Journal: Frontiers in Plant Science

Article Title: Supplemental Light-Emitting Diode Inter-Lighting Increases Tomato Fruit Growth Through Enhanced Photosynthetic Light Use Efficiency and Modulated Root Activity

doi: 10.3389/fpls.2019.01656

Figure Lengend Snippet: Schematic diagram of the installation of the light-emitting diode lamps and the positions and orientations of the LP9021 PAR sensor used to measure light intensity (PAR) and the JAZ-COMBO (Ocean Optics) (JAZ) used to determine the spectral properties. The distance between rows was 180 cm. The position and orientation of the light intensity and spectral sensors was the same in the control treatment.

Article Snippet: Light intensity was measured at the top and at the bottom of the canopy using an LP9021 PAR sensor connected to an HD 9021 logger (Delta OHM SRL, Padova, Italy).

Techniques: Control

Journal: bioRxiv

Article Title: Molecular Mechanism and Structural Models of Protein-Mediated Copper Transfer to the Arabidopsis thaliana Ethylene Receptor ETR1 at the ER Membrane

doi: 10.1101/2025.01.21.634023

Figure Lengend Snippet: A: Multiple sequence alignment of ATX1, the N-terminal metal binding domains (MBD) of CCH (CCHΔ), and MBDs of HMA5 and HMA7 (RAN1) from Arabidopsis thaliana . Amino acids are colored according to the Clustal X color scheme. Cysteines forming the copper binding motif (CBM) in ATX1, CCHΔ, and in MBD1-2 in HMA5 and HMA7 are highlighted by a red box. Note that these cysteines are missing in MBD3 of HMA5 and HMA7. The amino acids of the individual domains, which refer to their positions in the corresponding full-length proteins (given in brackets), represent the sequences of heterologously expressed and purified proteins used in this study. B: SDS-PAGE of all proteins used for in vitro experiments in this study. MBD1-3 refer to the MBDs of HMA7 as shown in ( A ). A truncation mutant of ETR1 containing the transmembrane- and GAF-domains (ETR1_GAF, aa 1-316) was used for subsequent interaction studies. C: Crystal structure of the RAN1 MBD3 from Arabidopsis thaliana at a resolution of 1.98 Å (PDB ID 8RNZ). D: Structure of the C-terminal region of the RAN1 MBD3 containing the SSRS sequence motif. Amino acid sidechains of this sequence motif are shown as sticks.

Article Snippet: At present, two computational models of the transmembrane domain of ETR1 are available ( Jumper et al ., 2021 ; Schott-Verdugo et al ., 2019 ; Varadi et al ., 2022 ).

Techniques: Sequencing, Binding Assay, Purification, SDS Page, In Vitro, Mutagenesis

Journal: bioRxiv

Article Title: Molecular Mechanism and Structural Models of Protein-Mediated Copper Transfer to the Arabidopsis thaliana Ethylene Receptor ETR1 at the ER Membrane

doi: 10.1101/2025.01.21.634023

Figure Lengend Snippet: A: Far-UV CD-spectra of MBDs 1 to 3. B: Copper transfer from the chromophoric Cu(I)-BCA 2 complex to MBDs 1 to 3 as a function of protein concentration. Competition for copper is monitored at 562 nm. C: Control samples used in the copper binding assay. DTT (positive control), MSP1E3 (His-tag control), and bleed-through (BT) control testing for unremoved DTT in MBD samples. Data from B and C were fit to a four-parameter logistic function and EC50-values are reported in the figure. D: Interaction of RAN1 MBDs 1 to 3 with ETR1_GAF 1-316 -studied by microscale thermophoresis (MST). ETR1_GAF 1-316 is the labeled protein. Data were fit to a one-site binding model and the obtained dissociation constants ( K D ) are reported in the figure. In all subfigures, symbols represent experimental data and solid lines represent fitted data. All measurements were performed at least in triplicate.

Article Snippet: At present, two computational models of the transmembrane domain of ETR1 are available ( Jumper et al ., 2021 ; Schott-Verdugo et al ., 2019 ; Varadi et al ., 2022 ).

Techniques: Circular Dichroism, Protein Concentration, Control, Binding Assay, Positive Control, Microscale Thermophoresis, Labeling

Journal: bioRxiv

Article Title: Molecular Mechanism and Structural Models of Protein-Mediated Copper Transfer to the Arabidopsis thaliana Ethylene Receptor ETR1 at the ER Membrane

doi: 10.1101/2025.01.21.634023

Figure Lengend Snippet: The darker red color and thicker lines in the putty representation of ETR1_GAF indicate a higher probability of interactions with the chaperones or MBDs. ATX1 and CCHβ, as well as MBD1 and MBD2 of RAN1, show interactions at the CBM (vertical lines at residues 13 and 16, 67 and 70, 144 and 147, respectively) with the linker region and GAF-domain of ETR1. Additionally, interactions are proposed for the residues at the beginning of the second β-sheet (vertical lines at residues 27 and 33, 235 and 243, respectively) with the ETR1 linker region and GAF domain. The latter interactions are not present for MBD1 and MBD2. For MBD3, no interaction at the degenerate CBM is indicated. Overall, MBD3 displays a similar pattern to ATX1 and CCH, but with higher prediction confidence, showing interactions of the second β-sheet with the ETR1 linker region and GAF domain.

Article Snippet: At present, two computational models of the transmembrane domain of ETR1 are available ( Jumper et al ., 2021 ; Schott-Verdugo et al ., 2019 ; Varadi et al ., 2022 ).

Techniques:

Journal: bioRxiv

Article Title: Molecular Mechanism and Structural Models of Protein-Mediated Copper Transfer to the Arabidopsis thaliana Ethylene Receptor ETR1 at the ER Membrane

doi: 10.1101/2025.01.21.634023

Figure Lengend Snippet: A-E: full-length ab initio ETR1. F-J: full-length ColabFold ETR1. Density representation of all ATX1 (A, F: dark green), CCH (B, G: yellow-green), MBD1 (C, H: purple), MBD2 (D, I: blue), and MBD3 (E, J: cyan) poses with ETR1 (gray) and the accordingly selected best-scored complex with the corresponding zoom. Amino acids forming the CBM in the chaperone are colored yellow. Residues of ETR1 able to complex Cu(I)-ions, such as cysteine, histidine, methionine, and serine are colored orange.

Article Snippet: At present, two computational models of the transmembrane domain of ETR1 are available ( Jumper et al ., 2021 ; Schott-Verdugo et al ., 2019 ; Varadi et al ., 2022 ).

Techniques:

Journal: bioRxiv

Article Title: Molecular Mechanism and Structural Models of Protein-Mediated Copper Transfer to the Arabidopsis thaliana Ethylene Receptor ETR1 at the ER Membrane

doi: 10.1101/2025.01.21.634023

Figure Lengend Snippet: The models indicate binding positions of the individual MBDs as obtained in previous results ( , ) and the orientation of RAN1 and ETR1 in relation to the membrane. The three MBDs are colored purple (MBD1), blue (MBD2), and cyan (MBD3). An alternative interaction site of MBD1 in the vicinity of the GAF domain is predicted. MBD2 and MBD3 bind to the same domains as in the initial docking approach. A: Membrane orientation of RAN1 and full-length ab initio ETR1 after docking. B: Truncated RAN1 lacking MBD1 and MBD1 were collectively docked to full-length ab initio ETR1. The remaining domains of RAN1 are hidden for the sake of clarity. C: Density representation of MBD1, MBD2, and MBD3 poses at full-length ab initio ETR1 D: Membrane orientation of RAN1 and full-length ColabFold ETR1 after docking. E: Truncated RAN1 and MBD1 docked to full-length ColabFold ETR1. The remaining domains of RAN1 are hidden for the sake of clarity. F: Density representation of MBD1, MBD2, and MBD3 poses at full-length ColabFold ETR1.

Article Snippet: At present, two computational models of the transmembrane domain of ETR1 are available ( Jumper et al ., 2021 ; Schott-Verdugo et al ., 2019 ; Varadi et al ., 2022 ).

Techniques: Binding Assay, Membrane