BUSCADOR RECOLECTA

Digital.CSIC. Repositorio Institucional del CSIC

oai:digital.csic.es:10261/311509

Material For modeling AlphaFold2_multimer was used. AlphaFold2 was downloaded from https://github.com/deepmind/alphafold/releases. Full length amino acid sequences of human PHF14 and HMG20A were used: >NP_001291433.1 high mobility group protein 20A isoform a [Homo sapiens] >NP_001007158.1 PHD finger protein 14 isoform 1 [Homo sapiens] To perform PHF14-HMG20A complex models we used Alphafold_multimers (v2.1.1) with --db_preset=reduced_dbs, --model_preset=multimer --max_template_date=2021-11-01, and default parameters. Computation was performed in the CESGA Supercomputing Center. RCSB PDB (https://www.rcsb.org/3d-view) or Swiss PDB viewer (DeepView) were used for structure viewing. Procedure Full lenth amino-acid protein sequences were obtained form NCBI Protein. Then, to perform PHF14-HMG20A complex models we used Alphafold_multimers (v2.1.1) with --db_preset=reduced_dbs, --model_preset=multimer --max_template_date=2021-11-01, and default parameters. A PAE plot (Predicted Aligned Error Plot) is uploaded. PAE plot "reports AlphaFold’s expected position error at residue x, when the predicted and true structures are aligned on residue y. This is useful for assessing confidence in global features, especially domain packing. For residues x and y drawn from two different domains, a consistently low PAE at (x, y) suggests AlphaFold is confident about the relative domain positions" (https://deepmind.com/research/publications/2021/enabling-high-accuracy-protein-structure-prediction-at-the-proteome-scale). A distogram (Matrix of distances between different parts of the proteins) is also uploaded., Structural modeling by using the AlphaFold2_multimer software, indicated that HMG20A forms a complex with PHF14 through the establishment of a two-stranded alpha-helical coiled-coil structure, Peer reviewed