Abstract
Amaç: Modifiye edilmemiş amino asitler içeren ve antimikrobiyal aktiviteye sahip olan Grup IIA bakteriyosinler çok geniş bir gruptur. Bu gruptaki sakasinler, Lactobacillus sakei tarafından üretilen bakteriyosinlerdir. En iyi bilinen sakasinler Sakacin A, G, K, P ve Q'dur. Özellikle Sakacin A ve P, iyi karakterize edilmiştir. Bu çalışma, PVA polimerinin tek bir monomeri ile Sakacin P bakteriyosin arasındaki etkileşimi incelemeyi amaçlamaktadır.
Yöntem: Bu çalışmada suda çözünebilen, biyouyumlu sentetik polimerlerden PVA polimerinin tek bir monomeri ile protein yapıya sahip Sakacin P bakteriyosinin etkileşimi moleküler yerleştirme yöntemi ile incelenmiştir.
Bulgular: Moleküler docking çalışması sonucunda ligand olarak seçilen PVA'nın C2H4O monomeri ile reseptör olarak seçilen Sakacin P proteini arasında bağlanma afinitesinin varlığı belirlenmiştir.
Sonuç: Analiz sonuçlarına göre ligand ile hedef arasında güçlü bir inhibitör varlığı tespit edilmiştir. Bu nedenle bu çalışma, laboratuvarda üretilecek polimer-bakteriosin materyalleri için bir şablon görevi görebilir.
References
- 1. Gurkan-Alp AS, Buyukbingol E. Docking studies of some retinoidal compounds to RXRα protein. Journal of Faculty of Pharmacy of Ankara University. 2009;38(3):155-166.
- 2. Bransden BH, Joachain CJ. Physics of Atoms and Molecules. 2nd ed. Prentice-Hall; 2003.
- 3. Parente E, Ricciardi A. Production, recovery and purification of bacteriocins from lactic acid bacteria. Appl Microbiol Biotechnol. 1999;52(5):628-638. doi: 10.1007/s002530051570.
- 4. De Martinis ECP, Alves VF, Franco BDGM. Fundamentals and perspectives for the use of bacteriocins produced by lactic acid bacteria in meat products. Food Rev Int. 2002;18(2-3):191-208. doi: 10.1081/fri-120014688.
- 5. Eijsink VG, Skeie M, Middelhoven PH, Brurberg MB, Nes IF. Comparative studies of class IIa bacteriocins of lactic acid bacteria. Appl Environ Microbiol. 1998;64(9):3275-3281. doi: 10.1128/AEM.64.9.3275-3281.1998.
- 6. Namazi H, Mosadegh M. Preparation and properties of starch/ nanosilicate layer/ polycaprolactone composites. J Polym Environ. 2011;19(4):980-987. doi: 10.1007/s10924-011-0366-5.
- 7. Chaouat M, Le Visage C, Baille WE, et al. A novel cross-linked poly (vinyl alcohol) (PVA) for vascular grafts. Adv Funct Mater. 2008;18(19):2855-2861. doi: 10.1002/adfm.200701261.
- 8. Kumar A, Negi YS, Bhardwaj NK, Choudhary V. Synthesis and characterization of methylcellulose/ PVA based porous composite. Carbohydr Polym. 2012;88(4):1364-1372. doi: 10.1016/j.carbpol.2012.02.019.
- 9. Morris GM, Huey R, Olson AJ. Using AutoDock for ligand-receptor docking. Curr Protoc Bioinformatics. 2008;8(1):8.14. doi: 10.1002/0471250953.bi0814s24.
- 10. Huey R, Morris GM, Forli S. Using AutoDock 4 and AutoDock vina with AutoDockTools: A tutorial. California 92037-1000 USA: The Scripps Research Institute Molecular Graphics Laboratory; 2012.
- 11. Singh S, Florez H. Coronavirus disease 2019 drug discovery through molecular docking. F1000Res. 2020;9:502. doi: 10.12688/f1000research.24218.1.
- 12. Oberholser K, Proteopedia entry: Ramachandran plots. Biochemistry and Molecular Biology Education. 2010;38(6):430. doi: 10.14576/381225.1772128.
Abstract
Aim: Group IIA bacteriocins, which contain unmodified amino acids and have antimicrobial activity, are a very broad group. Sakacins in this group are bacteriocins produced by Lactobacillus sakei. The most well-known sakacins are Sakacin A, G, K, P, and Q. In particular, Sakacin A and P are well characterized. This study aims to examine the interaction between a single monomer of PVA polymer and Sakacin P bacteriocin.
Method: In t this study, the interaction of a single monomer of PVA polymer, which is among the water-soluble, biocompatible synthetic polymers, and Sakacin P bacteriocin, which has a protein structure, was investigated by molecular docking method.
Results: As a result of our molecular docking study, the presence of binding affinity between the C2H4O monomer of PVA selected as the ligand and the Sakacin P protein selected as the receptor was determined.
Conclusion: According to the results of the analysis, the presence of a strong inhibitor was detected between the ligand and the target. Therefore, this study can serve as a template for polymer-bacteriocin materials to be produced in the laboratory.
Keywords
References
- 1. Gurkan-Alp AS, Buyukbingol E. Docking studies of some retinoidal compounds to RXRα protein. Journal of Faculty of Pharmacy of Ankara University. 2009;38(3):155-166.
- 2. Bransden BH, Joachain CJ. Physics of Atoms and Molecules. 2nd ed. Prentice-Hall; 2003.
- 3. Parente E, Ricciardi A. Production, recovery and purification of bacteriocins from lactic acid bacteria. Appl Microbiol Biotechnol. 1999;52(5):628-638. doi: 10.1007/s002530051570.
- 4. De Martinis ECP, Alves VF, Franco BDGM. Fundamentals and perspectives for the use of bacteriocins produced by lactic acid bacteria in meat products. Food Rev Int. 2002;18(2-3):191-208. doi: 10.1081/fri-120014688.
- 5. Eijsink VG, Skeie M, Middelhoven PH, Brurberg MB, Nes IF. Comparative studies of class IIa bacteriocins of lactic acid bacteria. Appl Environ Microbiol. 1998;64(9):3275-3281. doi: 10.1128/AEM.64.9.3275-3281.1998.
- 6. Namazi H, Mosadegh M. Preparation and properties of starch/ nanosilicate layer/ polycaprolactone composites. J Polym Environ. 2011;19(4):980-987. doi: 10.1007/s10924-011-0366-5.
- 7. Chaouat M, Le Visage C, Baille WE, et al. A novel cross-linked poly (vinyl alcohol) (PVA) for vascular grafts. Adv Funct Mater. 2008;18(19):2855-2861. doi: 10.1002/adfm.200701261.
- 8. Kumar A, Negi YS, Bhardwaj NK, Choudhary V. Synthesis and characterization of methylcellulose/ PVA based porous composite. Carbohydr Polym. 2012;88(4):1364-1372. doi: 10.1016/j.carbpol.2012.02.019.
- 9. Morris GM, Huey R, Olson AJ. Using AutoDock for ligand-receptor docking. Curr Protoc Bioinformatics. 2008;8(1):8.14. doi: 10.1002/0471250953.bi0814s24.
- 10. Huey R, Morris GM, Forli S. Using AutoDock 4 and AutoDock vina with AutoDockTools: A tutorial. California 92037-1000 USA: The Scripps Research Institute Molecular Graphics Laboratory; 2012.
- 11. Singh S, Florez H. Coronavirus disease 2019 drug discovery through molecular docking. F1000Res. 2020;9:502. doi: 10.12688/f1000research.24218.1.
- 12. Oberholser K, Proteopedia entry: Ramachandran plots. Biochemistry and Molecular Biology Education. 2010;38(6):430. doi: 10.14576/381225.1772128.
Details
| Primary Language | English |
|---|---|
| Subjects | Clinical Sciences |
| Journal Section | Articles |
| Authors | |
| Early Pub Date | April 27, 2024 |
| Publication Date | April 30, 2024 |
| Acceptance Date | February 29, 2024 |
| Published in Issue | Year 2024 Issue: 22 |
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