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Article ; Online: Correction to: Nanostructured biosensing platforms for the detection of food- and water‑borne pathogenic Escherichia coli.

Zhou, Qiang / Natarajan, Bharathi / Kannan, Palanisamy

2023 Volume 415, Issue 16, Page(s) 3297

Language	English
Publishing date	2023-05-25
Publishing country	Germany
Document type	Published Erratum
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-023-04765-w
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Article: Illuminating the functions of the understudied Fructosamine-3-kinase (FN3K) using a multi-omics approach reveals new links to lipid, carbon, and co-factor metabolic pathways.

Shrestha, Safal / Taujale, Rahil / Katiyar, Samiksha / Kannan, Natarajan

Research square

2024

Abstract: Fructosamine-3-kinases (FN3Ks) are a conserved family of repair enzymes that phosphorylate reactive sugars attached to lysine residues in peptides and proteins. Although FN3Ks are present across the tree of life and share detectable sequence similarity ... ...

Abstract	Fructosamine-3-kinases (FN3Ks) are a conserved family of repair enzymes that phosphorylate reactive sugars attached to lysine residues in peptides and proteins. Although FN3Ks are present across the tree of life and share detectable sequence similarity to eukaryotic protein kinases, the biological processes regulated by these kinases are largely unknown. To address this knowledge gap, we leveraged the FN3K CRISPR Knock-Out (KO) cell line alongside an integrative multi-omics study combining transcriptomics, metabolomics, and interactomics to place these enzymes in a pathway context. The integrative analyses revealed the enrichment of pathways related to oxidative stress response, lipid biosynthesis (cholesterol and fatty acids), carbon and co-factor metabolism. Moreover, enrichment of nicotinamide adenine dinucleotide (NAD) binding proteins and localization of human FN3K (HsFN3K) to mitochondria suggests potential links between FN3Ks and NAD-mediated energy metabolism and redox balance. We report specific binding of HsFN3K to NAD compounds in a metal and concentration-dependent manner and provide insight into their binding mode using modeling and experimental site-directed mutagenesis. By identifying a potential link between FN3Ks, redox regulation, and NAD-dependent metabolic processes, our studies provide a framework for targeting these understudied kinases in diabetic complications and metabolic disorders where redox balance is altered.
Language	English
Publishing date	2024-02-16
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3934957/v1
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Article ; Online: Oral physicians in the management of head and neck cancers

Natarajan Kannan

Journal of Indian Academy of Oral Medicine and Radiology, Vol 32, Iss 4, Pp 322-

2020 Volume 322

Keywords	Dentistry ; RK1-715 ; Medical physics. Medical radiology. Nuclear medicine ; R895-920
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Nanostructured biosensing platforms for the detection of food- and water-borne pathogenic Escherichia coli.

Zhou, Qiang / Natarajan, Bharathi / Kannan, Palanisamy

Analytical and bioanalytical chemistry

2023 Volume 415, Issue 16, Page(s) 3111–3129

Abstract: Pathogenic bacterial infection is one of the principal causes affecting human health and ecosystems. The accurate identification of bacteria in food and water samples is of significant interests to maintain safety and health for humans. Culture-based ... ...

Abstract	Pathogenic bacterial infection is one of the principal causes affecting human health and ecosystems. The accurate identification of bacteria in food and water samples is of significant interests to maintain safety and health for humans. Culture-based tests are practically tedious and may produce false-positive results, while viable but non-culturable microorganisms (NCMs) cannot be retrieved. Thus, it requires fast, reliable, and low-cost detection strategies for on-field analysis and point-of-care (POC) monitoring. The standard detection methods such as nucleic acid analysis (RT-PCR) and enzyme-linked immunosorbent assays (ELISA) are still challenging in POC practice due to their time-consuming (several hours to days) and expensive laboratory operations. The optical (surface plasmon resonance (SPR), fluorescence, and surface-enhanced Raman scattering (SERS)) and electrochemical-based detection of microbes (early stage of infective diseases) have been considered as alternative routes in the emerging world of nanostructured biosensing since they can attain a faster and concurrent screening of several pathogens in real samples. Moreover, optical and electrochemical detection strategies are opening a new route for the ability of detecting pathogens through the integration of cellphones, which is well fitted for POC analysis. This review article covers the current state of sensitive mechanistic approaches for the screening and detection of Escherichia coli O157:H7 (E. coli) pathogens in food and water samples, which can be potentially applied in clinical and environmental monitoring.
MeSH term(s)	Humans ; Biosensing Techniques/methods ; Ecosystem ; Surface Plasmon Resonance/methods ; Escherichia coli O157/chemistry ; Water ; Food Microbiology
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2023-05-12
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-023-04731-6
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Article ; Online: Chaperone-mediated MHC-I peptide exchange in antigen presentation.

Jiang, Jiansheng / Natarajan, Kannan / Margulies, David H

IUCrJ

2024 Volume 11, Issue Pt 3, Page(s) 287–298

Abstract: This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, ... ...

Abstract	This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.
MeSH term(s)	Antigen Presentation/immunology ; Histocompatibility Antigens Class I/immunology ; Histocompatibility Antigens Class I/metabolism ; Histocompatibility Antigens Class I/chemistry ; Humans ; Molecular Chaperones/metabolism ; Molecular Chaperones/chemistry ; Molecular Chaperones/immunology ; Peptides/immunology ; Peptides/chemistry ; Peptides/metabolism ; Receptors, Antigen, T-Cell/immunology ; Receptors, Antigen, T-Cell/metabolism ; Receptors, Antigen, T-Cell/chemistry ; Crystallography, X-Ray
Chemical Substances	Histocompatibility Antigens Class I ; Molecular Chaperones ; Peptides ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2024-05-01
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2754953-7
ISSN	2052-2525 ; 2052-2525
ISSN (online)	2052-2525
ISSN	2052-2525
DOI	10.1107/S2052252524002768
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Article ; Online: Gravimetric weight loss of steel in self-compacting concrete blended with wood ash and silica fume.

V, Kannan / Natarajan, Karthiga Shenbagam

Environmental science and pollution research international

2022 Volume 30, Issue 4, Page(s) 9483–9495

Abstract: The present research work deals with the development of self-compacting concrete (SCC) containing wood ash (WA), silica fume (SF) and their combination (1:1 ratio). Several research studies have reported on the performance of WA and SF-blended SCC. ... ...

Abstract	The present research work deals with the development of self-compacting concrete (SCC) containing wood ash (WA), silica fume (SF) and their combination (1:1 ratio). Several research studies have reported on the performance of WA and SF-blended SCC. However, very limited information is available on the effects of silica dioxide (SiO
MeSH term(s)	Humans ; Silicon Dioxide ; Steel ; Compressive Strength ; Dust ; Gases ; Weight Loss
Chemical Substances	Silicon Dioxide (7631-86-9) ; Steel (12597-69-2) ; calcium silicate (S4255P4G5M) ; Dust ; Gases
Language	English
Publishing date	2022-09-03
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-22780-9
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Article ; Online: Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings.

Yeung, Wayland / Zhou, Zhongliang / Li, Sheng / Kannan, Natarajan

Briefings in bioinformatics

2023 Volume 24, Issue 1

Abstract: Protein language modeling is a fast-emerging deep learning method in bioinformatics with diverse applications such as structure prediction and protein design. However, application toward estimating sequence conservation for functional site prediction has ...

Abstract	Protein language modeling is a fast-emerging deep learning method in bioinformatics with diverse applications such as structure prediction and protein design. However, application toward estimating sequence conservation for functional site prediction has not been systematically explored. Here, we present a method for the alignment-free estimation of sequence conservation using sequence embeddings generated from protein language models. Comprehensive benchmarks across publicly available protein language models reveal that ESM2 models provide the best performance to computational cost ratio for conservation estimation. Applying our method to full-length protein sequences, we demonstrate that embedding-based methods are not sensitive to the order of conserved elements-conservation scores can be calculated for multidomain proteins in a single run, without the need to separate individual domains. Our method can also identify conserved functional sites within fast-evolving sequence regions (such as domain inserts), which we demonstrate through the identification of conserved phosphorylation motifs in variable insert segments in protein kinases. Overall, embedding-based conservation analysis is a broadly applicable method for identifying potential functional sites in any full-length protein sequence and estimating conservation in an alignment-free manner. To run this on your protein sequence of interest, try our scripts at https://github.com/esbgkannan/kibby.
MeSH term(s)	Amino Acid Sequence ; Proteins/genetics ; Proteins/chemistry ; Computational Biology/methods ; Conserved Sequence
Chemical Substances	Proteins
Language	English
Publishing date	2023-01-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbac599
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Article ; Online: Informatic challenges and advances in illuminating the druggable proteome.

Taujale, Rahil / Gravel, Nathan / Zhou, Zhongliang / Yeung, Wayland / Kochut, Krystof / Kannan, Natarajan

Drug discovery today

2024 Volume 29, Issue 3, Page(s) 103894

Abstract: The understudied members of the druggable proteomes offer promising prospects for drug discovery efforts. While large-scale initiatives have generated valuable functional information on understudied members of the druggable gene families, translating ... ...

Abstract	The understudied members of the druggable proteomes offer promising prospects for drug discovery efforts. While large-scale initiatives have generated valuable functional information on understudied members of the druggable gene families, translating this information into actionable knowledge for drug discovery requires specialized informatics tools and resources. Here, we review the unique informatics challenges and advances in annotating understudied members of the druggable proteome. We demonstrate the application of statistical evolutionary inference tools, knowledge graph mining approaches, and protein language models in illuminating understudied protein kinases, pseudokinases, and ion channels.
MeSH term(s)	Proteome ; Informatics
Chemical Substances	Proteome
Language	English
Publishing date	2024-01-22
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	1324988-5
ISSN	1878-5832 ; 1359-6446
ISSN (online)	1878-5832
ISSN	1359-6446
DOI	10.1016/j.drudis.2024.103894
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Article ; Online: Gravimetric weight loss of steel in self-compacting concrete blended with wood ash and silica fume

V, Kannan / Natarajan, Karthiga Shenbagam

Environ Sci Pollut Res. 2023 Jan., v. 30, no. 4 p.9483-9495

2023

Abstract	The present research work deals with the development of self-compacting concrete (SCC) containing wood ash (WA), silica fume (SF) and their combination (1:1 ratio). Several research studies have reported on the performance of WA and SF-blended SCC. However, very limited information is available on the effects of silica dioxide (SiO₂) and subsequent formation of calcium-silicate-hydrate (C-S–H) gel and its benefit on the strength and durability enhancement of self-compacting concrete. In this work, wood ash (WA) and silica fume (SF) were used as cement replacement materials, and studies were carried out on the chemical composition and its contribution in the strength development of SCC. Compressive strength, ultrasonic pulse velocity and dynamic modulus of elasticity have been increased when the cement is replaced with WA, SF and WA + SF content up to 10%, 6% and 30 + 8% respectively than normal SCC. From the EDAX analysis, Ca content in the mixes, NSCC mix has higher Ca content (52.04%) whereas 10% WA SCC, 6% SF and 30% WA + 6% SF SCC has 41.78%, 33.64% and 28.77% respectively. Similarly, SiO₂ content 6% SF-blended SCC has higher value (38.03%) than other mixes. As 6% SF-blended SCC has a higher value of SiO₂, it gives the higher compressive strength and UPV values because of high reactivity and subsequent formation of C-S–H gel.
Keywords	cement ; chemical composition ; compression strength ; concrete ; durability ; gels ; modulus of elasticity ; silica ; steel ; ultrasonics ; weight loss ; wood ash
Language	English
Dates of publication	2023-01
Size	p. 9483-9495.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-22780-9
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Article ; Online: Using explainable machine learning to uncover the kinase-substrate interaction landscape.

Zhou, Zhongliang / Yeung, Wayland / Soleymani, Saber / Gravel, Nathan / Salcedo, Mariah / Li, Sheng / Kannan, Natarajan

Bioinformatics (Oxford, England)

2024 Volume 40, Issue 2

Abstract: Motivation: Phosphorylation, a post-translational modification regulated by protein kinase enzymes, plays an essential role in almost all cellular processes. Understanding how each of the nearly 500 human protein kinases selectively phosphorylates their ...

Abstract	Motivation: Phosphorylation, a post-translational modification regulated by protein kinase enzymes, plays an essential role in almost all cellular processes. Understanding how each of the nearly 500 human protein kinases selectively phosphorylates their substrates is a foundational challenge in bioinformatics and cell signaling. Although deep learning models have been a popular means to predict kinase-substrate relationships, existing models often lack interpretability and are trained on datasets skewed toward a subset of well-studied kinases. Results: Here we leverage recent peptide library datasets generated to determine substrate specificity profiles of 300 serine/threonine kinases to develop an explainable Transformer model for kinase-peptide interaction prediction. The model, trained solely on primary sequences, achieved state-of-the-art performance. Its unique multitask learning paradigm built within the model enables predictions on virtually any kinase-peptide pair, including predictions on 139 kinases not used in peptide library screens. Furthermore, we employed explainable machine learning methods to elucidate the model's inner workings. Through analysis of learned embeddings at different training stages, we demonstrate that the model employs a unique strategy of substrate prediction considering both substrate motif patterns and kinase evolutionary features. SHapley Additive exPlanation (SHAP) analysis reveals key specificity determining residues in the peptide sequence. Finally, we provide a web interface for predicting kinase-substrate associations for user-defined sequences and a resource for visualizing the learned kinase-substrate associations. Availability and implementation: All code and data are available at https://github.com/esbgkannan/Phosformer-ST. Web server is available at https://phosformer.netlify.app.
MeSH term(s)	Humans ; Peptide Library ; Protein Kinases/metabolism ; Phosphorylation ; Peptides/chemistry ; Machine Learning
Chemical Substances	Peptide Library ; Protein Kinases (EC 2.7.-) ; Peptides
Language	English
Publishing date	2024-01-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btae033
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