Biochemical, molecular and in silico characterization of arsenate reductase from Bacillus thuringiensis KPWP1 tolerant to salt, arsenic and a wide range of pH

2021 ◽  
Vol 204 (1) ◽  
Author(s):  
Paromita Banerjee ◽  
Ananya Chatterjee ◽  
Sushmita Jha ◽  
Nirbhay K. Bhadani ◽  
Partha P. Datta ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
In Silico ◽  
Arsenate Reductase ◽  
Wide Range ◽  
In Silico Characterization

scholarly journals Identification and in silico Characterization of Deleterious Single Nucleotide Variations in Human ZP2 Gene

2021 ◽  
Vol 9 ◽  
Author(s):  
Neha Rajput ◽  
Gagandeep Kaur Gahlay
Keyword(s):  
In Silico ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Computational Tools ◽  
Coding Regions ◽  
Wide Range ◽  
Genes Encoding ◽  
In Silico Characterization ◽  
Dbsnp Database

ZP2, an important component of the zona matrix, surrounds mammalian oocytes and facilitates fertilization. Recently, some studies have documented the association of mutations in genes encoding the zona matrix with the infertile status of human females. Single nucleotide polymorphisms are the most common type of genetic variations observed in a population and as per the dbSNP database, around 5,152 SNPs are reported to exist in the human ZP2 (hZP2) gene. Although a wide range of computational tools are publicly available, yet no computational studies have been done to date to identify and analyze structural and functional effects of deleterious SNPs on hZP2. In this study, we conducted a comprehensive in silico analysis of all the SNPs found in hZP2. Six different computational tools including SIFT and PolyPhen-2 predicted 18 common nsSNPs as deleterious of which 12 were predicted to most likely affect the structure/functional properties. These were either present in the N-term region crucial for sperm-zona interaction or in the zona domain. 31 additional SNPs in both coding and non-coding regions were also identified. Interestingly, some of these SNPs have been found to be present in infertile females in some recent studies.

scholarly journals Biochemical, molecular and in silico characterization of arsenate reductase from pH, salt and arsenic tolerant Bacillus thuringiensis KPWP1

2021 ◽  
Author(s):  
Paromita Banerjee ◽  
Ananya Chatterjee ◽  
Sushmita Jha ◽  
Nirbhay Bhadani ◽  
Partha Datta ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Bacillus Subtilis ◽  
Surface Water ◽  
Bacillus Thuringiensis ◽  
Bacillus Cereus ◽  
Binding Site ◽  
In Silico ◽  
Arsenate Tolerance ◽  
In Silico Characterization

Abstract The objective of the present study was to characterize aresenate reductase of pH, salt and arsenate tolerant Bacillus thuringiensis KPWP1, isolated from contaminated surface water. Interestingly, it was found that the arsC, arsB and arsR genes involved in arsenate tolerance are distributed in the genome of KPWP1. The inducible arsC gene was cloned, expressed and the purified ArsC protein showed profound enzyme activity with the KM and Kcat values as 25 µM and 0.00119 s− 1, respectively. In silico studies of KPWP1 ArsC revealed that in spite of 19–26% differences in gene sequences, the ArsC proteins of Bacillus thuringiensis, Bacillus subtilis and Bacillus cereus are structurally conserved and KPWP1 ArsC structure is close to nature. Docking and analysis of binding site showed that arsenate ion interacts with three cysteine residues of ArsC of KPWP1and predicts that the ArsC from B. thuringiensis reduces arsenate by using the triple Cys redox relay mechanism.

IN VITRO/IN SILICO CHARACTERIZATION OF ACTIVE AND PASSIVE STRESSES IN CARDIAC MUSCLE

2012 ◽  
Vol 10 (2) ◽  
pp. 171-188 ◽  
Author(s):  
Markus Boel ◽  
Oscar J. Abilez ◽  
Ahmed N Assar ◽  
Christopher K. Zarins ◽  
Ellen Kuhl
Keyword(s):  
Cardiac Muscle ◽  
In Silico ◽  
In Silico Characterization

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

scholarly journals In silico characterization of masitinib interaction with SARS‐CoV‐2 main protease

ChemMedChem ◽  
2021 ◽  
Author(s):  
Ulises Martínez-Ortega ◽  
Diego I. Figueroa-Figueroa ◽  
Francisco Hernández-Luis ◽  
Rodrigo Aguayo-Ortiz
Keyword(s):  
In Silico ◽  
Main Protease ◽  
In Silico Characterization

scholarly journals In silico characterization of mutations circulating in SARS-CoV-2 structural proteins

2021 ◽  
pp. 1-16
Author(s):  
Neha Periwal ◽  
Shravan B. Rathod ◽  
Ranjan Pal ◽  
Priya Sharma ◽  
Lata Nebhnani ◽  
...  
Keyword(s):  
In Silico ◽  
Structural Proteins ◽  
In Silico Characterization

Effect and in silico characterization of genetic variants associated with severe spermatogenic disorders in a large Iberian cohort

Andrology ◽  
2021 ◽  
Author(s):  
Miriam Cerván‐Martín ◽  
Lara Bossini‐Castillo ◽  
Rocío Rivera‐Egea ◽  
Nicolás Garrido ◽  
Saturnino Luján ◽  
...  
Keyword(s):  
Genetic Variants ◽  
In Silico ◽  
In Silico Characterization

scholarly journals Genome-wide identification and in silico characterization of chitinase gene family in Foxtail millet (Setaria italica)

2020 ◽  
Author(s):  
Motukuri S. R. Krishna ◽  
Nerella Dheeraj ◽  
Bathuru Jayasree ◽  
Chodisetty Bhavya ◽  
Nallamothu Jaswanthi
Keyword(s):  
Gene Family ◽  
In Silico ◽  
Foxtail Millet ◽  
Chitinase Gene ◽  
Setaria Italica ◽  
Genome Wide ◽  
In Silico Characterization
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