Modeling of Protein–Protein Interactions in Cytokinin Signal Transduction
Abstract
:1. Introduction
2. Results and Discussion
2.1. Dimerization Interfaces of the Sensor Module
2.2. HisKA (DHpD) Domain Dimerization Interfaces
2.3. Receptor–Phosphotransmitter Interactions
2.4. HPt–HPt Interface and Its Comparison to the HPt–HKrd Interface
2.5. RRrd–HPt Interface and Its Comparison to AHP–AHKrd Interface
2.6. Effect of Phosphorylation on the HKrd–HPt Interactions
3. Materials and Methods
3.1. Homology Modeling
3.2. Structure Optimization, Validation, and Modification
3.3. Interface Properties Investigation
3.4. Surface Coloring
3.5. Protein–Protein Docking
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
CK | Cytokinin |
MSP | Multistep phosphorelay system |
HK | Histidine kinase |
HPt | Histidine containing phosphotransfer protein (phosphotransmitter) |
RR | Response regulator |
TCS | Two component system |
SM | Sensor module |
TM | Transmembrane region |
HisKA | HK-dimerization domain |
RD | Receiver domain |
PPI | Protein–protein interaction |
ASA | Accessible surface area |
BSA | Buried surface area |
PQR | PQR file is a PDB file with the temperature and occupancy columns replaced by columns containing the per-atom charge (Q) and radius (R) |
aa | Amino acid |
RMSD | Root-mean-square deviation of atomic positions |
BiFC | Bimolecular fluorescence complementation |
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Protein–Protein Complex | ΔG (kcal/mol) | ΔG (kJ/mol) | Kd (μM) at 25 °C |
---|---|---|---|
AHK3rd–AHP2_Apo | −8 | −33.47 | 1.3 |
AHK3rd–AHP2_Mg2+ | −8.5 | −35.56 | 0.6 |
AHK3rd(P) –AHP2_Mg2+ | −8.8 | −36.82 | 0.35 |
AHK3rd–AHP2(P)_Mg2+ | −7.9 | −33.05 | 1.5 |
AHK3rd(P)–AHP2(P)_Mg2+ | −8.1 | −33.89 | 1.1 |
AHK3rd(D941E)–AHP2_Mg2+ | −8.5 | −35.56 | 0.54 |
AHK3rd–AHP2(H82E)_Mg2+ | −8.4 | −35.15 | 0.72 |
Modeled Structure | Template Structure | |||
---|---|---|---|---|
Complex | Chain/Counterpart | PDB ID/chain ID | Protein Name | Reference |
Sensory module dimers | chains AB | 3T4L/AB | AHK4 | [4] |
HisKA domain dimers | chains AB | 4MT8/AB | ERS1 | [6] |
HKrd–HPt complexes | HKrd (chainA) | 3MMN/A | CKI1 | [17] |
4EUK/A | CKI2(AHK5) | [19] | ||
HPt (chain B) | 4EUK/B | AHP1 | [19] | |
HPt–HPt dimers | chains AB | 1YVI/AB | OsHP1 | [23,24] |
RRrd–HPt complexes | RRrd (chain A) | 1CHN/A | CheY | [38] |
4EUK A | CKI2(AHK5) | [19] | ||
HPt (chain B) | 4EUK B | AHP1 | [19] |
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Arkhipov, D.V.; Lomin, S.N.; Myakushina, Y.A.; Savelieva, E.M.; Osolodkin, D.I.; Romanov, G.A. Modeling of Protein–Protein Interactions in Cytokinin Signal Transduction. Int. J. Mol. Sci. 2019, 20, 2096. https://doi.org/10.3390/ijms20092096
Arkhipov DV, Lomin SN, Myakushina YA, Savelieva EM, Osolodkin DI, Romanov GA. Modeling of Protein–Protein Interactions in Cytokinin Signal Transduction. International Journal of Molecular Sciences. 2019; 20(9):2096. https://doi.org/10.3390/ijms20092096
Chicago/Turabian StyleArkhipov, Dmitry V., Sergey N. Lomin, Yulia A. Myakushina, Ekaterina M. Savelieva, Dmitry I. Osolodkin, and Georgy A. Romanov. 2019. "Modeling of Protein–Protein Interactions in Cytokinin Signal Transduction" International Journal of Molecular Sciences 20, no. 9: 2096. https://doi.org/10.3390/ijms20092096