Structural characterization of cassava linamarase-linamarin enzyme complex: an integrated computational approach

Abstract

Cassava linamarase is a hydrolyzing enzyme that belongs to a glycoside hydrolase family 1 (GH1). It is responsible for breaking down linamarin to toxic cyanide. The enzyme provides a defensive mechanism for plants against herbivores and has various applications in many fields. Understanding the structure of linamarase at the molecular level is a key to avail its reaction mechanism. In this study, the three-dimensional (3D) structure of linamarase was built for the first time using homology modelling and used to study its interaction with linamarin. Molecular docking calculations established the binding and orientation nature of linamarin, while molecular dynamics (MD) simulation established protein-ligand complexes' stability. Binding-free energy based on MM/PBSA was further used to rescore the docking results. An ensemble structure was found to be relatively stable compared to the modelled structure. This study sheds light on the exploration of linamarase towards understanding its reaction mechanisms.

Communicated by Ramaswamy H. Sarma

Keywords:

• Linamarase
• Linamarin
• molecular dynamics simulation
• molecular docking
• Cassava

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The authors acknowledge The Nelson Mandela African Institution of Science and Technology (NM-AIST) through the African Development Bank (AfDB) with project 295 No. P-Z1-IA0-016 and grant No. 2100155032816 for financial support. DMS thanks the CHPC Lengau, South Africa, for the computational facility. LP thanks UDSM (DUCE) for granting study leave. LP further expresses his sincere thanks to Mr. Adam Mawenya and Ms. Joyce Martine for their dedicated assistance in computational facilities. Authors acknowledge Deogratius Geradius for reading and correcting the manuscript. FNK would also like to acknowledge funding from the German Academic Exchange Services (DAAD) for a guest professorship at TU Dresden.