Amycolatopsis sulphurea’dan Elde Edilen AsAlaDh’ın 3D Modellemesi ve Biyoinformatiği

Öz

Alanin dehidrogenaz (AlaDH) (E.C.1.4.1.1), piruvat ve alaninin birbirine dönüşümünü katalize eden bir enzimdir. Bu enzim, mikroorganizmanın sporlanması ve mikroorganizmalardaki birçok amino asit, protein ve peptidoglikan tabakasının sentezi için anahtar katalitik role sahiptir. Amycolatopsis sulphurea, Pseudonocardiaceae familyası içindeki Amycolatopsis cinsinin suşlarından biri olup, Ristosetin, Vankomisin ve Epoksiquinomisin gibi farklı antibiyotikler üretmenin yanı sıra biyoplastik (poli-laktik asit (PLA) filmlerini biyolojik olarak parçalama yeteneğine sahiptir). Amycolatopsis sulphurea'dan Alanin dehidrogenazın 3D homoloji modeli I-TASSER aracılığıyla gerçekleştirildi. L-alanin ile enzimin aktif bölge amino asitlerinin etkileşimi, AutoDock Vina programı ile in silico kenetlenerek belirlendi. Protein ikincil yapıları EMBOSS tool garnier ile tahmin edildi. AsAlaDH'nin yapısal ve fonksiyonel analizleri ve fiziko-kimyasal özelliklerinin belirlenmesi farklı biyoinformatik araçlar kullanılarak gerçekleştirilmiştir. Alanin dehidrogenazın ikincil yapısı ve çoklu hizalama analizi, AlaDH'lerin farklı mikroorganizmalardan korunmuş amino asit kalıntıları olduğunu göstermiştir.

Anahtar Kelimeler

• Alanine dehidrogenaz
• Amycolatopsis sulphurea
• 3D homoloji modelleme
• biyokatalist

Bioinformatics and 3D homology modelling of AsAlaDH from Amycolatopsis sulphurea

Abstract

Alanine dehydrogenase (AlaDH) (E.C.1.4.1.1) is an enzyme that catalyzes the interconversion of pyruvate and alanine. This enzyme has the key catalytic role for the sporulation of microorganism and synthesis of the many amino acids, proteins, and peptidoglycan layers in the microorganisms. Amycolatopsis sulphurea one of the strains of Amycolatopsis genus within the family Pseudonocardiaceae has capable to produce different antibiotics such as Ristocetin, Vancomycin, and Epoxyquinomicin as well as to biodegrade the bioplastic (poly-lactic acid (PLA) films). The 3D homology model of Alanine dehydrogenase from Amycolatopsis sulphurea was carried out through I-TASSER. The interaction of L-alanine and active site amino acids of the enzyme was determined by docking in silico via AutoDock Vina program. Protein secondary structures were predicted with EMBOSS tool garnier. Structural and functional analysis and determination of Physico-chemical properties of AsAlaDH were performed by using different bioinformatics tools. The secondary structure and multiple alignment analysis of alanine dehydrogenase displayed that there are conserved amino acid residues of AlaDH's from different microorganisms.

Keywords

• Alanine dehydrogenase
• Amycolatopsis sulphurea
• 3D homology modelling
• Biocatalyst

Kaynakça

1. Agren, D., Stehr, M., Berthold, C. L., Kapoor, S., Oehlmann, W., Singh, M., & Schneider, G. (2008). Three-dimensional structures of apo- and holo-L-alanine dehydrogenase from Mycobacterium tuberculosis reveal conformational changes upon coenzyme binding. J Mol Biol, 377(4), 1161-1173. doi:10.1016/j.jmb.2008.01.091
2. Aktaş, F. (2021). Heterologous Expression and Partial Characterization of a New Alanine Dehydrogenase from Amycolatopsis sulphurea. The Protein Journal, 40(3), 342-347. doi:10.1007/s10930-021-09982-9
3. Allaway, D., Lodwig, E. M., Crompton, L. A., Wood, M., Parsons, R., Wheeler, T. R., & Poole, P. S. (2000). Identification of alanine dehydrogenase and its role in mixed secretion of ammonium and alanine by pea bacteroids. Mol Microbiol, 36(2), 508-515. doi:10.1046/j.1365-2958.2000.01884.x
4. Buchan, D. W. A., & Jones, D. T. (2019). The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic acids research, 47(W1), W402-W407. doi:10.1093/nar/gkz297 %J Nucleic Acids Research
5. Dave, U. C., & Kadeppagari, R.-K. (2019). Alanine dehydrogenase and its applications – A review. Critical Reviews in Biotechnology, 39(5), 648-664. doi:10.1080/07388551.2019.1594153
6. Garnier, J., Osguthorpe, D. J., & Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol, 120(1), 97-120. doi:https://doi.org/10.1016/0022-2836(78)90297-8
7. Gräfe, U., Bocker, H., Reinhardt, G., Tkocz, H., & Thrum, H. (1974). [Activity of alanine dehydrogenase and production of antibiotic in cultures of Streptomyces hygroscopicus JA 6599 (author's transl)]. Z Allg Mikrobiol, 14(3), 181-192. doi:10.1002/jobm.3630140302
8. Haddad, Y., Adam, V., & Heger, Z. (2020). Ten quick tips for homology modeling of high-resolution protein 3D structures. PLOS Computational Biology, 16(4), e1007449. doi:10.1371/journal.pcbi.1007449

9. Jeong, J.-A., Baek, E.-Y., Kim, S. W., Choi, J.-S., & Oh, J.-I. (2013). Regulation of the ald Gene Encoding Alanine Dehydrogenase by AldR in Mycobacterium smegmatis. 195(16), 3610-3620. doi:10.1128/JB.00482-13 %J Journal of Bacteriology
10. Keradjopoulos, D., & Holldorf, A. W. (1979). Purification and properties of alanine dehydrogenase from Halobacterium salinarium. Biochimica et biophysica acta, 570(1), 1-10. doi:10.1016/0005-2744(79)90195-5
11. LECHEVALIER, M. P., PRAUSER, H., LABEDA, D. P., & RUAN, J.-S. (1986). Two New Genera of Nocardioform Actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. 36(1), 29-37. doi:https://doi.org/10.1099/00207713-36-1-29
12. Lee, S. D. (2009). Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis. 59(6), 1401-1404. doi:https://doi.org/10.1099/ijs.0.006577-0
13. Ling, B., Bi, S., Sun, M., Jing, Z., Li, X., & Zhang, R. (2014). Molecular dynamics simulations of mutated Mycobacterium tuberculosis L-alanine dehydrogenase to illuminate the role of key residues. J Mol Graph Model, 50, 61-70. doi:10.1016/j.jmgm.2014.03.008
14. Ling, B., Sun, M., Bi, S., Jing, Z., & Liu, Y. (2012). Molecular dynamics simulations of the coenzyme induced conformational changes of Mycobacterium tuberculosis L-alanine dehydrogenase. J Mol Graph Model, 35, 1-10. doi:10.1016/j.jmgm.2012.01.005
15. Lukežič, T., Lešnik, U., Podgoršek, A., Horvat, J., Polak, T., Šala, M., . . . Petković, H. (2013). Identification of the chelocardin biosynthetic gene cluster from Amycolatopsis sulphurea: a platform for producing novel tetracycline antibiotics. Microbiology (Reading), 159(Pt 12), 2524-2532. doi:10.1099/mic.0.070995-0
16. Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., . . . Lopez, R. (2019). The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic acids research, 47(W1), W636-W641. doi:10.1093/nar/gkz268
17. McClerren, A. L., Cooper, L. E., Quan, C., Thomas, P. M., Kelleher, N. L., & van der Donk, W. A. (2006). Discovery and in vitro biosynthesis of haloduracin, a two-component lantibiotic. 103(46), 17243-17248. doi:10.1073/pnas.0606088103 %J Proceedings of the National Academy of Sciences
18. McCowen, S. M., & Phibbs, P. V. (1974). Regulation of Alanine Dehydrogenase in Bacillus licheniformis. 118(2), 590-597.
19. Naveed, M., Ahmed, I., Khalid, N., & Mumtaz, A. S. (2014). Bioinformatics based structural characterization of glucose dehydrogenase (gdh) gene and growth promoting activity of Leclercia sp. QAU-66. Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology], 45(2), 603-611. doi:10.1590/s1517-83822014000200031
20. Nitta, Y., Yasuda, Y., Tochikubo, K., & Hachisuka, Y. (1974). L-amino acid dehydrogenases in Bacillus subtilis spores. J Bacteriol, 117(2), 588-592. doi:10.1128/jb.117.2.588-592.1974
21. Nouioui, I., Carro, L., García-López, M., Meier-Kolthoff, J. P., Woyke, T., Kyrpides, N. C., . . . Göker, M. (2018). Genome-Based Taxonomic Classification of the Phylum Actinobacteria. 9(2007). doi:10.3389/fmicb.2018.02007
22. Pernil, R., Herrero, A., & Flores, E. (2010). Catabolic Function of Compartmentalized Alanine Dehydrogenase in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120. 192(19), 5165-5172. doi:10.1128/JB.00603-10 %J Journal of Bacteriology
23. Phogosee, S., Hibino, T., Kageyama, H., & Waditee-Sirisattha, R. (2018). Bifunctional alanine dehydrogenase from the halotolerant cyanobacterium Aphanothece halophytica: characterization and molecular properties. Arch Microbiol, 200(5), 719-727. doi:10.1007/s00203-018-1481-7
24. Porumb, H., Vancea, D., Mureşan, L., Presecan, E., Lascu, I., Petrescu, I., . . . Bârzu, O. (1987). Structural and catalytic properties of L-alanine dehydrogenase from Bacillus cereus. J Biol Chem, 262(10), 4610-4615.
25. Rehm, B. H. A., & Reinecke, F. (2005). Bioinformatic Tools for Gene and Protein Sequence Analysis. In J. M. Walker & R. Rapley (Eds.), Medical Biomethods Handbook (pp. 387-407). Totowa, NJ: Humana Press.
26. Rice, P., Longden, I., & Bleasby, A. (2000). EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet, 16(6), 276-277. doi:10.1016/s0168-9525(00)02024-2
27. Saintpierre-Bonaccio, D., Amir, H., Pineau, R., Tan, G. Y. A., & Goodfellow, M. (2005). Amycolatopsis plumensis sp. nov., a novel bioactive actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil. International Journal of Systematic and Evolutionary Microbiology, 55(5), 2057-2061. doi:10.1099/ijs.0.63630-0
28. Schultz, N. A., & Benson, D. R. (1990). Enzymes of ammonia assimilation in hyphae and vesicles of Frankia sp. strain CpI1. J Bacteriol, 172(3), 1380-1384. doi:10.1128/jb.172.3.1380-1384.1990
29. Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., . . . Higgins, D. G. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. 7(1), 539. doi:https://doi.org/10.1038/msb.2011.75
30. Tan, G. Y. A., Ward, A. C., & Goodfellow, M. (2006). Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Systematic and Applied Microbiology, 29(7), 557-569. doi:https://doi.org/10.1016/j.syapm.2006.01.007
31. Tripathi, S. M., & Ramachandran, R. (2008). Crystal structures of the Mycobacterium tuberculosis secretory antigen alanine dehydrogenase (Rv2780) in apo and ternary complex forms captures “open” and “closed” enzyme conformations. 72(3), 1089-1095. doi:https://doi.org/10.1002/prot.22101
32. Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461. doi:10.1002/jcc.21334
33. Voet, D., Voet, J. G., & Pratt, C. W. (2016). Fundamentals of biochemistry life at the molecular level.
34. Wilkins, M. R., Gasteiger, E., Bairoch, A., Sanchez, J. C., Williams, K. L., Appel, R. D., & Hochstrasser, D. F. (1999). Protein identification and analysis tools in the ExPASy server. Methods in molecular biology (Clifton, N.J.).
35. Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: protein structure and function prediction. Nat Methods, 12(1), 7-8. doi:10.1038/nmeth.3213
36. Yoshida, A., & Freese, E. (1965). Enzymic properties of alanine dehydrogenase of Bacillus subtilis. Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, 96(2), 248-262. doi:https://doi.org/10.1016/0005-2787(65)90588-5
37. Zdobnov, E. M., & Apweiler, R. (2001). InterProScan – an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17(9), 847-848. doi:10.1093/bioinformatics/17.9.847 %J Bioinformatics