Mechanistic Analysis of Factors Involved in Pancreatic Development and Other Disease Pathways

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This team works primarily on understanding the transcriptional networks determining cell fate, using a variety of biophysical tools, including X-ray crystallography.

The protein and structural biology group (PSB) works in collaboration with stem cell and bioinformatics groups both within and outside of QBRI to enable an integrated view of transcriptional networks. The group uses genomic knowledge to target specific transcription factors (TFs) and studies them in detail to understand the mechanisms used by TFs to make protein-protein and protein-DNA interactions. They are currently analyzing several TFs involved in pluripotency and are working with stem cell groups that are studying pancreatic beta cell differentiation in normal and Type 2 diabetes patients to target TFs with key roles in this process.

The team is also employing its group-specific technology to look at other disease mechanisms.

Latest Publications

  • Elbasir A, Mall R, Kunji K, Rawi R, Islam Z, Chuang GY, Kolatkar PR, Bensmail H. BCrystal: an interpretable sequence-based protein crystallization predictor. Bioinformatics. 2020 Mar 1;36(5):1429-1438. doi: 10.1093/bioinformatics/btz762.PMID: 31603511
  • Islam Z, Ali MH, Popelka A, Mall R, Ullah E, Ponraj J, Kolatkar PR. J Biomol Struct Dyn. 2020 Mar 10:1-10. Probing the fibrillation of lysozyme by nanoscale-infrared spectroscopy. doi: 10.1080/07391102.2020.1734091. Online ahead of print.PMID: 32131712
  • Gupta V, Sudhakaran IP, Islam Z, Vaikath NN, Hmila I, Lukacsovich T, Kolatkar PR, El-Agnaf OMA. PLoS One. 2020 Nov 6;15(11):e0241773. Expression, purification and characterization of α-synuclein fibrillar specific scFv from inclusion bodies. doi: 10.1371/journal.pone.0241773. eCollection 2020.PMID: 33156828
  • Chaudhary S, Islam Z, Mishra V, Rawat S, Ashraf GM, Kolatkar PR. Curr Protein Pept Sci. 2019;20(6):495-504. Sox2: A Regulatory Factor in Tumorigenesis and Metastasis. doi: 10.2174/1389203720666190325102255.PMID: 30907312
  • Kim HG, Rosenfeld JA, Scott DA, Bénédicte G, Labonne JD, Brown J, McGuire M, Mahida S, Naidu S, Gutierrez J, Lesca G, des Portes V, Bruel AL, Sorlin A, Xia F, Capri Y, Muller E, McKnight D, Torti E, Rüschendorf F, Hummel O, Islam Z, Kolatkar PR, Layman LC, Ryu D, Kong IK, Madan-Khetarpal S, Kim CH. Mol Autism. 2019 Oct 22;10:35. Disruption of PHF21A causes syndromic intellectual disability with craniofacial anomalies, epilepsy, hypotonia, and neurobehavioral problems including autism. doi: 10.1186/s13229-019-0286-0. eCollection 2019.PMID: 31649809
  • Elbasir A, Moovarkumudalvan B, Kunji K, Kolatkar PR, Mall R, Bensmail H. Bioinformatics. 2019 Jul 1;35(13):2216-2225. DeepCrystal: a deep learning framework for sequence-based protein crystallization prediction. doi: 10.1093/bioinformatics/bty953.PMID: 30462171
  • Ali MHM, Toor SM, Rakib F, Mall R, Ullah E, Mroue K, Kolatkar PR, Al-Saad K, Elkord E. Vaccines (Basel). 2019 Sep 9;7(3):109. Investigation of the Effect of PD-L1 Blockade on Triple Negative Breast Cancer Cells Using Fourier Transform Infrared Spectroscopy. doi: 10.3390/vaccines7030109.PMID: 31505846