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A novel search engine for proteins involved in Notch crosstalk signaling pathways

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Abstract

To regulate biological activity in humans, the Notch signaling pathway (NSP) plays an essential role in a wide array of cellular development and differentiation process. In recent years, many studies have reported that aberrant activation of Notch is associated with the tumor process; but no appropriate database exists to fill this significant gap. To address this, we created a pioneering database NCSp, which is open access and comprises intercommunicating pathways and related protein mutations. This allows scientists to understand better the cause of single amino acid mutations in proteins. Therefore, NCSp provides information on the predicted functional effect of human protein mutations, which aids in understanding the importance of mutations linked to the Notch crosstalk signaling pathways in cancerous and non-cancerous systems. This database might be helpful for therapeutic mutation analysis, molecular biology, and structural biology researchers. The NCSp database can be accessed through https://bioserver3.physics.iisc.ac.in/cgi-bin/nccspd/.

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Abbreviations

AKT1:

RAC-alpha serine/threonine-protein kinase

AMPK:

adenosine monophosphate-activated protein kinase

EGF:

epidermal growth factor

EGFR:

epidermal growth factor receptor

ErbB-2:

epidermal growth factor receptor-2

GLI2:

GLI-Kruppel family member GLI2

Hh:

hedgehog

IKK:

IkappaB kinase

JAK-STAT:

janus kinases - signal transducer and activator of transcription proteins

KEGG:

Kyoto Encyclopedia of Genes and Genomes

KRAS:

GTPase KRas

MAPK:

mitogen-activated protein kinase

mTOR:

mammalian target of rapamycin

NCSp:

Notch crosstalk signaling pathway

NF-κB:

nuclear transcriptional factor kappa B

NFAT:

nuclear factors of activated T-cells

NICD:

Notch intracellular domain

NSP:

Notch signaling pathway

PI3K:

phosphatidylinositol-3-kinase

P53:

phosphoprotein 53

TGF-β:

transforming growth factor beta

TNF-α:

tumor necrosis factor-alpha

TCR:

T cell receptor

VEGF:

vascular endothelial growth factor

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Acknowledgements

The authors (KS, SR and DR) thank the ‘An Indian Initiative on setting up a high-fidelity structural data archival/retrieval system for Life Sciences-(PDBi)’ project, funded by CDAC (Center for Development of Advanced Computing). JJ and MS acknowledge the MHRD-RUSA 2.0, (F.24-51/2014-U, Policy (TN Multi-Gen), Department of Education, Government of India (Dt.09.10.2018). JJ acknowledges the financial grant supported by DBT-BIC (BT/PR40154/BTIS/137/34/2021, Dt. 07.03.2022). CNR acknowledges the Dr. D.S. Kothari Postdoctoral Fellowship (DSKPDF) (Ref.No. BL/20-21/0172 (S-90)), funded by the University Grants Commission (UGC). Also, the funding by the Department of Biotechnology (DBT) is gratefully acknowledged.

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Authors and Affiliations

  1. Structural Biology and Bio Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, 630004, India

    Madhumathi Sanjeevi, Chandrasekar Narayanan Rahul & Jeyakanthan Jeyaraman

  2. Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, India

    Santhosh Rajendran, Dhanalakshmi Ramachandran & Sekar Kanagaraj

Authors
  1. Madhumathi Sanjeevi
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  2. Santhosh Rajendran
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  3. Dhanalakshmi Ramachandran
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  4. Chandrasekar Narayanan Rahul
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  5. Jeyakanthan Jeyaraman
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  6. Sekar Kanagaraj
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Contributions

JJ conceptualised the problem. MS and SR devised the methodology. MS and DR designed the front end of the database. MS and CNR wrote the manuscript. KS reviewed the manuscript.

Corresponding authors

Correspondence to Jeyakanthan Jeyaraman or Sekar Kanagaraj.

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The authors have no conflicts of interest to disclose.

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Corresponding editor: Susmita Roy

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Sanjeevi, M., Rajendran, S., Ramachandran, D. et al. A novel search engine for proteins involved in Notch crosstalk signaling pathways. J Biosci 49, 8 (2024). https://doi.org/10.1007/s12038-023-00395-7

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