Journal: Communications Chemistry

Article Title: Human O- GlcNAcase catalytic-stalk dimer anchors flexible histone binding domains

doi: 10.1038/s42004-025-01813-7

Figure Lengend Snippet: Potential binding sites of the pHAT domains to nucleosomes, highlighting proximity and spacing of the H3K36 residues ( a ) as well as the H3K36 and H4K 5,8,12, and 16 residues ( b ) in the nucleosome (PDBID:1kx5: gray). OGA is colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and HAT-like domain: green. The distance between K36 residues (red) is 73.5 Å, and the total distance between pHAT densities is 107 Å (green). The distance between the K36 residue and the H4K 5,8,12,16 is 72.8 Å (pink). c OGA-L pHAT binding to histone modifications such as H3K36 Me and acetylated H4 tails would facilitate recruitment to sites of active transcription and DNA repair. The structural features identified for OGA-L are likely to increase the local concentration of tihe OGA-L and allow flexible movement of the catalytic domain to facilitate O- GlcNAc removal from proteins in proximity. The OGA model is shown with unstructured linkers added from the Alphafold2 colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and pHAT domain, green.

Article Snippet: Additional data compared in this study from the protein databank: Alphafold2 Multimer, PDB ID: 5M7R, PDB ID: 5VVO, PDB ID:5UHK, PDB ID: 5M7S, PDBID:5UN9, PDB ID:5UHL, PDB ID: 5M7T, PDB ID: 5UHO, PDB ID: 8P0L, PDB ID: 9BA8, 9BA9, PDB ID: 1KX5 .

Techniques: Binding Assay, Residue, Concentration Assay

Journal: Cancer Gene Therapy

Article Title: Predicting colorectal cancer risk in FAP patients using patient-specific organoids

doi: 10.1038/s41417-025-00923-7

Figure Lengend Snippet: A Description of the type and location of APC germline mutations in each of the three FAP-hESC lines and their effect on the protein sequence. RYI – (R-Arginine, Y-Tyrosine, I-Isoleucine); LVISLE – (L-Leucine, V-Valine, I-Isoleucine, S-Serine, L-Leucine, E-Glutamine acid). B Model of the secondary protein structure of the full APC protein and the truncated forms of FAP1, FAP2 and FAP3. The AlphaFold2 model based on dLDDT of the APC full domain and the truncated forms of FAP1, FAP2 and FAP3. Model confidante is indicated in a color scale ranging from very low in orange to very high in blue. C The APC- FAP3, FAP1 and FAP2 model is showcased, delineating the various domains: APC is highlighted in gray, FAP1 in green and purple, FAP3 in green, and FAP2 in a combination of green, purple, and pink.

Article Snippet: In order to model the secondary protein structure of the full-length APC (FL-APC) protein and to provide insights into the spatial organization of the truncated proteins, the AlphaFold2 (AF) algorithm developed by DeepMind [ , ] was utilized.

Techniques: Sequencing

Journal: Cancer Gene Therapy

Article Title: Predicting colorectal cancer risk in FAP patients using patient-specific organoids

doi: 10.1038/s41417-025-00923-7

Figure Lengend Snippet: A The APC:FAP3 heterodimer. a The dotted circle marks the ‘FAP3’ domain. The AlphaFold2 results show the confidence of APC: FAP3 heterodimer, at least in most parts of the protein. b , c The two monomers are shown in red (FAP3) and gray (APC). Effect of the mutation on dimer formation of APC: FAP3, based on chemical bonds at the truncated protein. Salt bridges between APC and FAP3, the interacting residues are indicated: Arg24-Glu19; Glu19-Arg24; Arg187-Glu74. B The APC:FAP1 heterodimer. a The AlphaFold2 results show high confidence in the model. b The two monomers are shown: in pink (1-330 FAP1 truncated protein) and gray (full APC). c The depicted images represent magnified views of the enclosed regions of interaction. Salt bridges between FAP1- APC are shown in balls: Arg24-Glu19; Glu19-Arg24; Arg187-Asp183; Asp183-Arg187. C The APC:FAP2 heterodimer. a The AlphaFold2 shows the confidence of the model. b The two monomers are shown: in red (FAP2) and gray (APC). The three additional residues RYI (R-Arginine, Y-Tyrosine, I-IsoLeucine) characterizing the truncated FAP2 protein are shown in yellow. The residues involved with heterodimer formations are from FAP3 and FAP1 but not beyond residue 330. c The depicted images represent magnified views of the enclosed regions of interaction and the salt bridge formation between FAP2: APC is illustrated, with the interacting residues indicated. D Effect of salt bridges on the heterodimer structure—a table summarizing protein length, number of contacts within the dimer and the type & number of contacts within the APC homodimer/heterodimers.

Article Snippet: In order to model the secondary protein structure of the full-length APC (FL-APC) protein and to provide insights into the spatial organization of the truncated proteins, the AlphaFold2 (AF) algorithm developed by DeepMind [ , ] was utilized.

Techniques: Mutagenesis, Residue

Journal: BMC Medical Genomics

Article Title: Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy

doi: 10.1186/s12920-023-01780-9

Figure Lengend Snippet: The MED12 pathogenic variant is responsible for dilated cardiomyopathy (DCM). (A) The image presents the pedigree of the family with DCM. Variant carriers: black; relatives without the variant: white; slashed line: the deceased member; square: male; circle: female; arrow: proband; triangle: spontaneous abortion. (B) The cardiac magnetic resonance imaging image (CMR) presents dilated cardiomyopathy in the index patient. (C) Direct Sanger-sequencing chromatograms show the MED12 variant sequence in the father, the mother, and the DCM-affected son. The arrow shows the nucleotide position of G/A in the wild-type homozygous father, the heterozygous mother, and the hemizygous patient. (D) The CLUSTALW server was used to compare the alignment of MED12 residues among various MED12 orthologs. The valine amino acids are shown in box

Article Snippet: Since it was impossible to model a huge MED12 protein with AlphaFold2 ( https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ) methods [ ], the InterPro ( https://www.ebi.ac.uk/interpro/ ) web server [ ] was first employed to identify and select the desired domains of the MED12 protein according to the study of Klatt, et al. [ ].

Techniques: Variant Assay, Magnetic Resonance Imaging, Sequencing

Journal: BMC Medical Genomics

Article Title: Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy

doi: 10.1186/s12920-023-01780-9

Figure Lengend Snippet: The image depicts the structural prediction of the MED12 protein. (A) The image presents the domain prediction, performed with the InterPro web server. (B) The computational model of the normal MED12 protein constructed with the aid of the AlphaFold2 web server is presented herein. The surface yellow color shows the normal amino acid. (C) The computational model of the variant MED12 protein constructed with the use of the AlphaFold2 web server is presented herein. The surface green color shows the variant amino acid. (D) Superimposed AlphaFold2 models of MED12 (amino acid 1–800) as normal (green), Val417Ile (pink)

Article Snippet: Since it was impossible to model a huge MED12 protein with AlphaFold2 ( https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ) methods [ ], the InterPro ( https://www.ebi.ac.uk/interpro/ ) web server [ ] was first employed to identify and select the desired domains of the MED12 protein according to the study of Klatt, et al. [ ].

Techniques: Structural Proteomics, Construct, Variant Assay

Journal: BMC Medical Genomics

Article Title: Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy

doi: 10.1186/s12920-023-01780-9

Figure Lengend Snippet: Confidence metrics for the forecasted structure of (A) normal MED12 structure and (B) Val417Ile variant. The Ramachandran plot illustrates the energetically permissible regions for backbone dihedral angles ψ and ϕ of amino acid residues in the MED12 structure (the normal and the Val417Ile variant). The favored, and allowed regions are depicted in green and blue, respectively. (C) The image indicates the possible functions of the native MED12 domains, predicted with the aid of the AlphaFold2 and VAST web servers

Article Snippet: Since it was impossible to model a huge MED12 protein with AlphaFold2 ( https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ) methods [ ], the InterPro ( https://www.ebi.ac.uk/interpro/ ) web server [ ] was first employed to identify and select the desired domains of the MED12 protein according to the study of Klatt, et al. [ ].

Techniques: Variant Assay

Journal: BMC Medical Genomics

Article Title: Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy

doi: 10.1186/s12920-023-01780-9

Figure Lengend Snippet: The image demonstrates the molecular docking analysis of the MED12 protein (the normal and variant amino acids) with the CDK8 protein (PDB: 4F6U) by using PyMOL v.2.5.2. (A) The image illustrates the protein-protein interactions between the normal MED12 protein and the CDK8 protein (CDK8: purple; normal MED12: green). (B) The protein-protein interactions between the MED12 variant and the CDK8 protein (CDK8: purple; variant MED12: yellow) are shown herein

Article Snippet: Since it was impossible to model a huge MED12 protein with AlphaFold2 ( https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ) methods [ ], the InterPro ( https://www.ebi.ac.uk/interpro/ ) web server [ ] was first employed to identify and select the desired domains of the MED12 protein according to the study of Klatt, et al. [ ].

Techniques: Variant Assay, Protein-Protein interactions

Journal: BMC Medical Genomics

Article Title: Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy

doi: 10.1186/s12920-023-01780-9

Figure Lengend Snippet: A schematic interaction of the best docking results of the normal (A) and variant MED12 (B) with CDK8 presented by LigPlus + v.2.2.4 is shown herein. Hydrogen bonding is demonstrated in green

Article Snippet: Since it was impossible to model a huge MED12 protein with AlphaFold2 ( https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ) methods [ ], the InterPro ( https://www.ebi.ac.uk/interpro/ ) web server [ ] was first employed to identify and select the desired domains of the MED12 protein according to the study of Klatt, et al. [ ].

Techniques: Variant Assay

Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Article Title: Fine mapping, introgression, and KASP marker development for powdery mildew resistance in watermelon using an interspecific RIL population ( Citrullus mucosospermus × C. lanatus )

doi: 10.1007/s00122-025-05079-4

Figure Lengend Snippet: Predicted tertiary structures of the ClCG02G015730 protein from the resistant (USVL531-MDR) and susceptible (USVL677-PMS) watermelon genotypes. Protein 3D models were generated using AlphaFold2 (DeepMind; https://alphafoldserver.com ). Both alleles exhibited nearly identical α-helical architectures with high per-residue confidence scores (pLDDT > 90), indicating well-defined and stable folding. The resistant allele (USVL531-MDR) differed from the susceptible allele (USVL677-PMS) by a single conservative Met ↔ Val substitution located within a flexible surface loop. This substitution does not alter the overall fold but may influence local flexibility or modify protein–protein interaction potential associated with powdery mildew resistance

Article Snippet: Protein structure prediction for ClCG02G015730 was performed using the AlphaFold2 model (DeepMind; https://alphafoldserver.com ).

Techniques: Generated, Residue