Investigation of Polyvinyl Alcohol (PVA)-Sakacin P Interaction by Molecular Docking Method

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

• Sakacin P
• molecular docking
• polyvinyl alcohol

Moleküler Yerleştirme Yöntemi ile Polivinil Alkol (PVA)-Sakasin P Etkileşiminin İncelenmesi

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.

Keywords

• Sakacin P
• moleküler yerleştirme
• polivinil alkol

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