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Browsing Department of Biological Sciences by Author "Chowdhury, Shibasish"

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Ab initio Folding Simulation of the Trp-cage Mini-protein Approaches NMR Resolution

Chowdhury, Shibasish (Elsiever, 2003-03-28)

Here, we report a 100 ns molecular dynamics simulation of the folding process of a recently designed autonomous-folding mini-protein designated as tc5b with a new AMBER force field parameter set developed based on ...
Analysis of seven putative Na+/H+ antiporters of Arthrospira platensis NIES-39 using transcription profiling and in silico studies: an indication towards alkaline pH acclimation

Chowdhury, Shibasish; Bhagavatula, Vani (Springer, 2019-09)

Na+/H+ antiporters mediated pH regulation is one of the known mechanism(s), which advocates a possible role of the antiporters in the alkaline pH tolerance of Arthrospira platensis NIES-39. Seven putative Na+/H+ antiporters ...
Analysis of seven putative Na+/H+ antiporters of Arthrospira platensis NIES-39 using transcription profiling and in silico studies: an indication towards alkaline pH acclimation

Bhagavatula, Vani; Chowdhury, Shibasish (Springer, 2019-09)

Na+/H+ antiporters mediated pH regulation is one of the known mechanism(s), which advocates a possible role of the antiporters in the alkaline pH tolerance of Arthrospira platensis NIES-39. Seven putative Na+/H+ antiporters ...
Autophagy Regulated by Gain of Function Mutant p53 Enhances Proteasomal Inhibitor-Mediated Cell Death through Induction of ROS and ERK in Lung Cancer Cells

Chowdhury, Shibasish; Chowdhury, Rajdeep; Mukherjee, Sudeshna (Hindawi, 2019)

Mutations in p53, especially gain of function (GOF) mutations, are highly frequent in lung cancers and are known to facilitate tumor aggressiveness. Yet, the links between mutant GOF-p53 and lung cancers are not well ...
Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide

Chowdhury, Shibasish (Wiley, 2002-11-25)

The formation mechanism of an alanine-based peptide has been studied by all-atom molecular dynamics simulations with a recently developed all-atom point-charge force ﬁeld and the Generalize Born continuum solvent model ...
Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations

Chowdhury, Shibasish (ACS, 2004)

In this study, the detailed mechanisms of the rapid-folding Trp-cage mini-protein were investigated by extensive all-atom molecular dynamics simulations of both wild-type and mutant proteins using a recently developed ...
Common and Unique microRNAs in Multiple Carcinomas Regulate Similar Network of Pathways to Mediate Cancer Progression

Chowdhury, Rajdeep; Chowdhury, Shibasish; Majumder, Syamantak; Majumder, Syamantak (Springer Nature, 2020)

Cancer is a complex disease with a fatal outcome. Early detection of cancer, by monitoring appropriate molecular markers is very important for its therapeutic management. In this regard, the short non-coding RNA molecules, ...
Cyanobacterial Stresses: An Ecophysiological, Biotechnological and Bioinformatic Approach

Chowdhury, Shibasish (LAMBERT Academic Publishing, 2014-02-26)

From time immemorial cyanobacteria have been acquiring an inquisitive field of burgeoning research owing to their ecological adaptivity, ubiquitous presence and efficient source of compounds of biotechnological significance. ...
Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A

Chowdhury, Shibasish (ACS, 2005-04)

The folding mechanism of the G29A mutant of the B-domain of protein A (BdpA) has been studied by all-atom molecular dynamics simulation using AMBER force field (ff03) and generalized Born continuum solvent model. Started ...
Differential response of photosynthetic apparatus towards alkaline pH treatment in NIES-39 and PCC 7345 strains of Arthrospira platensis

Chowdhury, Shibasish; Bhagavatula, Vani (Springer, 2021-05)

Alkaline stress is one of the severe abiotic stresses, which is not well studied so far, especially among cyanobacteria. To affirm the characteristics of alkaline stress and the subsequent adaptive responses in Arthrospira ...
Drug Tolerant Cells: An Emerging Target With Unique Transcriptomic Features

Chowdhury, Rajdeep; Majumder, Syamantak; Chowdhury, Shibasish (Sage, 2019)

Long-term outcome of cancer therapy is often severely perturbed by the acquisition of drug resistance. Recent evidence point toward the survival of a subpopulation of tumor cells under acute drug stress that over time can ...
Dynamic alterations of H3K4me3 and H3K27me3 at ADAM17 and Jagged-1 gene promoters cause an inflammatory switch of endothelial cells

Chowdhury, Shibasish; Majumder, Syamantak (Wiley, 2021-09-14)

Histone protein modifications control the inflammatory state of many immune cells. However, how dynamic alteration in histone methylation causes endothelial inflammation and apoptosis is not clearly understood. To examine ...
Dysregulated expression but redundant function of the long non-coding RNA HOTAIR in diabetic kidney disease

Chowdhury, Shibasish; Majumder, Syamantak (Springer, 2019-08-09)

Long non-coding RNAs (lncRNAs) are garnering increasing attention for their putative roles in the pathogenesis of chronic diseases, including diabetic kidney disease (DKD). However, much about in vivo lncRNA functionality ...
Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Chowdhury, Shibasish (Taylor & Francis, 2012-05-15)

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model ...
Evolution of endonuclease IV protein family: an in silico analysis

Chowdhury, Shibasish (Springer, 2019-04-06)

DNA repair is one of the key cellular events which balances between evolvability and integrity of the genome. Endonuclease IV enzymes are class II AP endonucleases under base excision repair pathway which act on abasic ...
Evolutionary pattern of four representative DNA repair proteins across six model organisms: an in silico analysis

Chowdhury, Shibasish; Mehrotra, Rajesh (INFOFNA, 2014)

DNA repair refers to a collection of processes by which a cell identifies and corrects damage to DNA molecules that encodes its genome. In this study, we examined evolution of O6-Methylguanine DNA alkyltransferase (MGMT), ...
Exploring the Structural Repertoire of Guanine-Rich DNA Sequences: Computer Modelling Studies

Chowdhury, Shibasish (Elsiever, 1999)
Fs-21 Peptides Can Form Both Single Helix and Helix−Turn−Helix

Chowdhury, Shibasish (ACS, 2004)

Detailed folding processes and mechanisms of two alanine-based peptides (Fs-21 and MABA-Fs) were investigated by all atom molecular dynamic simulation with a new AMBER force field and Generalized Born continuum solvent ...
G-Quadruplex Structure Can Be Stable with Only Some Coordination Sites Being Occupied by Cations: A Six-Nanosecond Molecular Dynamics Study

Chowdhury, Shibasish (ACS, 2001)

Guanine tetrads are formed spontaneously by guanine rich sequences in the presence of certain cations. Various quadruplex helical structures, stabilized by such tetrads, apparently play an important biological role in vivo. ...
A global transcriptomic pipeline decoding core network of genes involved in stages leading to acquisition of drug-resistance to cisplatin in osteosarcoma cells

Chowdhury, Rajdeep; Chowdhury, Shibasish; Majumder, Syamantak; Mukherjee, Sudeshna (OUP, 2019)

Traditional cancer therapy is focused on eradicating fast proliferating population of tumor cells. However, existing evidences suggest survival of sub-population of cancer cells that can resist chemotherapy by entering a ...

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