structure of the binding site remained stable throughout the simulation. For each RM-FA simulation, the RMSD profile of the binding site region with respect to the crystal structure of the inactive state (PDB id: 2RH1) showed that stability has been reached at around 4–4.5 ˚ A.

Genetic structure and diversity of Adonis L. (Ranunculaceae) populations collected from Turkey by inter-primer binding site (iPBS) retrotransposon markers

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To identify the genetic diversity of 62 Adonis ecotypes collected from different regions in Turkey, the interprimer binding site (iPBS) retrotransposon system was used.. Of the 83 iPBS primers used, 10 provided sufficient polymorphic data, generating a total of 204 alleles. The highest average number of alleles, Nei’s genetic diversity (h), and Shannon’s information index (I) were obtained from A.

RBPsuite: RNA-protein binding sites prediction suite based on deep learning

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Table 2 The expected runtime of predicting binding sites of a specific RBP on a linear RNA and a circRNA using RBPsuite for sequences with different lengths. In the table, the detected motif on the predicted binding site is marked in red.

SalMotifDB: A tool for analyzing putative transcription factor binding sites in salmonid genomes

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Evaluating tools for transcription factor binding site prediction. https://doi.org/10.1186/. Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, et al. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. org/10.1371/journal.pone.0000807.. Positional distribution of human transcription factor binding sites. https://doi.org/1 0.1093/nar/gkn752..

Protein targets of thiazolidinone derivatives in Toxoplasma gondii and insights into their binding to ROP18

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Figure 10b shows the noticeable conformational change induced by 30C in the surface of the active site, modifying and exposing hydrophobic regions of this ATP-binding site to ease its molecular docking.. Due to this, it contacts hydrophobic residues of the binding site of TgROP18 and also can bury deeper than ATP. 10 Structural changes on the TgROP18 protein caused by the action of the 30C ligand in one of the two possible states..

Corrupted DNA-binding specificity and ectopic transcription underpin dominant neomorphic mutations in KLF/SP transcription factors

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To confirm aberrant binding was intrinsic to the variant KLF1-E339K-ER protein, we performed in vitro DNA- binding assays to compare the affinities of KLF1-zf and KLF1-E339K-zf (see Methods). We measured DNA-binding af- finities for GST-purifiedKLF1-zf and KLF1-E339K-zf to probes for all four nucleotide variants at position 5 within an otherwise identical Alas2DNA-binding site..

EcRBPome: A comprehensive database of all known E. coli RNA-binding proteins

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This proves that proteins belonging to the same structural family are capable of binding to the same RNA, but per- haps with differential RNA-binding affinities, as seen in our previous studies also [21].. On the analysis of the NADP-bound structure of this protein (PDB code: 2O7P), it was seen that RibD uses a different site to bind the oxidised NADP + cofac- tor, which does not overlap with the RNA-binding site that we have proposed here.

Computational investigation of influenza A virus M2 protein inhibition mechanism by ion channel blockers

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Binding energy of AMA in this binding site was computed as 16.0 kcal/mol (Table 5). Binding at this site resulted in constriction of one distance at each part of the channel, which was observed for the first time in this study. Binding site 3, the second novel binding site for AMA, was located at the exit of the channel, towards the intracellular space.

TrawlerWeb: An online de novo motif discovery tool for next-generation sequencing datasets

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For each ChIP-seq dataset, and for each program, motifs with the. shortest distance to the expected binding site were identi- fied as the closest motif. 2a-e), and corresponding distance to the expected binding site (Fig. 2d), TrawlerWeb and RSAT peak-motifs identified the same primary motif, which interestingly, is different to the expected binding site. 2e), RSAT peak-motifs dis- covered a similar motif to the known binding site, whereas TrawlerWeb found motifs that are quite different. 1b, d)

Evaluation of quercetin as a potential β-lactamase CTX-M-15 inhibitor via the molecular docking, dynamics simulations, and MMGBSA

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Throughout the simulation, Tazobactam was replaced in the hydrophobic cavity to which it was bound, forming hydrogen bonds with THR234 and SER236 residues in three beta-sheet structures in the binding site (Figure 5).. The 3 aromatic rings perfectly overlapped the binding site of the CTX-M-15 with the molecular docking method and inter- acted with ASN131 and SER219 (Figure 5).

Biochemistry, 4th Edition P103

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This illustration highlights residues in or near the ATP-binding site of the ATPase domain. Events in the ATP-binding site of the ATPase domain are communicated to the protein-binding site of the peptide-binding domain through K70 and E171, which act as ATP sensors. and R151, which is part of the lever that relays the events from the ATPase domain to the other domain..

Biochemistry, 4th Edition P50

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FIGURE 15.6 Sigmoid v versus [S] plot. a binding site distinct from the substrate-binding site. Thus, allosteric enzymes typically have more than one S-binding site and more than one effector-binding site per enzyme molecule.. The working hypothesis is that, by some means, interaction of an allosteric en- zyme with effectors alters the distribution of conformational possibilities or sub- unit interactions available to the enzyme.

The inconsistent regulation of HOXC13 on different keratins and the regulation mechanism on HOXC13 in cashmere goat (Capra hircus)

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Furtherly, in order to verify the binding site of HOXC13 in the promoter of HOXC13 itself, the predicted binding site (TT(A/T)ATNPuPu) in the opti- mal promoter (HOXC13P365) was mutated by introdu- cing a EcoR Ι recognition site (HOXC13P365 mut), we found that the luciferase activity was not totally recovered in the group with mutational binding site (HOXC13P365 mut) compared with the wild type bind- ing site (HOXC13P365) (Fig. 5c), which suggested that another binding site of HOXC13 may be existent

Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

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Overall, panel C shows the co- ordinate plane of the predicted (axis X) and the measured (axis Y) ratio of K D;MUT /K D;WT values of minor versus. of the human ESR2 gene promoter retrieved from dbSNP, rel. b and c The results from our Web service SNP_TATA_Comparator [53] for the two SNP markers of reproductive potential: known marker rs and candidate marker rs766797386 near the known TBP-binding site (boxed) of the human ESR2 gene promoter.

Chapter 127. Treatment and Prophylaxis of Bacterial Infections (Part 3)

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Streptogramin B binds to a ribosomal site similar to the binding site for macrolides and lincosamides, whereas streptogramin A binds to a different ribosomal site, blocking the late phase of protein synthesis. This antibiotic binds reversibly to the 50S portion of the bacterial ribosome at a site close to but not identical with the binding sites for the macrolides and lincosamides, inhibiting peptide bond formation..

Investigation of the structural and physicochemical requirements of quinoline-arylamidine hybrids for the growth inhibition of K562 and Raji leukemia cells

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The binding site of the protein was defined according the bonded ligand (PDB ID: G6H). number of solution or poses:. Each compound in the library was docked into the binding site and protein–compound interaction profiles of electrostatic (Elec), hydrogen-bonding (Hbond), and vdW interactions were generated. The authors gratefully acknowledge the financial support from the J.

Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model

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To accomplish, we first considered a large number of molecular features related to miRNA-mRNA binding sites including sequence pairing [26], evolutionary conservation [37], free energy of the miRNA-mRNA heteroduplex [38], target site accessi- bility [39], and the flanking sequence of the target site on mRNA. In addition, several statistics related to binding site were also assessed, e.g., the number of complementary pairs within seed region and/or within the whole biding site.

Prostereoisomerism and biological activity: possible implications for drug design

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The answer would be ‘three’, assuming that the binding site can be considered as a chiral surface.. The view of an enzyme active site as a chiral surface appears unexceptional, considering that the binding site somewhat resembles a mousetrap, i.e. one side is completely shielded, so the entry and exit of the substrate are restricted to the opposite side!

Improving CLIP-seq data analysis by incorporating transcript information

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This suggests a general agreement in the amount of exon binding across cell lines. Sequence context influences binding site prediction performances. Based on the considerable amount of sites near exon bor- ders, we further investigated whether different sequence contexts could also influence the performances of bind- ing site prediction tools.

Chapter 080. Cancer Cell Biology and Angiogenesis (Part 5)

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Competitive inhibitor of the ATP binding site of the EGFR.. Inhibitor of EGFR tyrosine kinase.