Milan Senćanski1*, Ivana Prodić1, Ana Pantelić1, and Marija Vidović1
1Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
milan.sencanski [at] imgge.bg.ac.rs
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 DNA-dehydrin 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.
Keywords: intrinsically disordered proteins, dehydrins, DNA, drought, molecular dynamics, Ramonda serbica.
Acknowledgement: This research was funded by the Ministry of Science, Technological Development and Innovation of the Republic of Serbia, grant number 451-03-47/2023-01/200042.
