Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica – in silico approach

Abstract

Ramonda serbica Panc. is a resurrection plant that can survive long desiccation periods (extreme loss of cellular water). The accumulation of late embryogenesis abundant proteins (LEAPs) is a crucial step in desiccation tolerance mechanism. Based on in vitro studies, LEAPs can be involved in antioxidative defense, ion sequestration, structural stabilization of both membranes and enzymes during freezing or drying, while by forming intracellular proteinaceous condensates they increase structural integrity and intracellular viscosity of cells during desiccation. Here we investigated the antioxidative potential of LEAPs identified by de novo transcriptomics of R. serbica, based on their primary and secondary confirmation. In our previous work [1], we displayed the antioxidative capacity of 20 free proteogenic amino acids (FAA) through determining their hydroxyl radical (•OH, generated in Fenton reaction) scavenging rate by using electron paramagnetic resonance. These results served as a basis for generating a model for prediction of •OH scavenging activity for selected proteins. In addition, the model was built based on protein primary sequences, hydrophobicity, 3D structure and predicted solvent accessible area. Manually curated data for peptides and proteins with experimentally determined •OH scavenging rate were used for training and testing. The model was fed into machine learning algorithm and •OH scavenging potential scale was created using IC50 values. By applying our model, we classified 164 LEAPs according to their potential for •OH scavenging. Further work will focus on the experimental evaluation of the obtained model by measuring of the rate of • OH scavenging in the presence of recombinantly produced LEAPs.