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Your search keyword '"Xu, Rui-Ming"' showing total 325 results
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325 results on '"Xu, Rui-Ming"'

3. Topography of histone H3–H4 interaction with the Hat1–Hat2 acetyltransferase complex

Author

Yue, Ye, Yang, Wen-Si, Zhang, Lin, Liu, Chao-Pei, and Xu, Rui-Ming

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Generic health relevance, Acetylation, Cell Cycle Proteins, Chromatin, Histone Acetyltransferases, Histone Chaperones, Histones, Molecular Chaperones, histones, acetyltransferase, structure, enzymatic activity, histone chaperone, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract

Chaperones influence histone conformation and intermolecular interaction in multiprotein complexes, and the structures obtained with full-length histones often provide more accurate and comprehensive views. Here, our structure of the Hat1-Hat2 acetyltransferase complex bound to Asf1-H3-H4 shows that the core domains of H3 and H4 are involved in binding Hat1 and Hat2, and the N-terminal tail of H3 makes extensive interaction with Hat2. These findings expand the knowledge about histone-protein interaction and implicate a function of Hat2/RbAp46/48, which is a versatile histone chaperone found in many chromatin-associated complexes, in the passing of histones between chaperones.

Published
2022

16. Mechanism of DYRK1ain myocardial ischemia–reperfusion injury by regulating ferroptosis of cardiomyocytes

Author

Wang, Jing, Xu, Rui‐Ming, Cao, Qiu‐Mei, Ma, Bing‐Chen, Zhang, Hao, and Hao, Hua‐Peng

Abstract

This study aimed to explore the role and mechanism of DYRK1a regulating ferroptosis of cardiomyocytes during myocardial ischemia–reperfusion injury (MIRI). H9c2 cells treated with oxygen–glucose deprivation/reoxygenation (OGD/R) were used as MIRI cell models and transfected with sh‐DYRK1a or/and erastin. Cell viability, apoptosis, and DYRK1a mRNA/protein expression were measured accordingly. The levels of reactive oxygen species (ROS), iron, malondialdehyde (MDA), and glutathione (GSH) were determined. The expression of ferroptosis‐related proteins (GPX4, SLC7A11, ACSL4, and TFR1) was detected using western blotting. The MIRI rat model was established to explore the possible role of DYRK1a suppression in cell injury and ferroptosis. OGD/R cells showed elevated mRNA and protein expression for DYRK1a. OGD/R cells transfected with sh‐DYRK1a showed elevated cell viability, GSH content, increased GPX4 and SLC7A11 expression, suppressed iron content, MDA, ROS, ACSL4, and TFR1 expression, and reduced apoptosis rate, whereas co‐transfection of sh‐DYRK1a with erastin reversed the attenuation of sh‐DYRK1a on MIRI. The suppressive effect of sh‐DYRK1a on MI/R injury was confirmed in an MIRI rat model. DYRK1a mediates ferroptosis of cardiomyocytes to deteriorate MIRI progression.

Published
2023
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17. Energy landscape quantifications of histone H3.3 recognition by chaperone DAXX reveal an uncoupled binding specificity and affinity.

Author

Liu, Fei, Wang, Jin, Xu, Rui-Ming, and Yang, Na

Abstract

Histone variant H3.3 differs from the canonical histone H3.1 by only five amino acids, yet its chaperone death domain-associated protein (DAXX) can specifically recognize H3.3 over H3.1, despite having a large DAXX-interacting surface on the H3.3–H4 heterodimer common to that on the H3.1–H4 complex. This observation gives rise to the question of, from the binding energy point view, how high binding specificity may be achieved with small differences of the overall binding energy for protein–protein interactions in general. Here we investigate the mechanism of coupling of binding specificity and affinity in protein–protein interactions using the DAXX–H3.3–H4 complex as a model. Using a multi-scale method, we found that the hydrophobic interactions between DAXX and the H3.3-specific region contributed to their initial binding process. And the structural flexibility of the interacting partners contributed to the binding affinity after their encounter. By quantifying the free energy landscape, we revealed that the interaction between the specific residues of H3.3 and DAXX decreased the encounter barrier height while the folding of H3.3–H4 and DAXX increased the depth of the free energy basin of the final binding state. The encounter barrier height, which is not coupled to the thermodynamic stability of the final binding state, had a marked effect on the initial binding rate of flexible histones and chaperones. Based on the energy landscape theory, we found that the intrinsic binding energy funnel of this uncoupled recognition process was affected by the structural flexibility and the flexibility modulated the degree of coupling between binding specificity and affinity. Our work offers a biophysical explanation of the specific recognition between the histones and their chaperones, and also extends the use of energy landscape theory for understanding molecular recognitions in general. [ABSTRACT FROM AUTHOR]

Published
2023
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23. The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas

Author

Fang, Dong, Gan, Haiyun, Lee, Jeong-Heon, Han, Jing, Wang, Zhiquan, Riester, Scott M., Jin, Long, Chen, Jianji, Zhou, Hui, Wang, Jinglong, Zhang, Honglian, Yang, Na, Bradley, Elizabeth W., Ho, Thai H., Rubin, Brian P., Bridge, Julia A., Thibodeau, Stephen N., Ordog, Tamas, Chen, Yue, van Wijnen, Andre J., Oliveira, Andre M., Xu, Rui-Ming, Westendorf, Jennifer J., and Zhang, Zhiguo

Published
2016

32. Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation

Author

Zhang, Jing, primary, Zhang, Yan, additional, You, Qinglong, additional, Huang, Chang, additional, Zhang, Tiantian, additional, Wang, Mingzhu, additional, Zhang, Tianwei, additional, Yang, Xiaocheng, additional, Xiong, Jun, additional, Li, Yingfeng, additional, Liu, Chao-Pei, additional, Zhang, Zhuqiang, additional, Xu, Rui-Ming, additional, and Zhu, Bing, additional

Published
2022
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41. Crystal structure of a SIR2 homolog-NAD complex

Author

Min, Jinrong, Landry, Joseph, Sternglanz, Rolf, and Xu, Rui-Ming

Subjects
Cell research -- Analysis, Niacinamide -- Physiological aspects, Nucleotides -- Physiological aspects, Zinc -- Physiological aspects, Proteins -- Physiological aspects, Biological sciences
Abstract

Research has been conducted on the nicotineamide-adenine dinucleotide (NAD)-dependent protein deacetylases from the SIR2 protein family. The determination of the crystal structures of the SIR2 homolog from Archaeglobus fulgidus complexed with NAD has been carried out and the results indicate that the protein has a domain with the Rossmann fold and a smaller domain with the three-stranded zinc ribbon motif.

Published
2001

44. Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA

Author

Ding, Jianzhong, Hayahsi, Mariko K., Zhang, Ying, Manche Lisa, Krainer, Adrian R., and Xu, Rui-Ming

Subjects
Telomeres -- Research, RNA -- Analysis, X-ray crystallography -- Usage, Heredity, Human -- Research, Crystals -- Structure, Genetic disorders -- Research, Chromosome mapping -- Usage, Biological sciences
Abstract

The crystal structure of the two-RNA-recognition motif (two-RRM) domain of hnRNP A1 (UP1), or unwinding protein, the amino-terminal domain of human hnRNP A1, has been determined at resolution of 2.1 angstrom. The structure of the complex shows structure responsible for sequence-specific recognition by hnRNP A1 of the single-stranded overhangs of human telomeres. Human hnRNP is a versatile nucleic acid-binding protein with one strand. It acts in some parts of mRNA maturation and in length regulation for telomeres. Models for juxtaposition of other possible 5' splice sites and for regular packaging of telomere 3' overhangs are suggested.

Published
1999

48. Additional file 1: of UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells

Author

Chaoyang Xiong, Zengqi Wen, Yu, Juan, Chen, Jun, Chao-Pei Liu, Xiaodong Zhang, Chen, Ping, Xu, Rui-Ming, and Guohong Li

Abstract

Figure S1. The HRD domain is conserved in UBN1 and UBN2. Figure S2. UBN1 mediates the interaction between HIRA subunit and histone variant H3.3. Figure S3. Residues Ala87 and Gly90 of H3.3 are important for recognition and binding of H3.3 by HIRA complex. Figure S4. UBN1 and UBN2 co-exist in mESC. Figure S5. UBN1 and UBN2 cooperatively deposit H3.3 at cis-regulatory elements in mESC. Figure S6. UBN1- and UBN2-mediated H3.3 deposition is involved in neuron progenitor cell differentiation. Table S1. Primers used for ChIP-qPCR. Table S2. Primers used for real-time RT-qPCR. (DOCX 1184 kb)

Published
2018
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