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Figure 8.5: Illustration of the interaction of the phytochelatin molecules with protein 1HJO.
Figure 8.6: Illustration of the interaction of the rutin molecule with protein 1HJO.
Figure 8.7: Illustration of the interaction of the salicylic acid molecule with protein 1HJO.
Chapter 8 Metabolic and hormonal responses of medicinal and aromatic plants 313
314 Esra Uçar et al.
Glide
posenum
Glide
einternal
Glide
energy
Glide
emodel
Glide
ecoul
Glide
evdw
Table 8.2: Numerical values of the docking parameters of the molecule against protein.
Glide
hbond
Glide ligand
efficiency
score
YET Docking
Abscisic acid −. −. −. −. −. . −. −. .
Aminocyclopropane carboxylic acid −. −. −. −. −. −. −. −. .
Ascorbic acid −. −. −. −. −. . −. −. .
Benzyladenine −. −. −. −. −. −. −. −. .
Citric acid −. −. −. −. −. −. −. −. .
EDTA −. −. −. −. −. −. −. −. .
Epigallocatechin gallate −. −. −. −. −. −. −. −. .
Geldanamycin −. −. −. −. −. −. −. −. .
Glutathione −. −. −. −. −. . −. −. .
Jasmonic acid −. −. −. −. −. . −. −. .
Kinetin −. −. −. −. −. −. −. −. .
Phytochelatins −. −. −. −. −. . −. −. .
Proline −. −. −. −. −. . −. −. .
Quercetin −. −. −. −. −. . −. −. .
Radicicol −. −. −. −. −. . −. −. .
Rutin −. −. −. −. −. −. −. −. .
Salicylic acid −. −. −. −. −. . −. −. .
trans-Zeatin −. −. −. −. −. −. −. −. .
Trehalose −. −. . −. −. . −. −. .
Trolox −. −. . −. −. . −. −. .
Figure 8.8: Illustration of the interaction of the epigallocatechin gallate molecule with protein 1YET.
Chapter 8 Metabolic and hormonal responses of medicinal and aromatic plants 315
bolic processes of plants and lead to the buildup of damaging chemicals termed ROS. If
ROS accumulates, it may harm cellular membranes, proteins, and DNA.
The 1YET protein enhances the ability of plants to defend themselves against the
buildup of ROS by improving their antioxidant defense systems. This protein is critical
for intracellular signaling pathways, detects stress signals, and controls the production of genes that help plants adapt [128]. Furthermore, the 1YET protein helps to minimize the consequences of oxidative stress by maintaining the redox equilibrium in
cells (Table 8.2).
Under abiotic stress conditions, such as drought or salinity, the 1YET protein activates
mechanisms that support the retention of water within the cell. In addition, the protein regulates ion balance and alleviates the negative effects of salinity stress. Against
biotic stresses, the 1YET protein increases the production of phenolic compounds and
phytochemicals as part of the plant’s defense response.
This protein also regulates plant growth processes and energy metabolism. It increases the plant’s chances of survival by ensuring the optimal use of energy resources under stress conditions [129]. Increasing the 1YET protein through genetic engineering approaches is a promising strategy for developing plant species with high
stress tolerance in agricultural production (Figures 8.8–8.10).
The 3KDJ protein is a protein that helps plants defend themselves against environmental stress situations [130]. This protein is vital for the plant stress response and is
useful in helping plants adapt to both biotic and abiotic stressors. Abiotic stressors
are generated by environmental variables such drought, salt, high heat, cold, and ultraviolet radiation. On the other hand, biotic stresses are induced by harmful organisms, diseases, and insects [131]. The 3KDJ protein helps to correct cellular abnormalities that are produced by various stress events.
Figure 8.9: Illustration of the interaction of the geldanamycin molecule with protein 1YET.
Figure 8.10: Illustration of the interaction of the geldanamycin molecule with protein 1YET.
316 Esra Uçar et al.
ROS, which are damaging chemicals, build up in plants when they are under abiotic
stress conditions. Cell membranes, DNA, and proteins may all be harmed by these
chemicals. The 3KDJ protein is essential for detoxifying ROS and keeping cells in a state
of homeostasis [132]. This enables the plant to reduce the harmful impacts of stress and
continue to live. Furthermore, this protein modifies the plant’s metabolic activities via
controlling gene expression when the plant is under stress [133] (Table 8.3).
Under biotic stress conditions, the 3KDJ protein activates mechanisms that support the plant’s immune system. It increases the resistance of plants to harmful organisms, especially by increasing defense responses against pathogens [134]. In this process, the plant’s production of phenolic compounds and other defense metabolites
increases. In addition, this protein coordinates defense mechanisms in the plant by
regulating cellular signaling pathways [135].
Chapter 8 Metabolic and hormonal responses of medicinal and aromatic plants 317
Glide
posenum
Glide
einternal
Glide
energy
Glide
emodel
Glide
ecoul
Glide
evdw
Table 8.3: Numerical values of the docking parameters of the molecule against protein.
Glide
hbond
Glide ligand
efficiency
score
KDJ Docking
Abscisic acid −. −. −. −. −. −. −. −. .
Aminocyclopropane carboxylic acid −. −. −. −. −. −. −. −. .
Ascorbic acid −. −. −. −. −. −. −. −. .
Citric acid −. −. −. −. −. −. −. −. .
EDTA −. −. −. −. −. −. −. −. .
Jasmonic acid −. −. −. −. −. −. −. −. .
Kinetin −. −. −. −. −. . −. −. .
Radicicol −. −. −. −. −. . −. −. .
Salicylic acid −. −. −. −. −. −. −. −. .
Trehalose −. −. . −. −. . −. −. .
Figure 8.11: Illustration of the interaction of the molecule abscisic acid with protein 3KDJ.
Figure 8.12: Illustration of the interaction of the molecule abscisic acid with protein 3KDJ.
Figure 8.13: Illustration of the interaction of the molecule trehalose with protein 3KDJ.
318 Esra Uçar et al.
Increasing the 3KDJ protein through genetic modification may contribute to the
development of plants with high stress tolerance in agricultural production. Such pro-
Chapter 8 Metabolic and hormonal responses of medicinal and aromatic plants 319
teins are promising targets for maintaining plant productivity in adverse environmental conditions such as drought or salinity. In the future, a better understanding of
the molecular mechanisms of the 3KDJ protein may offer innovative solutions in the
field of plant biotechnology (Figures 8.11–8.13).
8.10 Conclusion
Plants develop various responses to stress factors at both hormonal and metabolic levels. Phytohormones such as ethylene, ABA, SA, and jasmonates function as key regulators of stress responses, while metabolic responses include the management of ROS,
osmolyte accumulation, and the activation of antioxidant defense mechanisms. These
adaptations are crucial for supporting plant survival and growth under stressful conditions.
Molecules with high binding energy to 3KDJ protein showed strong inhibitory
properties against plant stress. Molecules binding to 1YET protein showed mitigating
effects on plant stress responses by reducing ROS. Inhibition of 1HJO protein increased plant resistance under stress conditions by maintaining cellular homeostasis.
The tested molecules regulated stress signaling pathways by selectively binding to the
active sites of all three proteins. Molecular modeling of these proteins may increase
the usability of target-specific inhibitors in agricultural biotechnology.
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