Improving the catalytic efficiency and dimeric stability of Cu,Zn superoxide dismutase by combining structure-guided consensus approach with site-directed mutagenesis

Kumar, Sachin; Bhardwaj, Vijay Kumar; Guleria, Shweta; Purohit, Rituraj; Kumar, Sanjay

doi:10.1016/j.bbabio.2021.148505

Cited by 8 publications

(9 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Cluster analysis is a method to reveal major conformational changes in protein structure during MD simulation. 40–42 We observed 51 clusters each for BRD3-BD2_Apo, JQ-1, LY294002, BCH14, and BCH4 complexes, while the BCH12 complex only showed 48 clusters (Fig. 5).…”

Section: Resultsmentioning

confidence: 86%

Evaluation of plant-derived semi-synthetic molecules against BRD3-BD2 protein: a computational strategy to combat breast cancer

Kumar

Bhardwaj

Singh

et al. 2022

Mol. Syst. Des. Eng.

Self Cite

View full text Add to dashboard Cite

show abstract

Section: Resultsmentioning

confidence: 86%

Evaluation of plant-derived semi-synthetic molecules against BRD3-BD2 protein: a computational strategy to combat breast cancer

Kumar

Bhardwaj

Singh

et al. 2022

Mol. Syst. Des. Eng.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The RMSF was used to measure the fluctuation of Cα atoms from their average positions 41,46,47 . We plotted the RMSF graphs of selected complexes with the residues on the x ‐axis and fluctuations on the y ‐axis for both chains (Figure 3).…”

Section: Resultsmentioning

confidence: 99%

“…The RMSF was used to measure the fluctuation of Cα atoms from their average positions. 41,46,47 We plotted the RMSF graphs of selected complexes with the residues on the x-axis and fluctuations on the y-axis for both chains (Figure 3). The DSPD3 and DSPD6 complexes showed the lowest flexibility for the crucial residues of the binding site (highlighted in Figure 3) as compared to cocrystallized ST-148 and other DSPD complexes.…”

Section: Structural Flexibility Analysismentioning

confidence: 99%

Identification of acridinedione scaffolds as potential inhibitor of DENV‐2 C protein: An in silico strategy to combat dengue

Kumar

Bhardwaj

Singh

et al. 2022

J of Cellular Biochemistry

Self Cite

View full text Add to dashboard Cite

Dengue is a prominent viral disease transmitted by mosquitoes to humans that affects mainly tropical and subtropical countries worldwide. The global spread of dengue virus (DENV) is mainly occurred by Aedes aegypti and Aedes albopictus mosquitoes. The dengue virus serotypes-2 (DENV-2) is a widely prevalent serotype of DENV, that causes the hemorrhagic fever and bleeding in the mucosa, which can be fatal. In the life cycle of DENV-2, a structural capsid (DENV-2 C) protein forms the nucleocapsid assembly and bind to the viral progeny RNA. For DENV-2 maturation, the nucleocapsid is a vital component. We used virtual ligand screening to filter out the best in-house synthesized acridinedione analogs (DSPD molecules) that could efficiently bind to DENV-2 C protein. The molecular docking and dynamics simulations studies were performed to analyze the effect of DSPD molecules on DENV-2 C protein after binding. Our findings showed that DSPD molecules strongly interacted with DENV-2 C protein, as evident from molecular interactions and several time-dependent molecular dynamics-driven analyses. Moreover, this study was also supported by the thermodynamic binding free energy and steered molecular dynamics simulations. Therefore, we intend to suggest that the DSPD3 molecule could be used as a potential therapeutic molecule against dengue complications as compared to the cocrystallized inhibitor ST-148. However, further studies are required to demonstrate the ability of DSPD3 to induce DENV-2 C tetramer formation.

show abstract

“…Biochemistry, genetics and molecular biology Study on the isolation and characterization [42][43][44][45], expression and purification [46][47][48][49][50], gene cloning, structural function analysis, improving catalytic efficiency, site-directed mutagenesis, protein crystallization, computational simulations, rational engineering to improve enzymes activity [51][52][53][54][55][56] preservation of enzymes, indigenous thermophilic exploration, cell-free enzymatic, polymerase synthesis, marine thermophiles, enzymatic purification and biodegradation [57][58][59]. The most important enzymes: Cellulose, xylanase, lipase and amylase.…”

Section: General Analysismentioning

confidence: 99%

Thermostable enzyme research advances: a bibliometric analysis

Hussian

Leong

2023

Journal of Genetic Engineering and Biotechnology

View full text Add to dashboard Cite

Thermostable enzymes are enzymes that can withstand elevated temperatures as high as 50 °C without altering their structure or distinctive features. The potential of thermostable enzymes to increase the conversion rate at high temperature has been identified as a key factor in enhancing the efficiency of industrial operations. Performing procedures at higher temperatures with thermostable enzymes minimises the risk of microbial contamination, which is one of the most significant benefits. In addition, it helps reduce substrate viscosity, improve transfer speeds, and increase solubility during reaction operations. Thermostable enzymes offer enormous industrial potential as biocatalysts, especially cellulase and xylanase, which have garnered considerable amount of interest for biodegradation and biofuel applications. As the usage of enzymes becomes more common, a range of performance-enhancing applications are being explored. This article offers a bibliometric evaluation of thermostable enzymes. Scopus databases were searched for scientific articles. The findings indicated that thermostable enzymes are widely employed in biodegradation as well as in biofuel and biomass production. Japan, the United States, China, and India, as along with the institutions affiliated with these nations, stand out as the academically most productive in the field of thermostable enzymes. This study’s analysis exposed a vast number of published papers that demonstrate the industrial potential of thermostable enzymes. These results highlight the significance of thermostable enzyme research for a variety of applications.

show abstract

Improving the catalytic efficiency and dimeric stability of Cu,Zn superoxide dismutase by combining structure-guided consensus approach with site-directed mutagenesis

Cited by 8 publications

References 40 publications

Evaluation of plant-derived semi-synthetic molecules against BRD3-BD2 protein: a computational strategy to combat breast cancer

Evaluation of plant-derived semi-synthetic molecules against BRD3-BD2 protein: a computational strategy to combat breast cancer

Identification of acridinedione scaffolds as potential inhibitor of DENV‐2 C protein: An in silico strategy to combat dengue

Thermostable enzyme research advances: a bibliometric analysis

Contact Info

Product

Resources

About