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排序方式: 共有899条查询结果,搜索用时 15 毫秒
1.
Hyun-Jin Kang Tuong Vy Thi Le Kyungmin Kim Jeonghwan Hur Kyeong Kyu Kim Hyun-Ju Park 《Journal of molecular biology》2014
Both G-quadruplex and Z-DNA can be formed in G-rich and repetitive sequences on genome, and their formation and biological functions are controlled by specific proteins. Z-DNA binding proteins, such as human ADAR1, have a highly conserved Z-DNA binding domain having selective affinity to Z-DNA. Here, our study identifies the Z-DNA binding domain of human ADAR1 (hZαADAR1) as a novel G-quadruplex binding protein that recognizes c-myc promoter G-quadruplex formed in NHEIII1 region and represses the gene expression. An electrophoretic migration shift assay shows the binding of hZαADAR1 to the intramolecular c-myc promoter G-quadruplex-forming DNA oligomer. To corroborate the binding of hZαADAR1 to the G-quadruplex, we conducted CD and NMR chemical shift perturbation analyses. CD results indicate that hZαADAR1 stabilizes the parallel-stranded conformation of the c-myc G-quadruplex. The NMR chemical shift perturbation data reveal that the G-quadruplex binding region in hZαADAR1 was almost identical with the Z-DNA binding region. Finally, promoter assay and Western blot analysis show that hZαADAR1 suppresses the c-myc expression promoted by NHEIII1 region containing the G-quadruplex-forming sequence. This finding suggests a novel function of Z-DNA binding protein as a regulator of G-quadruplex-mediated gene expression. 相似文献
2.
《Journal of molecular biology》2021,433(21):167224
Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin. 相似文献
3.
Vibrational optical coherence elastography (OCE) is a promising tool for extracting the mechanical property of soft tissue. Purpose of this study is focusing on settling the optimal frequency range for vibrational OCE with evenly distributed stress filed. A finite element model of 2% agar phantom was built by ANSYS with a vibration stimulation frequency range from 200 to 3000 Hz. Practical experiments were carried out for cross‐validation with the same frequencies and sample. Lateral and horizontal stress filed distributions under different frequencies were mathematically evaluated by coefficient of variance and degree of linearity. Results from simulation and practical experiment cross‐validated each other and 1000 Hz was set as the maximum ideal frequency for vibrational OCE, while the minimum frequency is set by theoretical calculation with a result of 250 Hz. An ex vivo biological sample was utilised to testify performance of vibrational OCE with excitation frequencies in and out of concluded optimal range, which showed that stiffness was better mapped out in optimal frequency range. 相似文献
4.
Joseph A. Marsh 《Journal of molecular biology》2009,391(2):359-318
Obtaining detailed structural models of disordered states of proteins under nondenaturing conditions is important for a better understanding of both functional intrinsically disordered proteins and unfolded states of folded proteins. Extensive experimental characterization of the drk N-terminal SH3 domain unfolded state has shown that, although it appears to be highly disordered, it possesses significant nonrandom secondary and tertiary structure. In our previous attempts to generate structural models of the unfolded state using the program ENSEMBLE, we were limited by insufficient experimental restraints and conformational sampling. In this study, we have vastly expanded our experimental restraint set to include 1H-15N residual dipolar couplings, small-angle X-ray scattering measurements, nitroxide paramagnetic relaxation enhancements, O2-induced 13C paramagnetic shifts, hydrogen-exchange protection factors, and 15N R2 data, in addition to the previously used nuclear Overhauser effects, amino terminal Cu2+-Ni2+ binding paramagnetic relaxation enhancements, J-couplings, chemical shifts, hydrodynamic radius, and solvent accessibility restraints. We have also implemented a new ensemble calculation methodology that uses iterative conformational sampling and seeks to calculate the simplest possible ensemble models. As a result, we can now generate ensembles that are consistent with much larger experimental data sets than was previously possible. Although highly heterogeneous and having broad molecular size distributions, the calculated drk N-terminal SH3 domain unfolded-state ensembles have very different properties than expected for random or statistical coils and possess significant nonnative α-helical structure and both native-like and nonnative tertiary structure. 相似文献
5.
Structural-Thermodynamic Relationships of Interactions in the N-Terminal ATP-Binding Domain of Hsp90
Sanjay Nilapwar Eleanor Williams Christosmos Prodromou Mark A. Williams 《Journal of molecular biology》2009,392(4):923-9317
Despite its importance as a target in anti-cancer therapeutics and the numerous rational-based inhibitor design efforts aimed at it, there are only limited data available on structural-thermodynamic relationships of interactions of the N-terminal ATP-binding domain of Hsp90 (N-Hsp90). Here, we redress this by presenting an investigation of binding of nucleotides and ansamycin compounds to this domain. Interactions of nucleotides with N-Hsp90 are relatively weak (> 10 μM) and are strongly enthalpy driven over the temperature range 10-25 °C. Geldanamycin (GA) and its analogues 17-AAG [17-(allylamino)-17-demethoxy-GA] and 17-DMAG (17-N,N-dimethylaminoethylamino-17-demethoxy-GA) bind more strongly and have a dominant favourable enthalpic contribution over the temperature range investigated. We investigated the temperature dependence of the enthalpic contribution to binding. We found that while the ansamycin compounds have the commonly observed negative value, the nucleotides show a negligible or even a positive ΔCp of binding. These data represent the first observation of a single binding site for which interactions with different ligands result in both negative and positive ΔCp values. By addressing the likely impact of the potential contributions from protein-ligand interactions, we are able to attribute the anomalous ΔCp for the nucleotides largely to a change in the conformation of the domain structure and local motion in the lid region of N-Hsp90 with the concomitant exposure of hydrophobic amino acid side chains. 相似文献
6.
Dickson Fenn 《FEBS letters》2008,582(30):4169-4175
Oxidation of guanine in DNA can lead to mutagenic lesions such as 7-hydro-8-oxoguanine (oG). Upon further oxidation, a more mutagenic lesion, spirominodihydantoin (Sp), can occur. In this study, nuclear magnetic resonance (NMR) investigations were performed to determine the structural features of DNA primer-template models with 5′-GG, 5′-G(oG), 5′-G(Sp) and 5′-T(Sp) templates, that mimic the situation in which the downstream G of the template has been oxidized to oG or hyperoxidized to Sp. Our results show that misalignment occurs only in the 5′-G(Sp) and 5′-T(Sp) templates, providing structural insights into the observed differences in mutagenicity of Sp and oG during DNA replication. 相似文献
7.
Aurein 1.2 is an antimicrobial and anticancer peptide isolated from an Australian frog. To improve our understanding of the mechanism of action, two series of peptides were designed. The first series includes the N-terminal membrane anchor of bacterial glucose-specific enzyme IIA, aurein 1.2, and a newly identified aurein 1.2 analog from human LL-37 (LLAA). The order of antibacterial activity is LLAA > aurein 1.2 >> the membrane anchor (inactive). The structure of LLAA in detergent micelles was determined by 1H NMR spectroscopy, including structural refinement by natural abundance 13Cα, 13Cβ, and 15N chemical shifts. The hydrophobic surface area of the 3D structure is related to the retention time of the peptide on a reverse-phase HPLC column. The higher activity of LLAA compared to aurein 1.2 was attributed to additional cationic residues that enhance the membrane perturbation potential. The second peptide series was created by changing the C-terminal phenylalanine (F13) of aurein 1.2 to either phenylglycine or tryptophan. A closer or further location of the aromatic rings to the peptide backbone in the mutants relative to F13 is proposed to cause a drop in activity. Phenylglycine with unique chemical shifts may be a useful NMR probe for structure-activity relationship studies of antimicrobial peptides. To facilitate potential future use for NMR studies, random-coil chemical shifts for phenylglycine (X) were measured using the synthetic peptide GGXGG. Aromatic rings of phenylalanines in all the peptides penetrated 2-5 Å below the lipid head group and are essential for membrane targeting as illustrated by intermolecular peptide-lipid NOE patterns. 相似文献
8.
E. P. Man’kovskaya 《Neurophysiology》2006,38(3):197-200
We compared changes in the EEG indices in healthy dextral volunteers performing static force grasps by the arm. Three test
modes were used: (i) performance of two successive grasps by the dominant (right) arm (test A), (ii) performance of two successive
grasps by the subdominant (left) arm (test B), and (iii) performance of the grasps first by the right arm and then by the
left arm (test C). Fourteen, six, and nine persons took part in tests A–C, respectively. In the course of grasps performed
by the right and left arms, bilateral increases in synchronization within the alpha 1 and alpha 2 ranges were frequently observed
in occipital regions in both the first and repeated grasps (P < 0.05). Consecutive grasps by the right arm were accompanied by clear desynchronization in a few anterior and central leads.
Alpha 2 desynchronization was observed in both realizations of the left-arm grasps (test B) performed by some subjects, but
intragroup modifications were not significant in this case. The coherence coefficients of the alpha 2 rhythm in most cases
increased for symmetric leads from the right and left hemispheres in the course of grasps by both the right and left hands.
The effect of intensification of interhemisphere links was manifested in the anterior and central cortical regions; this fact
showed that interhemisphere interaction increases in the course of the static effort. Changes in the coherence coefficients
for the alpha 2 range in the performance of the grasp efforts by the right arm and the left arm were most clear in the posterotemporal
(P = 0.02), parietal (P = 0.05), and anterofrontal (P = 0.06) lead pairs. Thus, we demonstrated the dependence between the side of performance of the muscle effort in the mode
close to isometric and lateralization of the EEG modifications.
Neirofiziologiya/Neurophysiology, Vol. 38, No. 3, pp. 235–238, May–June, 2006. 相似文献
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