Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica - in silico approach
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2021
Konferencijski prilog (Objavljena verzija)
Metapodaci
Prikaz svih podataka o dokumentuApstrakt
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 se...rved 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.
Ključne reči:
Ramonda serbica Panc. / Proteins LEAPsIzvor:
Free Radical Biology and Medicine, 2021, 177Izdavač:
- Elsevier Science Inc, New York
Finansiranje / projekti:
- Ministarstvo nauke, tehnološkog razvoja i inovacija Republike Srbije, institucionalno finansiranje - 200042 (Univerzitet u Beogradu, Institut za molekularnu genetiku i genetičko inženjerstvo) (RS-200042)
- Ministarstvo nauke, tehnološkog razvoja i inovacija Republike Srbije, institucionalno finansiranje - 200053 (Univerzitet u Beogradu, Institut za multidisciplinarna istraživanja) (RS-200053)
Institucija/grupa
Institut za multidisciplinarna istraživanjaTY - CONF AU - Milić Komić, Sonja AU - Stevanović, Strahinja AU - Vidović, Marija PY - 2021 UR - http://rimsi.imsi.bg.ac.rs/handle/123456789/1491 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. PB - Elsevier Science Inc, New York C3 - Free Radical Biology and Medicine T1 - Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica - in silico approach VL - 177 UR - https://hdl.handle.net/21.15107/rcub_rimsi_1491 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.", publisher = "Elsevier Science Inc, New York", journal = "Free Radical Biology and Medicine", title = "Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica - in silico approach", volume = "177", url = "https://hdl.handle.net/21.15107/rcub_rimsi_1491" }
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 Free Radical Biology and Medicine Elsevier Science Inc, New York., 177. https://hdl.handle.net/21.15107/rcub_rimsi_1491
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 Free Radical Biology and Medicine. 2021;177. https://hdl.handle.net/21.15107/rcub_rimsi_1491 .
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 Free Radical Biology and Medicine, 177 (2021), https://hdl.handle.net/21.15107/rcub_rimsi_1491 .