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Article ; Online: Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches.

Gupta, Swati / Pal, Debnath

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–11

Abstract: We compare the WebGeSTer and INtrinsic transcription TERmination hairPIN (INTERPIN) databases used for intrinsic transcription termination (ITT) site prediction in bacteria. The former deploys inverted nucleotide repeat detection for identification of ... ...

Abstract	We compare the WebGeSTer and INtrinsic transcription TERmination hairPIN (INTERPIN) databases used for intrinsic transcription termination (ITT) site prediction in bacteria. The former deploys inverted nucleotide repeat detection for identification of RNA hairpin, while the latter a pair-potential function - the hairpin energy score evaluation being identical for both. We find INTERPIN more sensitive than WebGeSTer with about 6% and 51% additional predictions for ITTs in chromosomal and plasmid operons, respectively. INTERPIN hairpins are relatively shorter in length with ungapped stem, and even located in AT-rich segments, compared to GC-rich longer hairpins with a gapped stem in WebGeSTer. The GC%, length, and energy score from INTERPIN transcription units (TUs) are best inter-correlated while the lowest energy
Language	English
Publishing date	2024-04-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2325107
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Article ; Online: microRNA Isolation, Expression Profiling, and Target Identification for Neuroprotection in Alzheimer's Disease.

Iqbal, Saleem / Pal, Debnath

Methods in molecular biology (Clifton, N.J.)

2024 Volume 2761, Page(s) 277–290

Abstract: Millions of people throughout the world are affected by neurodegenerative disorders like Alzheimer's disease (AD), making them a major public health concern. To create successful medicines, early diagnosis and illness monitoring are required. Emerging as ...

Abstract	Millions of people throughout the world are affected by neurodegenerative disorders like Alzheimer's disease (AD), making them a major public health concern. To create successful medicines, early diagnosis and illness monitoring are required. Emerging as possible diagnostic and treatment tools for neurodegenerative illnesses are biomarkers such as microRNAs (miRNAs). In the realm of neuroscience, miRNAs have been discovered to function as essential regulators of gene expression, with roles spanning development, differentiation, and illness. Several neurodegenerative diseases, including AD, have been linked to miRNA dysregulation. As high-throughput methods have been developed for monitoring miRNA expression and identifying miRNA targets, miRNAs have become a prime candidate for use in diagnostics and therapy. The techniques for isolating miRNAs and the most up-to-date computational methods for finding miRNA target transcripts are both described in this chapter. This chapter will be a helpful reference for anyone investigating the role of miRNAs in AD and related neurodegenerative illnesses.
MeSH term(s)	Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Alzheimer Disease/metabolism ; Neuroprotection ; Biomarkers/metabolism ; Gene Expression Profiling/methods
Chemical Substances	MicroRNAs ; Biomarkers
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3662-6_20
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Article ; Online: Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity.

Pal, Debnath

Journal of structural biology

2021 Volume 213, Issue 2, Page(s) 107713

Abstract: The high SARS-CoV-2 reproductive number driving the COVID-19 pandemic has been a mystery. Our recent in vitro, and in vivo coronaviral pathogenesis studies involving Mouse Hepatitis Virus (MHV-A59) suggest a crucial role for a small host membrane-virus ... ...

Abstract	The high SARS-CoV-2 reproductive number driving the COVID-19 pandemic has been a mystery. Our recent in vitro, and in vivo coronaviral pathogenesis studies involving Mouse Hepatitis Virus (MHV-A59) suggest a crucial role for a small host membrane-virus contact initiator region of the Spike protein, called the fusion peptide that enhances the virus fusogenicity and infectivity. Here I study the Spike from five human β-coronaviruses (HCoV) including the SARS-CoV-2, and MHV-A59 for comparison. The structural and dynamics analyses of the Spike show that its fusion loop spatially organizes three fusion peptides contiguous to each other to synergistically trigger the virus-host membrane fusion process. I propose a Contact Initiation Model based on the architecture of the Spike quaternary structure that explains the obligatory participation of the fusion loop in the initiation of the host membrane contact for the virus fusion process. Among all the HCoV Spikes in this study, SARS-CoV-2 has the most hydrophobic surface and the extent of hydrophobicity correlates with the reproductive number and infectivity of the other HCoV. Comparison between results from standard and replica exchange molecular dynamics reveal the unique physicochemical properties of the SARS-CoV-2 fusion peptides, accrued in part from the presence of consecutive prolines that impart backbone rigidity which aids the virus fusogenicity. The priming of the Spike by its cleavage and subsequent fusogenic conformational transition steered by the fusion loop may be critical for the SARS-CoV-2 spread. The importance of the fusion loop makes it an apt target for anti-virals and vaccine candidates.
Language	English
Publishing date	2021-03-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2021.107713
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Article ; Online: DREAMweb: An online tool for graph-based modeling of NMR protein structure.

Das, Niladri Ranajan / Chaudhury, Kunal Narayan / Pal, Debnath

Proteomics

2024 , Page(s) e2300379

Abstract: The value of accurate protein structural models closely conforming to the experimental data is indisputable. DREAMweb deploys an improved DREAM algorithm, DREAMv2, that incorporates a tighter bound in the constraint set of the underlying optimization ... ...

Abstract	The value of accurate protein structural models closely conforming to the experimental data is indisputable. DREAMweb deploys an improved DREAM algorithm, DREAMv2, that incorporates a tighter bound in the constraint set of the underlying optimization approach. This reduces the artifacts while modeling the protein structure by solving the distance-geometry problem. DREAMv2 follows a bottom-up strategy of building smaller substructures for regions with a larger concentration of experimental bounds and consolidating them before modeling the rest of the protein structure. This improves secondary structure conformance in the final models consistent with experimental data. The proposed method efficiently models regions with sparse coverage of experimental data by reducing the possibility of artifacts compared to DREAM. To balance performance and accuracy, smaller substructures (
Language	English
Publishing date	2024-04-17
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202300379
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Article ; Online: Identification of potential edible spices as EGFR and EGFR mutant T790M/L858R inhibitors by structure-based virtual screening and molecular dynamics.

Ahmad Ansari, Iqrar / Debnath, Bimal / Kar, Saikat / Patel, Harun M / Debnath, Sudhan / Zaki, Magdi E A / Pal, Pinaki

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 5, Page(s) 2464–2481

Abstract: Epidermal growth factor receptor (EGFR) tyrosine kinases are overexpressed in several human cancers and could serve as a promising anti-cancer drug target. With this in view, the main aim of the present study was to identify spices having the potential ... ...

Abstract	Epidermal growth factor receptor (EGFR) tyrosine kinases are overexpressed in several human cancers and could serve as a promising anti-cancer drug target. With this in view, the main aim of the present study was to identify spices having the potential to inhibit EGFR tyrosine kinase. The structure-based virtual screening of spice database consisting of 1439 compounds with EGFR tyrosine kinase (PDB ID: 3W32) was carried out using Glide. Top scored 18 hits (XP Glide Score ≥ -10.0 kcal/mol) was further docked with three EGFR tyrosine kinases and three EGFR T790M/L858R mutants using AutodockVina, followed by ADME filtration. The best three hits were further refined by Molecular Dynamics (MD) simulation and MM-GBSA-based binding energy calculation. The overall docking results of the selected hits with both EGFR and EGFR T790M/L858R were quite satisfactory and showed strong binding compared to the three coligands. Detailed MD analysis of CL_07, AC_11 and AS_49 also showed the stability of the protein-ligand complexes. Moreover, the hits were drug-like, and MM-GBSA binding free energy of CL_07 and AS_49 was established to be far better. AC_11 was found to be similar to the known inhibitor Gefitinib. Most of the potential hits are available in
MeSH term(s)	Humans ; Molecular Dynamics Simulation ; ErbB Receptors/metabolism ; Spices ; Molecular Docking Simulation ; Mutation ; Protein Kinase Inhibitors/chemistry ; Lung Neoplasms/drug therapy ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Tyrosine
Chemical Substances	ErbB Receptors (EC 2.7.10.1) ; Protein Kinase Inhibitors ; Antineoplastic Agents ; Tyrosine (42HK56048U) ; EGFR protein, human (EC 2.7.10.1)
Language	English
Publishing date	2023-06-22
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2223661
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Article ; Online: Cytochrome bc1-aa3 Oxidase Supercomplex As Emerging and Potential Drug Target Against Tuberculosis.

Sindhu, Thangaraj / Debnath, Pal

Current molecular pharmacology

2021 Volume 15, Issue 2, Page(s) 380–392

Abstract: The cytochrome bc1-aa3 supercomplex plays an essential role in the cellular respiratory system of Mycobacterium Tuberculosis. It transfers electrons from menaquinol to cytochrome aa3 (Complex IV) via cytochrome bc1 (Complex III), which reduces the oxygen. ...

Abstract	The cytochrome bc1-aa3 supercomplex plays an essential role in the cellular respiratory system of Mycobacterium Tuberculosis. It transfers electrons from menaquinol to cytochrome aa3 (Complex IV) via cytochrome bc1 (Complex III), which reduces the oxygen. The electron transfer from a variety of donors into oxygen through the respiratory electron transport chain is essential to pump protons across the membrane creating an electrochemical transmembrane gradient (proton motive force, PMF) that regulates the synthesis of ATP via the oxidative phosphorylation process. Cytochrome bc1-aa3 supercomplex in M. tuberculosis is, therefore, a major drug target for antibiotic action. In recent years, several respiratory chain components have been targeted for developing new candidate drugs, illustrating the therapeutic potential of obstructing energy conversion of M. tuberculosis. The recently available cryo-EM structure of mycobacterial cytochrome bc1-aa3 supercomplex with open and closed conformations has opened new avenues for understanding its structure and function for developing more effective, new therapeutics against pulmonary tuberculosis. In this review, we discuss the role and function of several components, subunits, and drug targeting elements of the supercomplex cytochrome bc1-aa3 and its potential inhibitors in detail.
MeSH term(s)	Drug Delivery Systems ; Electron Transport Complex III ; Electron Transport Complex IV/chemistry ; Electron Transport Complex IV/metabolism ; Humans ; Mycobacterium tuberculosis/metabolism ; Oxidoreductases ; Oxygen ; Tuberculosis/drug therapy
Chemical Substances	Oxidoreductases (EC 1.-) ; Electron Transport Complex IV (EC 1.9.3.1) ; Electron Transport Complex III (EC 7.1.1.8) ; Oxygen (S88TT14065)
Language	English
Publishing date	2021-10-01
Publishing country	United Arab Emirates
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ISSN	1874-4702
ISSN (online)	1874-4702
DOI	10.2174/1874467214666210928152512
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Article ; Online: MD DaVis: interactive data visualization of protein molecular dynamics.

Maity, Dibyajyoti / Pal, Debnath

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 12, Page(s) 3299–3301

Abstract: Summary: Molecular dynamics (MD) simulations have become an integral part of biomolecular study. Most MD software suites do not include analysis tools and those which do create very basic visualizations. Molecular Dynamics Data Visualizer (MD DaVis) is ... ...

Abstract	Summary: Molecular dynamics (MD) simulations have become an integral part of biomolecular study. Most MD software suites do not include analysis tools and those which do create very basic visualizations. Molecular Dynamics Data Visualizer (MD DaVis) is a python package developed to facilitate quick comparative analysis of MD trajectories of similar proteins or the same protein under different conditions. MD DaVis can quickly generate interactive visualization from molecular dynamics trajectories with a few simple steps. Interactive plots eliminate the need to make multiple plots for comparison, improving productivity and saving time. Availability and implementation: MD DaVis is an open-source Python 3 package (https://pypi.org/project/md-davis/) distributed under MIT license. The source code is available at https://github.com/djmaity/md-davis or https://doi.org/10.5281/zenodo.6227047. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Molecular Dynamics Simulation ; Data Visualization ; Software ; Proteins
Chemical Substances	Proteins
Language	English
Publishing date	2022-11-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac314
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Article: A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreatic

Deepa Maheshvare, M / Raha, Soumyendu / König, Matthias / Pal, Debnath

bioRxiv : the preprint server for biology

2023

Abstract: The pancreas plays a critical role in maintaining glucose homeostasis through the secretion of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by the ... ...

Abstract	The pancreas plays a critical role in maintaining glucose homeostasis through the secretion of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by the pancreatic
Language	English
Publishing date	2023-03-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.10.532028
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Article: A pathway model of glucose-stimulated insulin secretion in the pancreatic

Deepa Maheshvare, M / Raha, Soumyendu / König, Matthias / Pal, Debnath

Frontiers in endocrinology

2023 Volume 14, Page(s) 1185656

Abstract	The pancreas plays a critical role in maintaining glucose homeostasis through the secretion of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by the pancreatic
MeSH term(s)	Humans ; Animals ; Mice ; Rats ; Insulin Secretion ; Reproducibility of Results ; Insulin-Secreting Cells ; Glucose/pharmacology ; Adenosine Triphosphate
Chemical Substances	Glucose (IY9XDZ35W2) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2023-08-02
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2592084-4
ISSN	1664-2392
ISSN	1664-2392
DOI	10.3389/fendo.2023.1185656
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Article ; Online: INTERPIN: A repository for intrinsic transcription termination hairpins in bacteria.

Gupta, Swati / Padmashali, Namrata / Pal, Debnath

Biochimie

2023 Volume 214, Issue Pt B, Page(s) 228–236

Abstract: The large-scale detection of putative intrinsic transcription terminators is limited to only a few bacteria currently. We discovered a group of hairpins, called cluster hairpins, present within 15 nucleotides from each other. These are expected to work ... ...

Abstract	The large-scale detection of putative intrinsic transcription terminators is limited to only a few bacteria currently. We discovered a group of hairpins, called cluster hairpins, present within 15 nucleotides from each other. These are expected to work in tandem to cause intrinsic transcription termination (ITT), while the single hairpin can do the same alone. Therefore, exploring these ITT sites and the hairpins across bacterial genomes becomes highly desirable. INTERPIN is the largest archived collection of in silico inferred ITT hairpins in bacteria, covering 12745 bacterial genomes and encompassing ten bacterial phyla for ∼25 million hairpins. Users can obtain details on operons, individual cluster, and single ITT hairpins that were screened therein. Integrated Genome Viewer (IGV) software interactively visualizes hairpin secondary and tertiary structures in the genomic context. We also discuss statistics for the occurrence of cluster or single hairpins and other termination alternatives while showing the validation of predicted hairpins against in vivo detected hairpins. The database is freely available at http://pallab.cds.iisc.ac.in/INTERPIN/. INTERPIN (database and software) can make predictions for both AT and GC-rich genomes, which has not been achieved by any other program so far. It can also be used to improve genome annotation as well as to get predictions to improve the understanding of the ITT pathway by further analysis.
MeSH term(s)	Transcription, Genetic ; Bacteria/genetics ; Genomics ; Software ; Genome, Bacterial
Language	English
Publishing date	2023-07-26
Publishing country	France
Document type	Journal Article
ZDB-ID	120345-9
ISSN	1638-6183 ; 0300-9084
ISSN (online)	1638-6183
ISSN	0300-9084
DOI	10.1016/j.biochi.2023.07.018
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