In silico explorations of bacterial mercuric reductase as an ecofriendly bioremediator for noxious mercuric intoxications.

Mercury is a major pollutant in the environment due to its high concentration in the soil. In this study, a mercuric reductase was extracted from Pseudomonas aeruginosa. The sequence of the enzyme was retrieved from the literature and structural homologs were identified. The protein bonded with Mercuric compounds and their interaction was briefly studied. Autodock Vina was used to perform a molecular docking with the target protein. Results showed that the sequence consists of most of the random coil 44.74% followed by α-helix and B-turns. Moreover, the protein was predicted to have a FAD/NAD(P)-binding domain. The virulence factor prediction using different approaches of Virulentpred and VICMpred suggested that P00392 is non-toxic. Next, the mutational analyses were performed to predict the active site residues in the resulting models and to determine mutants. The results show that the enzyme is involved in the bioremediation of mercury by using in-silico techniques. Finally, molecular docking studies were conducted on the best-selected model to find the active site residues and to generate a pattern of interaction to understand the mode of action of the substrate and its catalytic activity which refers to the binding with mercury.

[1]  A. Alasmari,et al.  Halogens engineering-based design of agonists for boosting expression of frataxin protein in Friedreich's ataxia. , 2023, European review for medical and pharmacological sciences.

[2]  A. Alasmari,et al.  Side chain inset of neurogenerative amino acids to metalloproteins: a therapeutic signature for huntingtin protein in Huntington's disease. , 2023, European review for medical and pharmacological sciences.

[3]  Malathesh Pari,et al.  Transition metal chelates of novel ligand bearing Isatin moiety: Synthesis, Structural characterization, Voltammetric analysis of heavy metals, Molecular docking and Biological evaluation , 2023, Journal of Molecular Structure.

[4]  M. Chalot,et al.  The potential of microorganisms as biomonitoring and bioremediation tools for mercury-contaminated soils. , 2023, Ecotoxicology and environmental safety.

[5]  Urooj Ali,et al.  A reverse vaccinology approach to design an mRNA-based vaccine to provoke a robust immune response against HIV-1. , 2023, Acta biochimica Polonica.

[6]  A. Alasmari,et al.  Revolutionizing treatment for toxic shock syndrome with engineered super chromones to combat antibiotic-resistant Staphylococcus aureus. , 2023, European review for medical and pharmacological sciences.

[7]  S. Mishra,et al.  A review on emerging micro and nanoplastic pollutants, heavy metals and their remediation techniques , 2023, Nanofabrication.

[8]  Metab Alharbi,et al.  Chain-Engineering-Based De Novo Drug Design against MPXVgp169 Virulent Protein of Monkeypox Virus: A Molecular Modification Approach , 2022, Bioengineering.

[9]  E. Drăgoi,et al.  A comprehensive review on bio-stimulation and bio-enhancement towards remediation of heavy metals degeneration. , 2022, Chemosphere.

[10]  Hongzhe Sun,et al.  An ensemble 3D deep-learning model to predict protein metal-binding site , 2022, Cell Reports Physical Science.

[11]  T. Kathiresan,et al.  Docking simulation and ADMET prediction based investigation on the phytochemical constituents of Noni (Morinda citrifolia) fruit as a potential anticancer drug , 2022, In Silico Pharmacology.

[12]  T. Kathiresan,et al.  Docking simulation and ADMET prediction based investigation on the phytochemical constituents of Noni (Morinda citrifolia) fruit as a potential anticancer drug , 2022, In Silico Pharmacology.

[13]  K. C. Mondal,et al.  Hunt for α-amylase from metagenome and strategies to improve its thermostability: a systematic review , 2022, World Journal of Microbiology and Biotechnology.

[14]  M. Govarthanan,et al.  An insight into the mechanisms of homeostasis in extremophiles. , 2022, Microbiological research.

[15]  Hanqing Xu,et al.  Environmental pollution, a hidden culprit for health issues , 2022, Eco-Environment & Health.

[16]  Nikita Gupta,et al.  A Review on the Genetically Engineered Microbes for Bioremediation of THMs Namely Hg and Cr , 2022, ECS Transactions.

[17]  M. Al-Ansari,et al.  Biodetoxification mercury by using a marine bacterium Marinomonas sp. RS3 and its merA gene expression under mercury stress. , 2021, Environmental research.

[18]  Hirofumi Suzuki,et al.  Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data , 2021, Protein science : a publication of the Protein Society.

[19]  H. R. Dash,et al.  Cellular and genetic mechanism of bacterial mercury resistance and their role in biogeochemistry and bioremediation. , 2021, Journal of hazardous materials.

[20]  S. Chakraborty,et al.  Optimization of heavy metal (lead) remedial activities of fungi Aspergillus penicillioides (F12) through extra cellular polymeric substances. , 2021, Chemosphere.

[21]  Diogo Santos-Martins,et al.  AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings , 2021, J. Chem. Inf. Model..

[22]  L. Sembiring,et al.  Indigeneous Streptomyces spp. isolated from Cyperus rotundus rhizosphere indicate high mercuric reductase activity as a pontential bioremediation agent , 2021 .

[23]  Samsul Hadi,et al.  Pemodelan Protein dengan Homology Modeling menggunakan SWISS-MODEL , 2020, Jurnal Jejaring Matematika dan Sains.

[24]  P. Reddy,et al.  Homology modeling and validation of bacterial superoxide dismutase enzyme, an antioxidant , 2020 .

[25]  Silvio C. E. Tosatto,et al.  The InterPro protein families and domains database: 20 years on , 2020, Nucleic Acids Res..

[26]  Silvio C. E. Tosatto,et al.  Pfam: The protein families database in 2021 , 2020, Nucleic Acids Res..

[27]  Hafiz M.N. Iqbal,et al.  Biotransformation fate and sustainable mitigation of a potentially toxic element of mercury from environmental matrices , 2020 .

[28]  B. Gworek,et al.  Mercury in the terrestrial environment: a review , 2020, Environmental Sciences Europe.

[29]  H. A. Elnasri,et al.  Computational determination of human PPARG gene: SNPs and prediction of their effect on protein functions of diabetic patients , 2020, Clinical and Translational Medicine.

[30]  Tongbin Chen,et al.  Review on remediation technologies for arsenic-contaminated soil , 2019, Frontiers of Environmental Science & Engineering.

[31]  Mohit Kumar,et al.  Perspectives on arsenic toxicity, carcinogenicity and its systemic remediation strategies , 2019, Environmental Technology & Innovation.

[32]  Muhammad Naveed,et al.  In-Silico analysis of missense SNPs in Human HPPD gene associated with Tyrosinemia type III and Hawkinsinuria , 2019, Comput. Biol. Chem..

[33]  Gopal R Periyannan,et al.  Applicability of Instability Index for In vitro Protein Stability Prediction. , 2019, Protein and peptide letters.

[34]  Daniel W. A. Buchan,et al.  The PSIPRED Protein Analysis Workbench: 20 years on , 2019, Nucleic Acids Res..

[35]  Vipin Kumar,et al.  Mercury detoxification by absorption, mercuric ion reductase, and exopolysaccharides: a comprehensive study , 2019, Environmental Science and Pollution Research.

[36]  Ludwine Casteleyn,et al.  Mercury pollution in modern times and its socio-medical consequences. , 2019, The Science of the total environment.

[37]  N. Ma,et al.  Genetic and Physiological Adaptations of Marine Bacterium Pseudomonas stutzeri 273 to Mercury Stress , 2018, Front. Microbiol..

[38]  Gabriele Ausiello,et al.  Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities , 2011, BMC Bioinformatics.

[39]  Paper in press , 1985 .

[40]  Mohammad Basyuni,et al.  The estimated of 18.1 kDa class IV small heat shock protein (sHsp) from Hevea brasiliensis using of PHYRE2 and SWISS-MODEL software , 2021 .