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Sara Ibrahim Omar

Sara Ibrahim Omar
Proteic Bioscience

Doctor of Philosophy

About

19
Publications
4,044
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104
Citations
Additional affiliations
February 2019 - March 2020
University of Alberta
Position
  • PostDoc Position

Publications

Publications (19)
Article
Full-text available
The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem stru...
Preprint
Full-text available
The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem stru...
Article
Full-text available
Glioblastoma multiforme (GBM) is the most aggressive and deadly brain tumor, portending a median 13-month survival even following gross total resection with adjuvant chemotherapy and radiotherapy. This prognosis necessitates improved therapies for the disease. A target of interest for novel chemotherapies is the Warburg Effect, which describes the...
Article
Full-text available
One of the most important tumor suppressor proteins in eukaryotic cells is the transcription factor called p53. The importance of this protein in cells comes from the fact that it regulates a wide variety of cellular processes including the cell cycle, metabolism, DNA repair, senescence and apoptosis. In cancer cells, p53 is a major target as the m...
Conference Paper
Previously we have performed optical trapping and characterization of DNA and its interaction with tumor suppressing protein, p53. Here we extend the application of this technique to activators on mutant protein p53's interaction with DNA and establish a comparison with the wild type of the protein. The optical trapping setup uses an inverted micro...
Article
Full-text available
TP53 is the most mutated gene in all cancers. The mutant protein also accumulates in cells. The high frequency of p53 mutations makes the protein a promising target for anti-cancer therapy. Only a few molecules have been found, using in vitro screening, to reactivate the mutant protein. APR-246 is currently the most successful mutant p53 activator,...
Data
The PDB file of the minimized G245S-mp53 covalently bound to compound 2. (PDB)
Chapter
Full-text available
The main objective of this review chapter is to give the reader a practical toolbox for applications in quantitative biology and computational drug discovery. The computational technique of molecular dynamics is discussed, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. Addi...
Article
Full-text available
The cover image, by Niloofar Nayebi et al., is based on the Research Article A computational method for selecting short peptide sequences for inorganic material binding, DOI: 10.1002/prot.25356.
Article
Full-text available
The transcription factor p53 is a potent tumor suppressor dubbed as the “guardian of the genome” because of its ability to orchestrate protective biological outputs in response to a variety of oncogenic stresses. Mutation and thus inactivation of p53 can be found in 50% of human tumors. The majority are missense mutations located in the DNA binding...
Article
Discovering or designing biofunctionalized materials with improved quality highly depends on the ability to manipulate and control the peptide-inorganic interaction. Various peptides can be used as assemblers, synthesizers, and linkers in the material syntheses. In another context, specific and selective material-binding peptides can be used as rec...
Article
Calcium homeostasis is an essential physiological process requiring tight control in the normal cell. The dysregulation of calcium homeostasis may play a key role in the onset of Alzheimer's disease (AD) and other disorders, whether through the loss of calcium binding or calcium sensing capacity. Calbindin D28k (CB-D28k), a calcium binding protein...
Article
Protein-protein interaction networks associated with diseases have gained prominence as an area of research. We investigate algebraic and topo- logical indices for protein-protein interaction networks of 11 human cancers derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) data- base. We find a strong correlation between relative automor...
Article
Full-text available
A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas...
Article
The guardian of the genome, p53, is the most mutated protein found in all cancer cells. Restoration of wild-type activity to mutant p53 offers promise to eradicate cancer cells using novel pharmacological agents. Several molecules have already been found to activate mutant p53. While the exact mechanism of these compounds has not been fully underst...
Poster
Calbindin D28k is a calcium buffer and sensor. It is composed of six EF-hands (calcium binding domains) but only four of them can bind calcium. Calbindin D28k can also bind zinc ions. We used computational modelling to understand why EF-hands 2 and 6 lose their calcium binding ability. We also docked zinc ions to the protein to investigate the pote...

Projects

Project (1)