Dehydrins in the service of protecting the DNA helix from the aspect of molecular dynamics (MD)
Аутори
Senćanski, MilanProdić, Ivana
Pantelić, Ana
Vidović, Marija
Остала ауторства
Morić, IvanaĐorđević, Valentina
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
Метаподаци
Приказ свих података о документуАпстракт
Drought stress is one of the greatest threats to global food security, posing a major challenge
to agriculture. Understanding the molecular mechanisms underlying desiccation tolerance
in resurrection plants like Ramonda serbica Panc., can provide valuable insights for improving
crop resilience. Dehydrins are intrinsically disordered proteins known to accumulate in these
plants in response to desiccation. Among several proposed physiological roles, it has been
suggested that dehydrins can protect DNA from damage during water shortage. Here, we
have characterised dehydrins from R. serbica, selected a representative one and evaluated
its potential to interact with DNA.
Most of the R. serbica dehydrins were designated as hydrophilins (glycine content >6%;
GRAVY index <1). They exhibit a high disorder propensity, making them quite dynamic
in solution. Furthermore, they were predicted to localize in the nucleus. To examine the
potential interactions with DNA in silico, we have sel...ected a representative, highly hydrophilic
dehydrin (Gravy index: –1.29) containing a high percentage of glycine (22.6%) and charged
amino acids (lysine, glutamate and aspartate). Its 3D structures were determined using the
Phyre 2 intensive modelling and AlphaFold.
The dehydrin-DNA complex was manually adjusted, following molecular dynamic simulation
(MDS) in both cases of hydration and desiccation. To simulate complete hydration, the DNAdehydrin
complex was solvated in a water box, with final dimensions of 100×69×82 Å,
neutralised with 0.15 M NaCl. The system underwent a 10,000-step energy minimization,
consecutive 1250 ps equilibration NVE (constant number of atoms, volume and energy)
heating from 10 K to 298 K and 100 ns NPT (constant number of atoms, pressure and
temperature) MD production at 1 bar, and 1 fs integration step. In all simulations, periodic
boundary conditions (PBC) were implemented and the CHARMM36 force field was used.
The obtained results revealed that selected dehydrin can interact with both minor and major
DNA grooves. The phosphate groups from the DNA molecule form salt bridges with the
positively charged lysines from polylysine, K-segment, contributing to the complex stability.
Overall, we have provided evidence for possible dehydrin-DNA interactions. However, the
exact nature and significance of these interactions is still an area of active research in vitro.
Кључне речи:
intrinsically disordered proteins / dehydrins / DNA / drought / molecular dynamics / Ramonda serbicaИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 57-57Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Финансирање / пројекти:
- Министарство науке, технолошког развоја и иновација Републике Србије, институционално финансирање - 200042 (Универзитет у Београду, Институт за молекуларну генетику и генетичко инжењерство) (RS-MESTD-inst-2020-200042)
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Senćanski, Milan AU - Prodić, Ivana AU - Pantelić, Ana AU - Vidović, Marija PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1997 AB - Drought stress is one of the greatest threats to global food security, posing a major challenge to agriculture. Understanding the molecular mechanisms underlying desiccation tolerance in resurrection plants like Ramonda serbica Panc., can provide valuable insights for improving crop resilience. Dehydrins are intrinsically disordered proteins known to accumulate in these plants in response to desiccation. Among several proposed physiological roles, it has been suggested that dehydrins can protect DNA from damage during water shortage. Here, we have characterised dehydrins from R. serbica, selected a representative one and evaluated its potential to interact with DNA. Most of the R. serbica dehydrins were designated as hydrophilins (glycine content >6%; GRAVY index <1). They exhibit a high disorder propensity, making them quite dynamic in solution. Furthermore, they were predicted to localize in the nucleus. To examine the potential interactions with DNA in silico, we have selected a representative, highly hydrophilic dehydrin (Gravy index: –1.29) containing a high percentage of glycine (22.6%) and charged amino acids (lysine, glutamate and aspartate). Its 3D structures were determined using the Phyre 2 intensive modelling and AlphaFold. The dehydrin-DNA complex was manually adjusted, following molecular dynamic simulation (MDS) in both cases of hydration and desiccation. To simulate complete hydration, the DNAdehydrin complex was solvated in a water box, with final dimensions of 100×69×82 Å, neutralised with 0.15 M NaCl. The system underwent a 10,000-step energy minimization, consecutive 1250 ps equilibration NVE (constant number of atoms, volume and energy) heating from 10 K to 298 K and 100 ns NPT (constant number of atoms, pressure and temperature) MD production at 1 bar, and 1 fs integration step. In all simulations, periodic boundary conditions (PBC) were implemented and the CHARMM36 force field was used. The obtained results revealed that selected dehydrin can interact with both minor and major DNA grooves. The phosphate groups from the DNA molecule form salt bridges with the positively charged lysines from polylysine, K-segment, contributing to the complex stability. Overall, we have provided evidence for possible dehydrin-DNA interactions. However, the exact nature and significance of these interactions is still an area of active research in vitro. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Dehydrins in the service of protecting the DNA helix from the aspect of molecular dynamics (MD) EP - 57 SP - 57 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_1997 ER -
@conference{ author = "Senćanski, Milan and Prodić, Ivana and Pantelić, Ana and Vidović, Marija", year = "2023", abstract = "Drought stress is one of the greatest threats to global food security, posing a major challenge to agriculture. Understanding the molecular mechanisms underlying desiccation tolerance in resurrection plants like Ramonda serbica Panc., can provide valuable insights for improving crop resilience. Dehydrins are intrinsically disordered proteins known to accumulate in these plants in response to desiccation. Among several proposed physiological roles, it has been suggested that dehydrins can protect DNA from damage during water shortage. Here, we have characterised dehydrins from R. serbica, selected a representative one and evaluated its potential to interact with DNA. Most of the R. serbica dehydrins were designated as hydrophilins (glycine content >6%; GRAVY index <1). They exhibit a high disorder propensity, making them quite dynamic in solution. Furthermore, they were predicted to localize in the nucleus. To examine the potential interactions with DNA in silico, we have selected a representative, highly hydrophilic dehydrin (Gravy index: –1.29) containing a high percentage of glycine (22.6%) and charged amino acids (lysine, glutamate and aspartate). Its 3D structures were determined using the Phyre 2 intensive modelling and AlphaFold. The dehydrin-DNA complex was manually adjusted, following molecular dynamic simulation (MDS) in both cases of hydration and desiccation. To simulate complete hydration, the DNAdehydrin complex was solvated in a water box, with final dimensions of 100×69×82 Å, neutralised with 0.15 M NaCl. The system underwent a 10,000-step energy minimization, consecutive 1250 ps equilibration NVE (constant number of atoms, volume and energy) heating from 10 K to 298 K and 100 ns NPT (constant number of atoms, pressure and temperature) MD production at 1 bar, and 1 fs integration step. In all simulations, periodic boundary conditions (PBC) were implemented and the CHARMM36 force field was used. The obtained results revealed that selected dehydrin can interact with both minor and major DNA grooves. The phosphate groups from the DNA molecule form salt bridges with the positively charged lysines from polylysine, K-segment, contributing to the complex stability. Overall, we have provided evidence for possible dehydrin-DNA interactions. However, the exact nature and significance of these interactions is still an area of active research in vitro.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Dehydrins in the service of protecting the DNA helix from the aspect of molecular dynamics (MD)", pages = "57-57", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_1997" }
Senćanski, M., Prodić, I., Pantelić, A.,& Vidović, M.. (2023). Dehydrins in the service of protecting the DNA helix from the aspect of molecular dynamics (MD). in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 57-57. https://hdl.handle.net/21.15107/rcub_imagine_1997
Senćanski M, Prodić I, Pantelić A, Vidović M. Dehydrins in the service of protecting the DNA helix from the aspect of molecular dynamics (MD). in 4th Belgrade Bioinformatics Conference. 2023;4:57-57. https://hdl.handle.net/21.15107/rcub_imagine_1997 .
Senćanski, Milan, Prodić, Ivana, Pantelić, Ana, Vidović, Marija, "Dehydrins in the service of protecting the DNA helix from the aspect of molecular dynamics (MD)" in 4th Belgrade Bioinformatics Conference, 4 (2023):57-57, https://hdl.handle.net/21.15107/rcub_imagine_1997 .