Modeling and investigation of rhamnogalacturonidase enzyme interaction with appropriate substrate: Bacteroides xylanosalons bacteria, stomach microbiota

Moghadami, Foozieh; Kamelnia, Reyhane; Kamelnia, Elahe

doi:10.22034/ibhf.2024.482065.1008

Modeling and investigation of rhamnogalacturonidase enzyme interaction with appropriate substrate: Bacteroides xylanosalons bacteria, stomach microbiota

Document Type : Original Article

Authors

Foozieh moghadami ¹

Reyhane Kamelnia ²

elahe kamelnia ³

¹ Department of Biology, Payame Noor University, Tehran, Iran

² 1-Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 2-Department of Medicine, Faculty of Medicine, Mashhad Branch, Islamic Azad University, Mashhad, Iran

³ Department of biology, Faculty of sciences, Mashhad branch, Islamic Azad University, Mashhad, Iran

10.22034/ibhf.2024.482065.1008

Abstract

Bacteroides xylanosolvens, which belongs to gut microbiota digests the plant cell walls and causes the absorption of plant fibers by the human intestine. The bacterium performs this process by Rhamnogalacturonides enzyme which hydrolyses glycosidic linkages belongs to glycosile hydrolase enzymes. These enzymes digest the complex hydrocarbons such as cellulose, hemicelluloses and pectin. This protein has the role of an enzyme called Rhamnogalacturonides degradation RhiN extracted from the bacterium Bacteroides xylanosolus, and there are few reports on determining the structure of this enzyme. In this study to assessment of bacterial Rhamnogalacturonides, the structure of enzyme was modeled by modeller software (9.17) and after the selection of the best model, the energy minimization and qualitative assurance was done by computational methods. To evaluate the performance of the enzyme, the interaction with the suitable substrate (pectin) was analyzed by docking software. As results, important amino acids involved in enzyme connection to the pectin junctions were identified and the results showed that the proposed model to assess the interaction between enzyme-substrate was desirable.

Keywords

Gut microbiota

rhamnogalacturonidase

pectin

glycoside hydrolase

molecular dynamics simulation

Subjects