RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

Goodsell, David S.; Burley, S.K.

doi:10.1038/s41388-020-01461-2

Cited by 12 publications

(10 citation statements)

References 39 publications

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“…136 Given the public health importance of human papilloma viruses (HPV, a cause of genital warts and cervical, genital, anal, and oropharyngeal cancers), PDB‐101 developed related content in the form of (i) a molecular origami paper‐folding model of the reconstituted HPV capsid that has been used successfully for vaccine design, (ii) a Human Papillomavirus and Vaccines MotM article (May 2018) 137 ; and (iii) a Nature Oncogene review article focused on the biology of HPV viewed through the lens of the PDB. 138 …”

Section: Resultsmentioning

confidence: 99%

“…Previously published PDB‐101 activities related to cancer included MotM articles on p53 Tumor Suppressor (July 2002) 127 ; Estrogen Receptor (September 2003) 128 ; Epidermal Growth Factor (June 2010) 129 ; RAS Protein (April 2012) 130 ; RAF Protein Kinases (March 2016) 131 ; Programmed Cell Death Protein 1 (December 2016) 132 ; Chimeric Antigen Receptors (October 2017) 133 ; MDM2 (June 2019) 134 ; Cyclin and Cyclin Dependent Kinase (August 2019) 135 ; and Cisplatin and DNA (March 2021) 136 . Given the public health importance of human papilloma viruses (HPV, a cause of genital warts and cervical, genital, anal, and oropharyngeal cancers), PDB‐101 developed related content in the form of (i) a molecular origami paper‐folding model of the reconstituted HPV capsid that has been used successfully for vaccine design, (ii) a Human Papillomavirus and Vaccines MotM article (May 2018) 137 ; and (iii) a Nature Oncogene review article focused on the biology of HPV viewed through the lens of the PDB 138 …”

Section: Resultsmentioning

confidence: 99%

“…136 Given the public health importance of human papilloma viruses (HPV, a cause of genital warts and cervical, genital, anal, and oropharyngeal cancers), PDB-101 developed related content in the form of (i) a molecular origami paper-folding model of the reconstituted HPV capsid that has been used successfully for vaccine design, (ii) a Human Papillomavirus and Vaccines MotM article (May 2018) 137 ; and (iii) a Nature Oncogene review article focused on the biology of HPV viewed through the lens of the PDB. 138 Going beyond our biennial theme of Cancer Biology and Therapeutics, we use our PDB101.RCSB.org web portal and Service 4 social media channels (Twitter: @buildmodels; Facebook: RCSBPDB) to empower educators, students, and the general public to explore and understand how 3D biostructures are being used in research to address global health challenges of immediate concern. Compelling SARS-CoV-2 images created by Service 4 team member Professor David S. Goodsell (pdb101.rcsb.…”

Section: Searching the Pdb Archivementioning

confidence: 99%

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RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Burley

Bhikadiya

et al. 2022

Protein Science

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Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal (http://RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (http://PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via http://RCSB.org; and (v) supports training, outreach, and education via http://PDB101.RCSB.org. New tools and features at http://RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Searching the Pdb Archivementioning

confidence: 99%

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RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Burley

Bhikadiya

et al. 2022

Protein Science

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“…The pKa obtained for M ≈ 3.4 and G ≈ 3.6 ( Figure 1(a) ) was consistent with those reported by Chuang et al [ 25 ]. The atomic coordinates of the GSH molecule were obtained from the cocrystallized structure of the glutathione transferase enzyme deposited in the Protein Data Bank (PDB id: 2VCV) [ 26 , 27 ]. Similarly, the pKa of GSH was evaluated with Epik [ 24 ].…”

Section: Methodsmentioning

confidence: 99%

Structural Effects of pH Variation and Calcium Amount on the Microencapsulation of Glutathione in Alginate Polymers

Bustos

Hernández-Rodríguez

Castro

et al. 2022

BioMed Research International

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Reduced glutathione (GSH) has a high antioxidant capacity and is present in nearly every cell in the body, playing important roles in nutrient metabolism, antioxidant defense, and regulation of cellular events. Conversely, alginate is a macromolecule that has been widely used in the food, pharmaceutical, biomedical, and textile industries due to its biocompatibility, biodegradability, nontoxicity, and nonimmunogenicity as well as for its capabilities of retaining water and stabilizing emulsions. The primary goal of this study was to characterize and optimize the formation of a molecular complex of calcium alginate with GSH using a computational approach. As methods, we evaluated the influence of varying the amount of calcium cations at two different pHs on the structural stability of Ca2+-alginate complexes and thus on GSH liberation from these types of nanostructures. The results showed that complex stabilization depends on pH, with the system having a lower Ca2+ amount that produces the major GSH release. The systems at pH 2.5 retain more molecules within the calcium-alginate complex, which release GSH more slowly when embedded in more acidic media. In conclusions, this study demonstrates the dependence of the amount of calcium and the stabilizing effect of pH on the formation and subsequent maintenance of an alginate nanostructure. The results presented in this study can help to develop better methodological frameworks in industries where the release or capture of compounds, such as GSH in this case, depends on the conditions of the alginate nanoparticle.

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“…The target proteins' 3D crystal structures in PDB format was provided by the Protein Data Bank (PDB; http://www. rcsb.org/pdb/) (40). The water molecules and excess ligands were removed by PyMOL software (41).…”

Section: Molecular Dockingmentioning

confidence: 99%

Systemic and local pharmacological effects of melatonin targeting polycystic ovary syndrome based on network pharmacology

Cheng¹,

Zhu²,

Zong³

et al. 2023

Ann Transl Med

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Background: Polycystic ovary syndrome (PCOS) is the most common cause of anovulatory infertility in women of childbearing age. Emerging evidence has demonstrated that melatonin (MT) is a promising therapeutic drug for PCOS. However, the specific therapeutic mechanisms are largely unknown. This study explores MT's potential pharmacological targets and pathways for PCOS using a systematic pharmacology approach.Methods: MT's potential pharmacological targets were obtained from the Traditional Chinese Medicine Systems Pharmacology (TCMSP), DrugBank, PharmMapper, and SwissTargetPrediction databases. The PCOS targets were obtained from the GeneCards, DisGeNET, and National Center for Biotechnology Information (NCBI) Gene databases. The protein-protein interaction (PPI) network was constructed with the STRING database. The Cytoscape plugin "CytoHubba" identified the hub genes using a Maximal Clique Centrality (MCC) topological analysis. The predicted therapeutic targets were imported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools to perform the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The results were visualized by an online bioinformatics tool, and the network construction was visualized using Cytoscape software. Molecular docking was performed via AutoDock Vina and PyMOL.Results: A total of 37 potential therapeutic targets were obtained, which were involved in biological processes (BP) closely related to hormone synthesis and transcriptional regulation in cells, such as the intracellular steroid hormone receptor signaling pathway, steroid catabolic process, and regulation of transcription from RNA polymerase II promoter. Using the Cytoscape network analysis, ten hub targets [ESR1, androgen receptor (AR), matrix metalloproteinase 9 (MMP9), CYP19A1, IGF1R, progesterone receptor (PGR), CYP1A1, NR3C1, ESR2, MDM2] were discovered by the MCC algorithm of the "CytoHubba" plugin. Molecular docking also showed high affinity between these ten hub targets with MT, indicating that these targets might play key roles in treating PCOS. The top ten KEGG pathways interacted with the 37 potential therapeutic targets and were classified into four functional modules: circadian rhythm, reproductive process, metabolic process, and oocyte maturation.Conclusions: As a critical rhythm synchronizer, MT may alleviate symptoms of reproductive and metabolic disorders of PCOS systemically. At a localized level, it may protect oocytes from oxidative stress due to its strong antioxidant effects.

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RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

Cited by 12 publications

References 39 publications

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Structural Effects of pH Variation and Calcium Amount on the Microencapsulation of Glutathione in Alginate Polymers

Systemic and local pharmacological effects of melatonin targeting polycystic ovary syndrome based on network pharmacology

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