Ke Ruan

University of Science and Technology of China

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Jihui Wu

University of Science and Technology of China

Jia Gao

University of Rochester

Jiahai Zhang

Hefei National Center for Physical Sciences at Nanoscale

Yunyu Shi

University of Science and Technology of China

Rongsheng Ma

Jiaxing University

Xuebiao Yao

University of Science and Technology of China

Fudong Li

Shanghai Changzheng Hospital

Xing Liu

University of Science and Technology of China

Zhiyong Zhang

Wuxi People's Hospital

Yaqian Liu

First Affiliated Hospital of Xinxiang Medical University

Cooperative Institutions

University of Science and Technology of China

209

Chinese Academy of Sciences

137

Hefei National Center for Physical Sciences at Nanoscale

121

Peking University

University of Chinese Academy of Sciences

Center for Excellence in Molecular Cell Science

Shanghai Jiao Tong University

Shandong University

Sun Yat-sen University

Zhejiang University

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NMR Residual Dipolar Couplings as Probes of Biomolecular Dynamics

Chemical Reviews (2006)

Joel R. Tolman Ke Ruan

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNMR Residual Dipolar Couplings as Probes of Biomolecular DynamicsJoel R. Tolman and Ke RuanView Author Information Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 Cite this: Chem. Rev. 2006, 106, 5, 1720–1736Publication Date (Web):April 8, 2006Publication History Received29 July 2005Revised21 February 2006Published online8 April 2006Published inissue 1 May 2006https://pubs.acs.org/doi/10.1021/cr040429zhttps://doi.org/10.1021/cr040429zresearch-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views3164Altmetric-Citations230LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Elements,Magnetic properties,Order,Peptides and proteins,Quantum mechanics Get e-Alerts

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10.1021/cr040429z

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Citations (252)

Effect of bromide salts on cationic micellar catalysis

Colloid & Polymer Science (2001)

Ke Ruan Zeang Zhao Jinghong Ma

Cationic polymerization

Molar concentration

10.1007/s003960100515

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Citations (15)

Primary structure of human thromboxane synthase determined from the cDNA sequence.

Journal of Biological Chemistry (1992)

Kazuteru Ohashi Ke Ruan Richard J. Kulmacz Kenneth K. Wu Lee‐Ho Wang

Polymerase chain reaction techniques have been used to isolate a cDNA clone containing the entire protein coding region of thromboxane A2 synthase (EC 5.3.99.5) from a human lung cDNA library.The cDNA clone hybridizes with a single 2.1-kilobase mRNA species in phorbol ester-induced human erythroleukemia and monocytic leukemia cell lines.A second cDNA, differing only by an insert of 163 base pairs near the 3'-end of the translated region, was also found to be present in the same library.The proteins predicted from both nucleic acid sequences include the three polypeptide sequences determined from amino acid se- quencing of the purified human platelet enzyme, five potential sites for N-glycosylation, and a hydrophobic region that may serve to anchor the synthase in the endoplasmic reticulum membrane.The longer predicted protein, designated thromboxane synthase-I, contains 534 amino acids, with a M, of 60,684, whereas the shorter protein, designated thromboxane synthase-11, contains 460 amino acids and has a M, of 52,408.Although thromboxane synthase-I1 lacks the conserved cysteine that serves as the proximal heme ligand in the other cytochromes, significant sequence similarities exist among thromboxane synthase-I and -11 and several P450s, particularly those in family 3.The overall amino acid identity is considerably less than 40%, making it likely that thromboxane synthase represents a previously undefined family of cytochrome P450.

Protein primary structure

Thromboxane-A synthase

Primary (astronomy)

Sequence (biology)

Complete sequence

10.1016/s0021-9258(18)48353-6

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Citations (99)

Interfacial tension of the aqueous two-phase systems of cationic-anionic surfactant mixtures

Acta Physico-Chimica Sinica (2006)

Ke Ruan Liming Zhang Jianxin Tang Jianzhong Xiao

Interfacial tensions of the aqueous two-phase systems formed by cationic-anionic surfactant mixtures were measured using spinning drop method. The effects of surfactant structure, molar ratio of cationic to anionic surfactants, surfactant concentration, salt, and temperature on the interfacial tensions were investigated. It was shown that the values of the interfacial tensions of the aqueous two-phase were in the scale of ultra-low interfacial tensions at certain molar ratios of cationic to anionic surfactants. Three types of interfacial tension curves were observed. The first curve comprised two curves that were located on either side of 1:1 molar ratio, and the interfacial tension decreased with the increase of excessive surfactant components. The second one was a saddle-shaped curve that strode over the 1:1 molar ratio. The third type was a saddle-shaped curve that was located beside the 1:1 molar ratio. The types of interfacial tensions depended on the molecular structure of the surfactants such as the hydrophilic groups and the lengths and symmetry of hydrophobic chains.

Cationic polymerization

Molar concentration

10.1016/s1872-1508(06)60074-0

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Citations (7)

Mitotic motor CENP-E cooperates with PRC1 in temporal control of central spindle assembly

Journal of Molecular Cell Biology (2019)

Xu Liu Leilei Xu Junying Li Phil Y. Yao Wanjuan Wang

Error-free cell division depends on the accurate assembly of the spindle midzone from dynamic spindle microtubules to ensure chromatid segregation during metaphase-anaphase transition. However, the mechanism underlying the key transition from the mitotic spindle to central spindle before anaphase onset remains elusive. Given the prevalence of chromosome instability phenotype in gastric tumorigenesis, we developed a strategy to model context-dependent cell division using a combination of light sheet microscope and 3D gastric organoids. Light sheet microscopic image analyses of 3D organoids showed that CENP-E inhibited cells undergoing aberrant metaphase-anaphase transition and exhibiting chromosome segregation errors during mitosis. High-resolution real-time imaging analyses of 2D cell culture revealed that CENP-E inhibited cells undergoing central spindle splitting and chromosome instability phenotype. Using biotinylated syntelin as an affinity matrix, we found that CENP-E forms a complex with PRC1 in mitotic cells. Chemical inhibition of CENP-E in metaphase by syntelin prevented accurate central spindle assembly by perturbing temporal assembly of PRC1 to the midzone. Thus, CENP-E-mediated PRC1 assembly to the central spindle constitutes a temporal switch to organize dynamic kinetochore microtubules into stable midzone arrays. These findings reveal a previously uncharacterized role of CENP-E in temporal control of central spindle assembly. Since CENP-E is absent from yeast, we reasoned that metazoans evolved an elaborate central spindle organization machinery to ensure accurate sister chromatid segregation during anaphase and cytokinesis.

Spindle checkpoint

Multipolar spindles

Spindle pole body

Mitotic exit

10.1093/jmcb/mjz051

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Citations (25)

Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2

The Journal of Physical Chemistry Letters (2020)

Jia Gao Liang Zhang Xiaodan Liu Fudong Li Rongsheng Ma

The coronavirus disease pandemic caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected the global healthcare system. As low-molecular-weight drugs have high potential to completely match interactions with essential SARS-CoV-2 targets, we propose a strategy to identify such drugs using the fragment-based approach. Herein, using ligand- and protein-observed fragment screening approaches, we identified niacin and hit 1 binding to the catalytic pocket of the main protease (Mpro) of SARS-CoV-2, thereby modestly inhibiting the enzymatic activity of Mpro. We further searched for low-molecular-weight drugs containing niacin or hit 1 pharmacophores with enhanced inhibiting activity, e.g., carmofur, bendamustine, triclabendazole, emedastine, and omeprazole, in which omeprazole is the only one binding to the C-terminal domain of SARS-CoV-2 Mpro. Our study demonstrates that the fragment-based approach is a feasible strategy for identifying low-molecular-weight drugs against the SARS-CoV-2 and other potential targets lacking specific drugs.

Drug repositioning

Coronavirus

Repurposing

10.1021/acs.jpclett.0c01894

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Citations (26)

Inhibitors against Two PDZ Domains of MDA-9 Suppressed Migration of Breast Cancer Cells

International Journal of Molecular Sciences (2023)

Heng Tang Lei Wang LI Shu-ju Xiaoli Wei Mengqi Lv

Melanoma differentiation-associated gene 9 (MDA-9) is a small adaptor protein with tandem PDZ domains that promotes tumor progression and metastasis in various human cancers. However, it is difficult to develop drug-like small molecules with high affinity due to the narrow groove of the PDZ domains of MDA-9. Herein, we identified four novel hits targeting the PDZ1 and PDZ2 domains of MDA-9, namely PI1A, PI1B, PI2A, and PI2B, using a protein-observed nuclear magnetic resonance (NMR) fragment screening method. We also solved the crystal structure of the MDA-9 PDZ1 domain in complex with PI1B and characterized the binding poses of PDZ1-PI1A and PDZ2-PI2A, guided by transferred paramagnetic relaxation enhancement. The protein–ligand interaction modes were then cross-validated by the mutagenesis of the MDA-9 PDZ domains. Competitive fluorescence polarization experiments demonstrated that PI1A and PI2A blocked the binding of natural substrates to the PDZ1 and PDZ2 domains, respectively. Furthermore, these inhibitors exhibited low cellular toxicity, but suppressed the migration of MDA-MB-231 breast carcinoma cells, which recapitulated the phenotype of MDA-9 knockdown. Our work has paved the way for the development of potent inhibitors using structure-guided fragment ligation in the future.

PDZ domain

10.3390/ijms24043431

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Citations (3)

Prostacyclin is an autocrine regulator in the contraction of oviductal smooth muscle

Human Reproduction (2002)

Farinaz Arbab Jennifer S. Goldsby Nena Matijevic‐Aleksic Gangxiong Huang Ke Ruan

It was recently discovered that prostacyclin constituted 40-50% of prostaglandins (PG) produced by minced human oviduct. It is well established that prostacyclin relaxes vascular smooth muscle, but whether oviductal smooth muscle synthesizes prostacyclin and whether its contraction is affected by prostacyclin remain unclear.Smooth muscle microdissected from human oviducts was used for the study. The expression of prostacyclin synthase (PGIS) and prostacyclin receptor (IP) was confirmed by Western blot analysis. Metabolites of [(3)H]PGH(2) were analysed for prostacyclin. Functional coupling of IP to adenyl cyclase was assessed by the accumulation of intracellular cAMP upon prostacyclin challenge. The presence of saturable, specific binding sites for prostacyclin was confirmed by binding assay. The identity of IP was further confirmed by RT-PCR and nucleotide sequence analysis. Finally, the effects of prostacyclin on muscle contraction were studied.Human oviductal smooth muscle expresses functionally active PGIS and IP. The IP expressed is the same as that cloned from human lung tissue. The ED(50) of prostacyclin to increase intracellular cAMP was 16 nmol/l. Prostacyclin dose-dependently decreased the amplitude of muscle contraction.Human oviductal smooth muscle produces prostacyclin, which, in turn, decreases its contractility. Prostacyclin may regulate embryo transport.

10.1093/humrep/17.12.3053

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Citations (37)

A Genetically Encoded Trimethylsilyl 1D¹H-NMR Probe for Conformation Change in Large Membrane Protein Complexes

bioRxiv (Cold Spring Harbor Laboratory) (2019)

Qi Liu Qing‐tao He Xiaoxuan Lyu Fan Yang Zhongliang Zhu

Abstract While one dimensional 1 H nuclear magnetic resonance (1D 1 H-NMR) spectroscopy is one of the most important and convenient method for measuring conformation change in biomacromolecules, characterization of protein dynamics in large membrane protein complexes by 1D 1 H-NMR remains challenging, due to the difficulty of spectra assignment, low signal-to-noise ratio (S/N) and the need for large amount of protein. Here we report the site-specific incorporation of 4-trimethylsilyl phenylalanine (TMSiPhe) into proteins, through genetic code expansion in Escherichia coli cells, and the measurement of multiple conformational states in membrane protein complex by 1D 1 H-NMR. The unique up-field 1 H-NMR chemical shift of TMSiPhe, highly efficient and specific incorporation of TMSiPhe enabled facile assignment of the TMSiPhe 1 H-NMR signal, and characterization of multiple conformational state in a 150 kilodalton (kD) membrane protein complex, using only 5 μM of protein and 20 min spectra accumulation time. This highly efficient and convenient methods should be broadly applicable for the investigation of dynamic conformation change of protein complexes.

Conformational change

Chemical shift

Trimethylsilyl

10.1101/2019.12.18.873729

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Citations (1)

A novel inhibitor of the new antibiotic resistance protein OptrA

Chemical Biology & Drug Design (2018)

Xiaobo Zhong Hua Xiang Tiedong Wang Ling Zhong Di Ming

The antibiotic resistance ( ARE ) subfamily of ABC ( ATP ‐binding cassette) proteins confers resistance to a variety of clinically important ribosome‐targeting antibiotics and plays an important role in infections caused by pathogenic bacteria. However, inhibitors of ARE proteins have rarely been reported. Here, OptrA, a new member of the ARE proteins, was used to study inhibitors of these types of proteins. We first confirmed that destroying the catalytic activity of OptrA could restore the sensitivity of host cells to antibiotics. Then, fragment‐based screening, a drug screening method, was used to screen for inhibitors of OptrA. The competitive saturation transfer difference experiments, docking, and molecular dynamics were used to determine the binding sites and mode of interactions between OptrA and fragment screening hits. In this study, we first find a novel and specific inhibitor of OptrA ( CP 1), which suppressed the ATP ase activity of OptrA in vitro by 30%. A hydrogen bond formed between the 8‐position phenylcyclic cyano group in CP 1 and the amino acid residue Lys‐271 allows CP 1 to form a stable complex with OptrA protein. These findings provide a theoretical basis for the further optimization of the inhibitor structure to obtain inhibitors with higher efficiencies.

Subfamily

Docking (animal)

10.1111/cbdd.13311

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Citations (11)