phosphorylation site prediction  (HealthTech Connex Inc)

Journal: Genes

Article Title: Functional and Bioinformatic Analysis of PDX2 from Ginkgo biloba

doi: 10.3390/genes16050609

Figure Lengend Snippet: The characterization of GbPDX2 proteins: ( A ) hydrophilic/hydrophobic analysis; ( B ) prediction of the transmembrane domain; ( C ) signal peptide prediction; ( D ) prediction of the phosphorylation site.

Article Snippet: https://services.healthtech.dtu.dk/services/NetPhos-3.1/ (accessed on 14 February 2025) , phosphorylation site prediction.

Techniques: Phospho-proteomics

Journal: bioRxiv

Article Title: Extending Prot2Token: Aligning Protein Language Models for Unified and Diverse Protein Prediction Tasks

doi: 10.1101/2025.03.03.641065

Figure Lengend Snippet:

Article Snippet: Building on the model’s ability to predict PTMs, we extended our approach to include proteinkinase phosphorylation site prediction, a task with significant real-world applications.

Techniques: Phospho-proteomics

Journal: Microbiology Spectrum

Article Title: An Atypical F-Actin Capping Protein Modulates Cytoskeleton Behaviors Crucial for Trichomonas vaginalis Colonization

doi: 10.1128/spectrum.00596-23

Figure Lengend Snippet: Ser2 phosphorylation regulates Tv FACPα actin binding. (A) Total lysates from TH17 trophozoites in the flagellate (Flg) and amoeboid (Amo) forms were fractionated for Western blotting. The ratio of the indicated protein signal in the pellet (P) to that in the supernatant (S) was quantified, as shown in the bar graph. (B) The immunoprecipitants from the total lysates from panel A were examined by Western blotting using anti- Tv FACPα antibody. The relative signal intensities of the indicated proteins were quantified, as shown in the bar graph. (C and D) Total lysates from nontransgenic control or TH17 trophozoites overexpressing HA- Tv FACPα and S2A (C) or S2D (D) were fractionated for Western blotting. The ratios of the indicated protein signals from the pellet fraction (P) to those in the supernatant fraction (S) were analyzed, as shown in the bar graph. (E and F) The total lysates from trophozoites overexpressing HA- Tv FACPα and S2A (E) or S2D (F) were immunoprecipitated by an anti-HA antibody for Western blotting. The relative intensities of the indicated protein signals were quantified, as shown in the bar graphs. All assays were performed with three biological repeats ( n = 3). Data are presented as means ± SD. Statistical significance for each group of data was measured by Student’s t test, as indicated ( n = 3) (**, P < 0.01; *, P < 0.05; ns, no significance).

Article Snippet: By using a phosphorylation site prediction algorithm (NetPhos 3.1 generic phosphorylation prediction [ https://Services.healthtech.dtu.dk/service.php?NetPhos-3.1 ]), Ser2, Ser46, Ser88, Ser106, and Ser223 were predicted to be CKII phosphorylation sites.

Techniques: Phospho-proteomics, Binding Assay, Western Blot, Control, Immunoprecipitation

Journal: Microbiology Spectrum

Article Title: An Atypical F-Actin Capping Protein Modulates Cytoskeleton Behaviors Crucial for Trichomonas vaginalis Colonization

doi: 10.1128/spectrum.00596-23

Figure Lengend Snippet: Proposed model for Tv FACPα function and regulation. Tv FACPα is an actin-binding protein containing a C-terminal actin-binding domain and CKII-dependent Ser2 phosphorylation. Tv FACPα interacts directly with G-actin and F-actin through the actin-binding domain, and Ser2 phosphorylation is the essential signal triggering the dissociation of Tv FACPα and α-actin. Tv FACPα colocalizes with actin at the leading edge of the peripheral motile protrusions, inhibiting actin filament polymerization (1), leading to the diminishment of flagellate-amoeboid transformation and motility switching (2), amoeboid migration (3), and cytoadherence (4) in this parasite. As expected, the above-mentioned behaviors were also inhibited by TBB and LatB, supporting the significance of CKII and cytoskeleton activities for parasitism. Tight adherence and immediate migration conversion may be approaches adopted by this parasite to counteract environmental fluctuations or evade host defenses. This novel mechanism of T. vaginalis cytoadherence may provide new therapeutic targets for future treatment.

Article Snippet: By using a phosphorylation site prediction algorithm (NetPhos 3.1 generic phosphorylation prediction [ https://Services.healthtech.dtu.dk/service.php?NetPhos-3.1 ]), Ser2, Ser46, Ser88, Ser106, and Ser223 were predicted to be CKII phosphorylation sites.

Techniques: Binding Assay, Phospho-proteomics, Transformation Assay, Migration, Biomarker Discovery