Journal: Journal of Experimental Botany

Article Title: Evidence for dual targeting control of Arabidopsis 6-phosphogluconate dehydrogenase isoforms by N-terminal phosphorylation

doi: 10.1093/jxb/erae077

Figure Lengend Snippet: A new medial GFP fusion of PGD2 is active but does not localize in peroxisomes. (A) PGD2 monomer (PDB file obtained from Alphafold, and modifed by Protean 3D) with a large dimer interface (dashed line), the C-terminally extended part with GFP insertion positions (position 476 of Eubel et al ., 2008 ), and C420 indicated by arrows. (B) PGD2 constructs with the medial GFP reporter (numbers refer to amino acids of the N- and C-terminal parts) and their analysis in Arabidopsis protoplasts isolated from leaves (48 h post-transfection). Note that old medial and new medial display opposite localization patterns with an influence on catalytic activity, indicated on the left. All images show maximal projections of ~35 single sections. GFP fusions are in green, peroxisomal marker (OFP–PGL3_ C-short ) in magenta, and chlorophyll autofluorescence in blue. Merge, co-localization of green and magenta, or very close signals (<200 nm), appear white. Scale bars 3 µm.

Article Snippet: Protein 3D models are based on AlphaFold predictions and were modified with DNASTAR Protean 3D v17.

Techniques: Construct, Isolation, Transfection, Activity Assay, Marker

Journal: Journal of Experimental Botany

Article Title: Evidence for dual targeting control of Arabidopsis 6-phosphogluconate dehydrogenase isoforms by N-terminal phosphorylation

doi: 10.1093/jxb/erae077

Figure Lengend Snippet: The phosphomimetic change T6E lowers PGD2 solubility and catalytic activity. (A) AlphaFold prediction of intramolecular bonds (within a radius of 5 Å) in the N-terminal part of PGD2. The magnification shows that Thr6 (red) is bound by surrounding Ile8, Ser32, Ser68, and Gln70 (green). (B) Relative protein amounts of PGD2 medial variants compared with endogenous PGD signals in cleared extracts of Arabidopsis protoplasts. Note that compared with PGD2_ new medial , T6E and old medial versions are depleted from the supernatant (SN) but less from the pellet (Pe) fractions, indicative of lower solubility. (C) Relative activity of the indicated PGD2–GFP fusions compared with the corresponding wild type (WT, 100%) upon pull-down from supernatant fractions; n.d., not detected. The immunoblot was developed with anti-PGD2 antiserum ( Hölscher et al. , 2016 ). Note that with N-terminal GFP, PGD2-T6E showed catalytic activity. Compilation of different blots (marked by outlines). The lighter lanes stem from the same blot from which empty lanes and the marker were removed. (D) SDS–PAGE of His-PGD2 variants from cleared E. coli BL21 minus extracts without (–) or with (+) SDS and DTT in the sample buffer (plus boiling at 100 °C). The immunoblot was developed with anti-His–HRP conjugate to visualize only recombinant PGD proteins. kDa, PageRuler™ Prestained Protein Ladder (Fermentas).

Article Snippet: Protein 3D models are based on AlphaFold predictions and were modified with DNASTAR Protean 3D v17.

Techniques: Solubility, Activity Assay, Western Blot, Marker, SDS Page, Recombinant

Journal: BMC Genomics

Article Title: Functional analysis of the FGF2 gene in horn development in sheep and identification of key regulatory variants

doi: 10.1186/s12864-025-12309-y

Figure Lengend Snippet: Phylogenetic analysis and three-dimensional structure prediction of the sheep FGF2 protein. ( A ) Phylogenetic tree of homologous FGF2 protein sequences from sheep and other species. Bootstrap values at each node represent the confidence level of the corresponding branch. The scale bar (0.05) reflects evolutionary distance, with longer branches indicating greater sequence divergence. ( B ) Prediction of the Three-Dimensional structure of sheep FGF2 protein with highlighted key residues and structural features ( C ) Protein–protein interaction network for sheep FGF2 obtained from the STRING database, indicating potential interacting partners involved in fibroblast growth factor signaling. ( D ) Three-dimensional structural prediction of the FGFR1 protein. ( E ) Three-dimensional structural prediction of the FGFR2 protein. ( F ) Predicted complex structure of FGF2 binding with FGFR1. FGF2 is shown in red, and FGFR1 is shown in green. The interaction confidence metrics from AlphaFold 3 are as follows: inter-chain predicted TM-score (ipTM) = 0.89 and predicted TM-score (pTM) = 0.49. ( G ) Predicted complex structure of FGF2 binding with FGFR2. FGF2 is depicted in red, and FGFR2 in blue. The interaction confidence metrics from AlphaFold 3 are as follows: inter-chain predicted TM-score (ipTM) = 0.85 and predicted TM-score (pTM) = 0.49

Article Snippet: To further explore the spatial conformation of the protein, the 3D structure of sheep FGF2 was predicted using AlphaFold3 (default parameters, https://deepmind.google/technologies/alphafold/alphafold-server/ ).

Techniques: Sequencing, Structural Proteomics, Binding Assay