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

Yıl 2021, Sayı: 25, 829 - 835, 31.08.2021

Fatih Aktaş

https://doi.org/10.31590/ejosat.971416

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

Öz

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.

Anahtar Kelimeler

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

Kaynakça

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