با همکاری مشترک دانشگاه پیام نور و انجمن فیزیولوژی و فارماکولوژی ایران

نوع مقاله : مقاله پژوهشی

نویسندگان

1 . دکتری، گروه علوم زیست‌شناسی، دانشکده علوم، دانشگاه پیام‌نور، تهران

2 دانشیار، پژوهشکده مواد و سوخت هسته‌ای، پژوهشگاه علوم و فنون هسته‌ای، سازمان انرژی اتمی، تهران

3 . استاد، گروه علوم زیست‌شناسی، دانشگاه پیام نور، تهران

4 استادیار، آزمایشگاه شیمی نوروارگانیک، مؤسسه بیوشیمی و بیوفیزیک (IBB)، دانشگاه تهران، تهران، ایران و گروه زیست‌شناسی، دانشکده علوم، دانشگاه زنجان

چکیده

چکیده
اسیدیتیوباسیلوس فرواکسیدانس یک باکتری اسیدوفیل بوده که در فرایند بیولیچینگ فلزات دخیل می باشد. Cytochrome c552 (Cyc1) یک پروتئین پری­پلاسمی در این باکتری است که نقش کلیدی در انتقال الکترون در زنجیره تنفسی دارد. حضور هِم A و B در ساختار Cyc1 و نقش آن در دریافت الکترون از پروتئین قبلی (Cyc2) و انتقال آن به پروتئین بعدی (CcO)، دلیل اصلی انتخاب این پروتئین است. در این تحقیق، با هدف بهبود فرآیند بیولیچینگ، گلوتامات 122 و هیستیدین 54 Cyc1 برای جهش نقطه‌ای در مطالعات بیوانفورماتیک انتخاب شد. ابتدا جهش‌ها توسط نرم‌افزار پایمول انجام و شبیه ‌سازی دینامیک مولکولی برای پروتئین‌های وحشی و جهش ‌یافته‌ E122D و H54I در Cyc1 صورت گرفت. تغییرات ساختار فضایی پروتئین‌های وحشی و جهش‌ یافته‌ توسط آنالیزهایRMSD ،RMSF ، Rg، SASA و پیوندهای هیدروژنی انجام شد. نتایج حاکی از پایداری دو پروتئین جهش‌ یافته پس از پایان شبیه ‌سازی بود. با تبدیل گلوتامات 122 به آسپارتات، یک مولکول اسیدی، اسیدی‌تر ‌شده و با کاهش بیش ‌از پیش پتانسیل ردوکس در مرکز راستی­سیانین، باعث سرعت انتقال الکترون به Cyc1 خواهد شد. همچنین، با کاهش پتانسیل ردوکس در محل جهش سرعت انتقال الکترون به هِم A نیز افزایش خواهد یافت. در صورت تبدیل هیستیدین 54 به ایزولوسین، حلقه ایمیدازول الکترواستاتیک به اسیدآمینه­ای باریشه بدون بار تغییر کرده و درنتیجه منجر به تشکیل یک پیوند هیدروژنه قوی بین دو اسیدآمینه می‌شود. بنابراین، انتقال الکترون بین Cyc1 و CcO از طریق یک مولکول آب (W79) بهبود یافته و به­دنبال آن احتمالاً سرعت بیولیچینگ افزایش خواهد یافت.
 

کلیدواژه‌ها

 
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.