Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica – in silico approach
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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.
Keywords:
desiccation tolerance / electron paramagnetic resonance (EPR) / intrinsically disordered proteins / machine learning / resurrection plants / secondary structureSource:
Annual Meeting, SFRR-E 2021 Belgrade, Serbia, 15-18 June, 2021, 214-214Funding / projects:
- LEAPSyn-SCI - Late Embryogenesis Abundant Proteins: Structural Characterisation and Interaction With Α-Synuclein (RS-ScienceFundRS-Promis-6039663)
Note:
- Organized by Society for Free Radical Research Europe (SFRR-E).
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Hemijski fakultet / Faculty of ChemistryTY - CONF AU - Milić Komić, Sonja AU - Stevanović, Strahinja AU - Vidović, Marija PY - 2021 UR - https://cherry.chem.bg.ac.rs/handle/123456789/4507 AB - 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. C3 - Annual Meeting, SFRR-E 2021 Belgrade, Serbia, 15-18 June T1 - Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica – in silico approach SP - 214 EP - 214 UR - https://hdl.handle.net/21.15107/rcub_cherry_4507 ER -
@conference{ author = "Milić Komić, Sonja and Stevanović, Strahinja and Vidović, Marija", year = "2021", 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.", journal = "Annual Meeting, SFRR-E 2021 Belgrade, Serbia, 15-18 June", title = "Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica – in silico approach", pages = "214-214", url = "https://hdl.handle.net/21.15107/rcub_cherry_4507" }
Milić Komić, S., Stevanović, S.,& Vidović, M.. (2021). Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica – in silico approach. in Annual Meeting, SFRR-E 2021 Belgrade, Serbia, 15-18 June, 214-214. https://hdl.handle.net/21.15107/rcub_cherry_4507
Milić Komić S, Stevanović S, Vidović M. Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica – in silico approach. in Annual Meeting, SFRR-E 2021 Belgrade, Serbia, 15-18 June. 2021;:214-214. https://hdl.handle.net/21.15107/rcub_cherry_4507 .
Milić Komić, Sonja, Stevanović, Strahinja, Vidović, Marija, "Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica – in silico approach" in Annual Meeting, SFRR-E 2021 Belgrade, Serbia, 15-18 June (2021):214-214, https://hdl.handle.net/21.15107/rcub_cherry_4507 .