Seeing the PDB

Richardson, Jane S.; Richardson, David C.; Goodsell, David S.

doi:10.1016/j.jbc.2021.100742

Cited by 16 publications

(10 citation statements)

References 68 publications

(54 reference statements)

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“…The virtual docking of key proteins and active components was performed using Discovery Studio 2020 software (College of Pharmacy, Henan University of Chinese Medicine) to study their interaction. For the top 20 targets with a higher degree value in the compound-target-pathway network, the corresponding 3D structure was downloaded in the RSCB PDB database (https://www.rcsb.org/) (Richardson et al, 2021), and 22 component structures were obtained from the PubChem database, and the components were prepared using the "Prepare Ligands" module to obtain the 3D structure. For protein preparation, crystallographic water molecules were removed and then used in the "Prepare Protein" module.…”

Section: Molecular Dockingmentioning

confidence: 99%

Network Pharmacology and Experimental Validation to Explore the Mechanism of Qing-Jin-Hua-Tan-Decoction Against Acute Lung Injury

et al. 2022

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Qing-Jin-Hua-Tan-Decoction (QJHTD), a classic famous Chinese ancient prescription, has been used for treatment of pulmonary diseases since Ming Dynasty. A total of 22 prototype compounds of QJHTD absorbed into rat blood were chosen as candidates for the pharmacological network analysis and molecular docking. The targets from the intersection of compound target and ALI disease targets were used for GO and KEGG enrichment analyses. Molecular docking was adopted to further verify the interactions between 22 components and the top 20 targets with higher degree values in the component–target–pathway network. In vitro experiments were performed to verify the results of network pharmacology using SPR experiments, Western blot experiments, and the PMA-induced neutrophils to produce neutrophil extracellular trap (NET) model. The compound–target–pathway network includes 176 targets and 20 signaling pathways in which the degree of MAPK14, CDK2, EGFR, F2, SRC, and AKT1 is higher than that of other targets and which may be potential disease targets. The biological processes in QJHTD for ALI mainly included protein phosphorylation, response to wounding, response to bacterium, regulation of inflammatory response, and so on. KEGG enrichment analyses revealed multiple signaling pathways, including lipid and atherosclerosis, HIF-1 signaling pathway, renin–angiotensin system, and neutrophil extracellular trap formation. The molecular docking results showed that baicalin, oroxylin A-7-glucuronide, hispidulin-7-O-β-D-glucuronide, wogonoside, baicalein, wogonin, tianshic acid, and mangiferin can be combined with most of the targets, which might be the core components of QJHTD in treatment of ALI. Direct binding ability of baicalein, wogonin, and baicalin to thrombin protein was all micromolar, and their KD values were 11.92 μM, 1.303 μM, and 1.146 μM, respectively, revealed by SPR experiments, and QJHTD could inhibit Src phosphorylation in LPS-activated neutrophils by Western blot experiments. The experimental results of PMA-induced neutrophils to produce NETs indicated that QJHTD could inhibit the production of NETs. This study revealed the active compounds, effective targets, and potential pharmacological mechanisms of QJHTD acting on ALI.

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Section: Molecular Dockingmentioning

confidence: 99%

Network Pharmacology and Experimental Validation to Explore the Mechanism of Qing-Jin-Hua-Tan-Decoction Against Acute Lung Injury

et al. 2022

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“…Then, after lastly getting a peek at the atomic world, scientists eagerly make graphical diagrams to show us what they saw: G. Lewis and his dot structures ( 33 ), J. Richardson’s ribbon diagrams ( 34 ), and C. Levinthal’s computer graphics ( 35 ). Taking one final step to make this imagery accessible to all people is now easier than ever.…”

Section: Resultsmentioning

confidence: 99%

Data for all: Tactile graphics that light up with picture-perfect resolution

et al. 2022

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People who are blind do not have access to graphical data and imagery produced by science. This exclusion complicates learning and data sharing between sighted and blind persons. Because blind people use tactile senses to visualize data (and sighted people use eyesight), a single data format that can be easily visualized by both is needed. Here, we report that graphical data can be three-dimensionally printed into tactile graphics that glow with video-like resolution via the lithophane effect. Lithophane forms of gel electropherograms, micrographs, electronic and mass spectra, and textbook illustrations could be interpreted by touch or eyesight at ≥79% accuracy ( n = 360). The lithophane data format enables universal visualization of data by people regardless of their level of eyesight.

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“…Both VC1371 and VcRfaH are able to profoundly activate mshH transcription in E. coli ; however, neither of these two proteins were predicted to contain a classical helix-turn-helix DNA-binding domain [36]. We tested the interaction between VC1371 or VcRfaH and the promoter region of mshH , and found that both of these proteins could bind to the nucleotide fragments non-specifically in vitro (Fig.…”

Section: Discussionmentioning

confidence: 99%

Two regulatory factors of Vibrio cholerae activating the mannose-sensitive haemagglutinin pilus expression is important for biofilm formation and colonization in mice

et al. 2021

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Vibrio cholerae the causative agent of cholera, uses a large number of coordinated transcriptional regulatory events to transition from its environmental reservoir to the host intestine, which is its preferred colonization site. Transcription of the mannose-sensitive haemagglutinin pilus (MSHA), which aids the persistence of V. cholerae in aquatic environments, but causes its clearance by host immune defenses, was found to be regulated by a yet unknown mechanism during the infection cycle of V. cholerae . In this study, genomic expression library screening revealed that two regulators, VC1371 and VcRfaH, are able to positively activate the transcription of MSHA operon. VC1371 is localized and active in the cell membrane. Deletion of vc1371 or VcrfaH genes in V. cholerae resulted in less MshA protein production and less efficiency of biofilm formation compared to that in the wild-type strain. An adult mouse model showed that the mutants with vc1371 or VcrfaH deletion colonized less efficiently than the wild-type; the VcrfaH deletion mutant showed less colonization efficiency in the infant mouse model. The findings strongly suggested that the two regulators, namely VC1371 and VcRfaH, which are involved in the regulation of MSHA expression, play an important role in V. cholerae biofilm formation and colonization in mice.

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Seeing the PDB

Cited by 16 publications

References 68 publications

Network Pharmacology and Experimental Validation to Explore the Mechanism of Qing-Jin-Hua-Tan-Decoction Against Acute Lung Injury

Network Pharmacology and Experimental Validation to Explore the Mechanism of Qing-Jin-Hua-Tan-Decoction Against Acute Lung Injury

Data for all: Tactile graphics that light up with picture-perfect resolution

Two regulatory factors of Vibrio cholerae activating the mannose-sensitive haemagglutinin pilus expression is important for biofilm formation and colonization in mice

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