Impact of mutation on podocin protein involved in type 2 nephrotic syndrome: Insights into docking and molecular dynamics simulation study

Sahu, Satya Narayan; Moharana, Maheswata; Sahu, Rojalin; Pattanayak, Subrat Kumar

doi:10.1016/j.molliq.2019.02.120

Cited by 26 publications

(3 citation statements)

References 58 publications

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“…Molecular dynamics (MD) simulations [ 68 , 69 ] were used to investigate the dynamic properties of the 6LU7-acacetin, 6Y2E-acacetin and spike RBD-acacetin systems. The root mean square deviation (RMSD) of the entire backbone atoms for the above systems was investigated using the gmx rms module.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking, ADMET properties and molecular dynamics simulation study

Moharana

Das

Sahu

et al. 2022

Journal of the Indian Chemical Society

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Section: Resultsmentioning

confidence: 99%

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking, ADMET properties and molecular dynamics simulation study

Moharana

Das

Sahu

et al. 2022

Journal of the Indian Chemical Society

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“…Moreover, GROMACS [274][275][276] and CHARMM [277,278] are valuable tools for conducting molecular dynamics simulations and free energy calculations. Furthermore, FireProt [279][280][281], FoldX [282,283], UniRep [284][285][286], and PredictSNP [287,288] offer essential features for predicting protein stability and the impact of mutations. Notably, computer software such as ScaffoldSeq [289],…”

Section: A Collaborative Approach Is the Best Approachmentioning

confidence: 99%

State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering

Chaisupa,

Wright

2023

Preprint

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Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems—biosensor-based controllers—in metabolic engineering. We also explore specifically protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We proposed that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.

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“…Mutation is a conventional way to alternate the interaction between a ligand and its receptor (Sahu, Moharana, Sahu, & Pattanayak, 2019), i.e. the binding of N-oligosaccharides on the N-terminal domain.…”

Section: Introductionmentioning

confidence: 99%

Mutation of the Flo1 flocculation protein for enhancing the oligomannose binding

Zhang¹,

Zhong²

Authorea

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Impact of mutation on podocin protein involved in type 2 nephrotic syndrome: Insights into docking and molecular dynamics simulation study

Cited by 26 publications

References 58 publications

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking, ADMET properties and molecular dynamics simulation study

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking, ADMET properties and molecular dynamics simulation study

State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering

Mutation of the Flo1 flocculation protein for enhancing the oligomannose binding

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