Document Type : Article
Authors
1 1. Ph. D., Department of Science, Payame Noor University, Tehran, Iran
2 . Associate Professor, Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
3 . Professor, Department of Biology, Payame Noor University, Tehran, Iran
4 Assistant Professor, Laboratory of Neuro-organic Chemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran and Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran
Abstract
Abstract
Acidithiobacillus ferrooxidans (Af) is an acidophilic bacterium involved in the bioleaching process. Cytochrome c552 (Cyc1) is a periplasmic protein that has a key role in the electron transportation in the respiratory chain. The presence of both heme A and B in the Cyc1 structure and its role in taking electrons from the previous protein and electron transfer to the next protein is the main reason for choosing this protein. In this research, with purpose of improving the bioleaching process, glutamate 122 and histidine 54 Cyc1 were selected for point mutation in bioinformatics studies. Mutations were performed by PYMOL software and simulated molecular dynamics for wild proteins, and mutant E122D, H54I in Cyc1. The conformational changes of mutated protein were investigated by SASA, Rg, NH bond analysis. Our results confirmed that the mutated proteins retained its stability during the simulation. By converting glutamate to aspartate, an acid molecule changed into a more acidic molecule leading to the further decreased redox potential at the rusticyanin midpoint resulted into the improved electron transfer from the Rcy to Cyc1 . This will also cause the increased electron transfer rate to heme A. In the case of converting histidine 54 to isoleucine, an electrostatic imidazole loop changed into an amino acid with the root of R with lack of charge which leads to the formation of a stronger hydrogen bond between the two amino acids. Therefore, probably the electron transfers between Cyc1 and CcO is improved through a water molecule (W79) leading to increased bioleaching rate.
Keywords
References
Abergel, C.; Nitschke, W.; Malarte, G.; Bruschi, M.; Claverie, J.-M.; Giudici-Orticoni, M.-T. (2003). The structure of Acidithiobacillus ferrooxidans c 4-cytochrome: a model for complex-induced electron transfer tuning. Structure; 11(5): 547-555.
Abergel, C.; Nitschke, W.; Malarte, G.; Bruschi, M.; Claverie, J.-M.; Giudici-Orticoni, M.-T. (2003). The structure of Acidithiobacillus ferrooxidans c4-cytochrome: a model for complex-induced electron transfer tuning. Structure; 11(5): 547-555.
Appia-Ayme, C.; Guiliani, N.; Ratouchniak, J.; Bonnefoy, V. (1999). Characterization of an Operon Encoding Two c-Type Cytochromes, an aa3-Type Cytochrome Oxidase, and Rusticyanin in Thiobacillus ferrooxidansATCC 33020. Applied and environmental microbiology; 65(11): 4781-4787.
Appia-Ayme, C.; Quatrini, R.; Denis, Y.; Denizot, F.; Silver, S. (2006). Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans. Hydrometallurgy;83(1-4): 273-280.
Barrett, M. L.; Harvey, I.; Sundararajan, M.; Surendran, R. (2006).Atomic resolution crystal structures, EXAFS, and quantum chemical studies of rusticyanin and its two mutants provide insight into its unusual properties. Biochemistry; 45(9): 2927-2939.
Benkert, P.; Künzli, M. Schwede, T. (2009). QMEAN server for protein model quality estimation. Nucleic acids research; 37(2): 510-514.
Bhatti, T. M.; Vuorinen, A.; Lehtinen, M.; O. H. Tuovinen. (1998). Dissolution of uraninite in acid solutions. Journal of Chemical Technology and Biotechnology; 73(3): 259-263.
Chen, L.; Gavini, N.; Tsuruta, H.; Eliezer, D.;... (1994). MgATP-induced conformational changes in the iron protein from Azotobacter vinelandii, as studied by small-angle x-ray scattering. Journal of Biological Chemistry; 269(5): 3290-3294.
Donati, E. R.; Sand, W. (2007) Microbial processing of metal sulfides. Springer.
Donati, E.; Pogliani, C.; Boiardi, J. (1997). Anaerobic leaching of covellite by Thiobacillus ferrooxidans. Applied Microbiology and Biotechnology; 47(6), 636-639.
Eisenberg, D.; Lüthy, R.; Bowie, J. U. (1997). [20] VERIFY3D: assessment of protein models with three-dimensional profiles. in Methods in enzymology; 277: 396-404.
Er, TK.; Chen, CC.; Liu, YY. (2011). Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif. BMC structural biology; 11(1): 43.
Farahmand, S.; Fatemi, F.; Haji Hosseini, R. (2019). [ Sequencing of the rus gene before and after the mutation with DES in the bacterial Acidithiobacillus ferrooxidans sp. FJ2] Nova Biologica Reperta]; in press.
Fatemi, F.; Miri, S.; Jahani, S. (2017). Effect of metal sulfide pulp density on gene expression of electron transporters in Acidithiobacillus sp. FJ2. Archives of microbiology; 199(4): 521-530.
Fatemi, F.; Rashidi, A.; Jahani, S. (2015). Isolation and identification of native sulfuroxidizing bacterium capable of uranium extraction. Progress in Biological Sciences; 5(2): 207-221.
Ghasemi, F.; Zomorodipour, A.; Karkhane, A. A.; Khorramizadeh, M. R. (2016). In silico designing of hyper-glycosylated analogs for the human coagulation factor IX. Journal of Molecular Graphics and Modelling; 68: 39-47.
Goodin, D. B.; McRee, D. E. (1993). The Asp-His-iron triad of cytochrome c peroxidase controls the reduction potential electronic structure, and coupling of the tryptophan free radical to the heme. Biochemistry; 32(13): 3313-3324.
Hess, B.; Kutzner, C.; Van Der Spoel, D. Lindahl, E. (2008). GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of chemical theory and computation; 4(3): 435-447.
Jafarpoor, R.; Fatemi, F.; Mehrnejad, F. (2018).Investigation the UV Effect on Uranium Bioleaching Process in Acidithiobacillus sp FJ2 and its Possible Consequences on the CoxB Gene Sequence. Biological Journal of Microorganisms; 7(27): 95-111.
Kanbi, L. D.; Antonyuk, S.; Hough, M. A.; Hall, J. F.; Dodd, F. E.; Hasnain, S. S. (2002). Crystal structures of the Met148Leu and Ser86Asp mutants of rusticyanin from Thiobacillus ferrooxidans: insights into the structural relationship with the cupredoxins and the multi copper proteins. Journal of molecular biology; 320(2): 263-275.
Lüthen, H.; Böttger, M. (1993). Hexachloroiridate IV as an electron acceptor for a plasmalemma redox system in maize roots. Plant physiology; 86(4): 1044-1047.
Muneeswaran, G.; Pandiaraj, M.; Kartheeswaran, S.; Sankaralingam, M.; Muthukumar, K.; Karunakaran, C. (2018). Molecular dynamics simulation approach to explore atomistic molecular mechanism of peroxidase activity of apoptotic cytochrome c mutants. Informatics in Medicine Unlocked; 11: 51-60.
Patra, M. C.; Pradhan, S. K.; Rath, S. N.; Maharana, J. (2013). Structural Analysis of Respirasomes in Electron Transfer Pathway of Acidithiobacillus ferrooxidans: A Computer-Aided Molecular Designing Study. ISRN Biophysic.
Quatrini, R.; Appia-Ayme, C.; Denis, Y.; Ratouchniak, J. (2006). Insights into the iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling. Hydrometallurgy; 83(1-4): 263-272.
Sand, W.; Gehrke T.; Jozsa, P.G.; Schippers, A. (2001). (Bio) chemistry of bacterial leaching-direct vs. indirect bioleaching. Hydrometallurgy; 59(2): 159-175.
Shu, C.; Xiao, K.; Sun, X. (2017). Structural Basis for the Influence of A1, 5A, and W51W57 Mutations on the Conductivity of the Geobacter sulfurreducens Pili. Crystals; 8(1): 10.
Smith, J. J.; Riddle, M. (2009). Sewage disposal and wildlife health in Antarctica. in Health of Antarctic Wildlife: Springer. pp. 271-315.
Srikumar, P.; Rohini, K. (2013). Exploring the structural insights on human laforin mutation K87A in Lafora disease-a molecular dynamics study. Applied biochemistry and biotechnology; 171(4): 874-882.
Tributsch, H. (2001). Direct versus indirect bioleaching. Hydrometallurgy; 59(2): 177-185.
Vera, M.; Schippers, A.; Sand, W. (2013). Progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation-part A. Applied Microbiology and Biotechnology; 97(17): 7529-7541.
Voet, D.; Voet, J. G.; Pratt, C. W. (2016). Fundamentals of biochemistry: life at the molecular level. Wiley New York.
Wang, W.; Xia, M.; Chen, J.; Deng, F. (2016).Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboretum. Data in brief; 9: 345-348.
Wiederstein, M.; Sippl, M. J. (2007). ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic acids research; 35 (2): 407-410.
Zhou, H.-X. (1994). Effects of mutations and complex formation on the reduction potentials of cytochrome c and cytochrome c peroxidase. Journal of the American Chemical Society; 116(23): 10362-10375.
References
Abergel, C.; Nitschke, W.; Malarte, G.; Bruschi, M.; Claverie, J.-M.; Giudici-Orticoni, M.-T. (2003). The structure of Acidithiobacillus ferrooxidans c 4-cytochrome: a model for complex-induced electron transfer tuning. Structure; 11(5): 547-555.
Abergel, C.; Nitschke, W.; Malarte, G.; Bruschi, M.; Claverie, J.-M.; Giudici-Orticoni, M.-T. (2003). The structure of Acidithiobacillus ferrooxidans c4-cytochrome: a model for complex-induced electron transfer tuning. Structure; 11(5): 547-555.
Appia-Ayme, C.; Guiliani, N.; Ratouchniak, J.; Bonnefoy, V. (1999). Characterization of an Operon Encoding Two c-Type Cytochromes, an aa3-Type Cytochrome Oxidase, and Rusticyanin in Thiobacillus ferrooxidansATCC 33020. Applied and environmental microbiology; 65(11): 4781-4787.
Appia-Ayme, C.; Quatrini, R.; Denis, Y.; Denizot, F.; Silver, S. (2006). Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans. Hydrometallurgy;83(1-4): 273-280.
Barrett, M. L.; Harvey, I.; Sundararajan, M.; Surendran, R. (2006).Atomic resolution crystal structures, EXAFS, and quantum chemical studies of rusticyanin and its two mutants provide insight into its unusual properties. Biochemistry; 45(9): 2927-2939.
Benkert, P.; Künzli, M. Schwede, T. (2009). QMEAN server for protein model quality estimation. Nucleic acids research; 37(2): 510-514.
Bhatti, T. M.; Vuorinen, A.; Lehtinen, M.; O. H. Tuovinen. (1998). Dissolution of uraninite in acid solutions. Journal of Chemical Technology and Biotechnology; 73(3): 259-263.
Chen, L.; Gavini, N.; Tsuruta, H.; Eliezer, D.;... (1994). MgATP-induced conformational changes in the iron protein from Azotobacter vinelandii, as studied by small-angle x-ray scattering. Journal of Biological Chemistry; 269(5): 3290-3294.
Donati, E. R.; Sand, W. (2007) Microbial processing of metal sulfides. Springer.
Donati, E.; Pogliani, C.; Boiardi, J. (1997). Anaerobic leaching of covellite by Thiobacillus ferrooxidans. Applied Microbiology and Biotechnology; 47(6), 636-639.
Eisenberg, D.; Lüthy, R.; Bowie, J. U. (1997). [20] VERIFY3D: assessment of protein models with three-dimensional profiles. in Methods in enzymology; 277: 396-404.
Er, TK.; Chen, CC.; Liu, YY. (2011). Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif. BMC structural biology; 11(1): 43.
Farahmand, S.; Fatemi, F.; Haji Hosseini, R. (2019). [ Sequencing of the rus gene before and after the mutation with DES in the bacterial Acidithiobacillus ferrooxidans sp. FJ2] Nova Biologica Reperta]; in press.
Fatemi, F.; Miri, S.; Jahani, S. (2017). Effect of metal sulfide pulp density on gene expression of electron transporters in Acidithiobacillus sp. FJ2. Archives of microbiology; 199(4): 521-530.
Fatemi, F.; Rashidi, A.; Jahani, S. (2015). Isolation and identification of native sulfuroxidizing bacterium capable of uranium extraction. Progress in Biological Sciences; 5(2): 207-221.
Ghasemi, F.; Zomorodipour, A.; Karkhane, A. A.; Khorramizadeh, M. R. (2016). In silico designing of hyper-glycosylated analogs for the human coagulation factor IX. Journal of Molecular Graphics and Modelling; 68: 39-47.
Goodin, D. B.; McRee, D. E. (1993). The Asp-His-iron triad of cytochrome c peroxidase controls the reduction potential electronic structure, and coupling of the tryptophan free radical to the heme. Biochemistry; 32(13): 3313-3324.
Hess, B.; Kutzner, C.; Van Der Spoel, D. Lindahl, E. (2008). GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of chemical theory and computation; 4(3): 435-447.
Jafarpoor, R.; Fatemi, F.; Mehrnejad, F. (2018).Investigation the UV Effect on Uranium Bioleaching Process in Acidithiobacillus sp FJ2 and its Possible Consequences on the CoxB Gene Sequence. Biological Journal of Microorganisms; 7(27): 95-111.
Kanbi, L. D.; Antonyuk, S.; Hough, M. A.; Hall, J. F.; Dodd, F. E.; Hasnain, S. S. (2002). Crystal structures of the Met148Leu and Ser86Asp mutants of rusticyanin from Thiobacillus ferrooxidans: insights into the structural relationship with the cupredoxins and the multi copper proteins. Journal of molecular biology; 320(2): 263-275.
Lüthen, H.; Böttger, M. (1993). Hexachloroiridate IV as an electron acceptor for a plasmalemma redox system in maize roots. Plant physiology; 86(4): 1044-1047.
Muneeswaran, G.; Pandiaraj, M.; Kartheeswaran, S.; Sankaralingam, M.; Muthukumar, K.; Karunakaran, C. (2018). Molecular dynamics simulation approach to explore atomistic molecular mechanism of peroxidase activity of apoptotic cytochrome c mutants. Informatics in Medicine Unlocked; 11: 51-60.
Patra, M. C.; Pradhan, S. K.; Rath, S. N.; Maharana, J. (2013). Structural Analysis of Respirasomes in Electron Transfer Pathway of Acidithiobacillus ferrooxidans: A Computer-Aided Molecular Designing Study. ISRN Biophysic.
Quatrini, R.; Appia-Ayme, C.; Denis, Y.; Ratouchniak, J. (2006). Insights into the iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling. Hydrometallurgy; 83(1-4): 263-272.
Sand, W.; Gehrke T.; Jozsa, P.G.; Schippers, A. (2001). (Bio) chemistry of bacterial leaching-direct vs. indirect bioleaching. Hydrometallurgy; 59(2): 159-175.
Shu, C.; Xiao, K.; Sun, X. (2017). Structural Basis for the Influence of A1, 5A, and W51W57 Mutations on the Conductivity of the Geobacter sulfurreducens Pili. Crystals; 8(1): 10.
Smith, J. J.; Riddle, M. (2009). Sewage disposal and wildlife health in Antarctica. in Health of Antarctic Wildlife: Springer. pp. 271-315.
Srikumar, P.; Rohini, K. (2013). Exploring the structural insights on human laforin mutation K87A in Lafora disease-a molecular dynamics study. Applied biochemistry and biotechnology; 171(4): 874-882.
Tributsch, H. (2001). Direct versus indirect bioleaching. Hydrometallurgy; 59(2): 177-185.
Vera, M.; Schippers, A.; Sand, W. (2013). Progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation-part A. Applied Microbiology and Biotechnology; 97(17): 7529-7541.
Voet, D.; Voet, J. G.; Pratt, C. W. (2016). Fundamentals of biochemistry: life at the molecular level. Wiley New York.
Wang, W.; Xia, M.; Chen, J.; Deng, F. (2016).Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboretum. Data in brief; 9: 345-348.
Wiederstein, M.; Sippl, M. J. (2007). ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic acids research; 35 (2): 407-410.
Zhou, H.-X. (1994). Effects of mutations and complex formation on the reduction potentials of cytochrome c and cytochrome c peroxidase. Journal of the American Chemical Society; 116(23): 10362-10375.
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