In-silico evaluation of peptide hybrids of di-31 as potential plant defense modulators via activation FLS2
Keywords:
FLS2; flagelina; híbridos esteroide-péptido; defensina; defensa de plantas.Abstract
In order to manage stress, plants must balance growth and defense processes at
molecular level. Some control over these processes, would allow mankind to develop an
efficient and sustainable agriculture. Within this field, the study of defense stimulators’ response steps out as possible substituents of agrochemicals. Thus, by hybridizing the steroidal biostimulant DI-31 with the γ-core motif of the antifungal defensin MtDef4
(GRCRGFRRRC), it was intended to potentiate the steroid bioactivity. Molecular docking studies of the designed hybrids against FLS2 receptor, as a potential way for inducing the immune response in plants, were carried out along with DFT calculations
including frontier molecular orbitals analysis for the ligands; pKd values for ligand-protein complex were also estimated with the neural network NNScore 2,0. The results displayed the possibility that mono-steroidal hybrid DI31-GMA4, could be recognized by the studied receptor and, subsequently, induce the corresponding biological activity as defense stimulator.
References
WANG, W.; WANG, Z.-Y. “At the intersection of plant growth and immunity“,
Cell host & microbe. 2014, 15, 400-402. DOI 10.1016/j.chom.2014.03.014.
FIGUEROA-MACÍAS, J.P.; COLL, Y.; NÚÑEZ, M.; DÍAZ, K.; OLEA, A.F.;
ESPINOZA, L. “Plant Growth-Defense Trade-Offs: Molecular Processes Leading to
Physiological Changes“, Int. J. Mol. Sci. 2021, 22, 693-711. DOI
3390/ijms22020693.
MATILLA, M.A. Chapter 10 - “Metabolic Responses of Plants Upon Different
Plant–Pathogen Interactions. In Plant Metabolites and Regulation Under Environmental
Stress“, Ahmad, P., Ahanger, M.A., Singh, V.P., Tripathi, D.K., Alam, P., Alyemeni,
M.N., Eds.; Academic Press: 2018; pp. 195-214.
CUI, H.; TSUDA, K.; PARKER, J.E. “Effector-triggered immunity: from
pathogen perception to robust defense“, Annu. Rev. Plant Biol. 2015, 66, 487–511. DOI
1146/annurev-arplant-050213-040012.
REIMER-MICHALSKI, E.M.; CONRATH, U. “Innate immune memory in
plants“, Semin Immunol. 2016, 28, 319-327. DOI 10.1016/j.smim.2016.05.006.
GÓMEZ-GÓMEZ, L.; BOLLER, T. “FLS2: An LRR Receptor–like Kinase
Involved in the Perception of the Bacterial Elicitor Flagellin in Arabidopsis“, Molecular
Cell. 2000, 5, 1003-1011. DOI 10.1016/s1097-2765(00)80265-8.
KANYUKA, K.; RUDD, J.J. “Cell surface immune receptors: the guardians of
the plant’s extracellular spaces“, J Current opinion in plant biology. 2019, 50, 1-8. DOI
1016/j.pbi.2019.02.005.
CHECKER, V.G.; KUSHWAHA, H.R.; KUMARI, P.; YADAV, S. “Role of
Phytohormones in Plant Defense: Signaling and Cross Talk. In Molecular Aspects of
Plant-Pathogen Interaction“, Singh, A., Singh, I.K., Eds.; Springer Nature Singapore Pte
Ltd: 2018. DOI 10.1007/978-981-10-7371-7_7.
SUN, Y.; LI, L.; MACHO, A.P.; HAN, Z.; HU, Z.; ZIPFEL, C.; ZHOU, J.M.;
CHAI, J. “Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1
immune complex“, Science. 2013, 342, 624-628. DOI 10.1126/science.1243825.
LOZANO-DURÁN, R.; ZIPFEL, C. “Trade-off between growth and immunity:
Role of brassinosteroids“, Trends Plant Sci. 2015, 20, 12-19. DOI
1016/j.tplants.2014.09.003.
SAGARAM, U.S.; EL-MOUNAD, K.; BUCHKO, G.W.; PANDURANGI, R.S.;
SMITH, T.J.; SHAH, D.M.; DANFORTH, D.; BERG, H.R.; KAUR, J. “Structural and
Functional Studies of a Phosphatidic AcidBinding Antifungal Plant Defensin MtDef4:
Identification of an RGFRRR Motif Governing Fungal Cell Entry“, PLoS ONE. 2013, 8,
e82485. DOI 10.1371/journal.pone.0082485.
SHER KHAN, R.; IQBAL, A.; MALAK, R.; SHEHRYAR, K.; ATTIA, S.;
AHMED, T.; ALI KHAN, M.; ARIF, M.; MII, M. “Plant defensins: types, mechanism
of action and prospects of genetic engineering for enhanced disease resistance in
plants“, 3 Biotech. 2019, 9, 192-204. DOI 10.1007/s13205-019-1725-5.
CAMPOS, M.L.; DE SOUZA, C.M.; DE OLIVEIRA, K.B.S.; DIAS, S.C.;
FRANCO, O.L. “The role of antimicrobial peptides in plant immunity“, J Exp Bot.
, 69, 4997-5011. DOI 10.1093/jxb/ery294.
KOVALEVA, V.; BUKHTEEVA, I.; KIT, O.Y.; NESMELOVA, I.V. “Plant
Defensins from a Structural Perspective“, Int J Mol Sci. 2020, 21, 5307-5331. DOI
3390/ijms21155307.
SAGARAM, U.S.; PANDURANGI, R.; KAUR, J.; SMITH, T.J.; SHAH, D.M.
“Structure-Activity Determinants in Antifungal Plant Defensins MsDef1 and MtDef4
with Different Modes of Action against Fusariumgraminearum“, PLoS ONE 2011, 6,
e18550. DOI 10.1371/journal.pone.0018550.
WEI, H.; MOVAHEDI, A.; XU, C.; SUN, W.; WANG, P.; LI, D.; YIN, T.;
ZHUGE, Q. “Characterization, Expression Profiling, and Functional Analysis of PtDef, a Defensin-Encoding Gene From Populus trichocarpa“, Front Microbiol. 2020, 11, 106-
DOI 10.3389/fmicb.2020.00106.
FURIO, R.N.; SALAZAR, S.M.; MARTÍNEZ-ZAMORA, G.M.; COLL, Y.;
HAEL-CONRAD, V.; DÍAZ-RICCI, J.C. “Brassinosteroids promote growth, fruit
quality and protection against Botrytis on Fragaria x ananassa“, Eur J Plant Pathol.
, 154, 801-810. DOI 10.1007/s10658-019-01704-3.
MORENO-CASTILLO, E.; RAMÍREZ-ECHEMENDÍA, D.P.; HERNÁNDEZ-
CAMPOALEGRE, G.; MESA-TEJEDA, D.; COLL-MANCHADO, F.; COLL-
GARCÍA, Y. “In silico identification of new potentially active brassinosteroid
analogues“, Steroids 2018, 138, 35-42. DOI 10.1016/j.steroids.2018.06.009.
ZHOU, P.; JIN, B.; LI, H.; HUANG, S.Y. “HPEPDOCK: a web server for blind
peptide-protein docking based on a hierarchical algorithm“, Nucleic Acids Res. 2018,
, W443-W450. DOI 10.1093/nar/gky357.
HALGREN, T.A. “Merck Molecular Force Field. I. Basis, Form, Scope,
Parameterization, and Performance of MMFF94“, J. Comput. Chem. 1996, 17, 490-519.
DOI 10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-p.
SEGONZAC C; NIMCHUK ZL; BECK M; et al. “The shoot apical meristem
regulatory peptide CLV3 does not activate innate immunity“, Plant Cell. 2012, 24,
–3192. DOI 10.1105/tpc.111.091264.
TROTT, O.; OLSON, A.J. “AutoDock Vina: Improving the Speed and Accuracy of
Docking with a New Scoring Function, Efficient Optimization and Multithreading“, J.
Comput. Chem. 2010, 31, 455-461. DOI 10.1002/jcc.21334.
DURRANT, J.D.; MCCAMMON, J.A. “NNScore 2.0: a neural-network
receptor-ligand scoring function“, J Chem Inf Model. 2011, 51, 2897-2903. DOI
1021/ci2003889.
DURRANT, J.D.; MCCAMMON, J.A. “BINANA: a novel algorithm for ligand-
binding characterization“, J Mol Graph Model. 2011, 29, 888-893. DOI
1016/J.JMGM.2011.01.004.
FRISCH, M.J.; TRUCKS, G.W.; SCHLEGEL, H.B. et al. Gaussian 09,
Gaussian Inc: Wallingford, CT, USA, 2009.
BECKE, A.D. “A new mixing of Hartree–Fock and local density‐functional
theories“. 1993, 98, 1372-1377. DOI 10.1063/1.464304.
GRIMME, S.; EHRLICH, S.; GOERIGK, L. “Effect of the damping function in
dispersion corrected density functional theory“, Journal of computational chemistry.
, 32, 1456-1465. DOI 10.1002/jcc.21759.
DENNINGTON, R.; KEITH, T.; MILLAM, J. Gauss View, Semichem Inc.:
Shawnee, KS, USA, 2009.
ROBATZEK, S.; WIRTHMUELLER, L. “Mapping FLS2 function to structure:
LRRs, kinase and its working bits“, Protoplasma. 2013, 250, 671-681. DOI
1007/s00709-012-0459-6.
WEI, Y.; BALACEANU, A.; RUFIAN, J.S.; SEGONZAC, C.; ZHAO, A.;
MORCILLO, R.J.L.; MACHO, A.P. “An immune receptor complex evolved in soybean
to perceive a polymorphic bacterial flagellin“, Nat Commun. 2020, 11, 3763-3774. DOI
1038/s41467-020-17573-y.
MUELLER K.; et al. “Chimeric FLS2 receptors reveal the basis for differential
flagellin perception in Arabidopsis and Tomato“, Plant Cell. 2012, 24, 2213–2224. DOI
1105/tpc.112.096073
LEE, H.; CHAH, O.K.; SHEEN, J. “Stem-cell-triggered immunity through
CLV3p-FLS2 signalling“, Nature. 2011, 473, 376-379. DOI 10.1038/nature09958.
FURIO, R.N.; MARTÍNEZ-ZAMORA, G.M.; SALAZAr, S.M.; COLL, Y.;
PERATO, S.M.; MARTOS, G.G.; DÍAZ RICCI, J.C. “Role of calcium in the defense
response induced by brassinosteroids in strawberry plants“, Scientia Horticulturae.
, 261. DOI 10.1016/j.scienta.2019.109010.
MUELLER K; CHINCHILLA D; ALBERT M; et al. “Contamination risks in
work with synthetic peptides: flg22 as an example of a pirate in commercial peptide
preparations“, Plant Cell. 2012, 24, 3193–3197. DOI 10.1105/tpc.112.096073.
MORRIS G.M.; HUEY R.; LINDSTROM W.; SANNER M.F.; BELEW R.K.;
GOODSELL D.S.; OLSON A.J. “AutoDock4 and AutoDockTools4: automated docking
with selective receptor flexibility“, J. Comput. Chem. 2009, 30, 2785–2791. DOI
1002/jcc.21256.
NASEEM, M.; SRIVASTAVA, M.; OSMANOGLU, O.; IQBAL, J.; HOWARi,
F.M.; ALREMEITHI, F.A.; DANDEKAR, T. “Molecular Modeling of the Interaction
Between Stem Cell Peptide and Immune Receptor in Plants“, Methods Mol Biol 2020,
, 67-77. DOI 10.1007/978-1-0716-0183-9_8.
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2024 Juan Pablo Figueroa-Macías, Fidel E-Morales, Yoana Perez-Badell, Yamilet-Coll Coll
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
This journal provides immediate open access to its content, based on the principle that offering the public free access to research helps a greater global exchange of knowledge. Each author is responsible for the content of each of their articles.
