Journal: Nutrients

Article Title: Role of Probiotics in the Management of COVID-19: A Computational Perspective

doi: 10.3390/nu14020274

Figure Lengend Snippet: Schematic representation for the reconstruction of PlnE and PlnF. The sequence of PlnE and PlnF were separately modeled using SWISS-MODEL server and AlphaFold Colab, followed by superimposing predicted structures with PlnE template (PDB ID: 2JUI) and PlnF template (PDB ID: 2RLW). The SWISS-MODEL predicted structures were chosen for further modeling due to the lower RMSD value with the templates compared to AlphaFold Colab predicted structures. A homology modeling approach was used to rebuild PlnE and PlnF as a single structure using MODELLER v10.1. The best structure was used to dock against SARS-CoV-2 helicase nsp13 using the protein-protein docking approach.

Article Snippet: AlphaFold Colab, a Google Colab notebook allowing users to predict protein structure, is a simplified version of AlphaFold v2.1.0, which has been developed by DeepMind [ , ].

Techniques: Sequencing

Journal: Nutrients

Article Title: Role of Probiotics in the Management of COVID-19: A Computational Perspective

doi: 10.3390/nu14020274

Figure Lengend Snippet: RMSD values of predicted structures of PlnE and PlnF modeled by AlphaFold Colab and SWISS-MODEL, in comparing with each other or with templates.

Article Snippet: AlphaFold Colab, a Google Colab notebook allowing users to predict protein structure, is a simplified version of AlphaFold v2.1.0, which has been developed by DeepMind [ , ].

Techniques:

Journal: mSystems

Article Title: Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer

doi: 10.1128/msystems.00375-24

Figure Lengend Snippet: Structural context of ApbE flavinylation sites. ( A ) Previously resolved crystal structure of a flavinylated monomeric protein from C. perfringens (FMN-Bind 1 , PDB: 3O6U ). ( B ) AlphaFold model of a double-flavinylated protein from Erysipelotrichaceae bacterium containing 2 FMN-bind 2 domains (left) and its structural alignment with FMN-bind 1 (right). Arrows highlight β1, β2, and β3 strands. ( C ) Previously resolved crystal structure of the B subunit from the Nqr complex (PDB: 4P6V ). ( D ) AlphaFold model of a Shewanella oneidensis protein with a flavinylated DUF2271 domain. ( E and F ) AlphaFold models of flavinylated Flavodoxin_4 ( E ) and flavinylated FMN reductase ( F ). Gray circles highlight the position of the flavinylated amino acid.

Article Snippet: AlphaFold models of the ApbE-associated Flavodoxin_4 proteins from Anaerocolumna xylanovorans ( ; National Center for Biotechnology Information [NCBI] accession SHO45324.1 ) and Desulfosporosinus lacus ( ; NCBI accession WP_073032509.1 ) resemble a crystal structure of a homologous non-covalent flavin-binding protein (PDB: 3KLB ) from Bacteroides fragilis ( ).

Techniques:

Journal: mSystems

Article Title: Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer

doi: 10.1128/msystems.00375-24

Figure Lengend Snippet: ApbE flavinylation evolved from non-covalent flavoproteins. ( A and B ) AlphaFold models for flavinylated Flavodoxin_4 proteins from Anaerocolumna xylanovorans ( A ) and Desulfosporosinus lacus ( B ). ( C ) Previously resolved crystal structure of a Flavodoxin_4 with non-covalently bound FMN (PDB: 3KLB ). ( D ) Structural alignments of Flavodoxin_4 proteins with and without predicted flavinylation site. Dashed oval highlights an inserted loop that is lacking in 3KLB (left). Right panel shows zoom-in view of non-covalent FMN molecule from 3KLB and surrounding residues. Arrow indicates the serine residue in flavinylated Flavodoxin_4 responsible for covalent FMN binding. ( E ) Taxonomic distribution of Flavodoxin_4 proteins in bacteria. ( F ) SDS-PAGE gel image of purified flavinylated Flavodoxin_4 from A. xylanovorans and D. lacus , visualized under UV. ( G and H ) AlphaFold models for flavinylated FMN reductases from Lactococcus lactis and Lactococcus taiwanensis . ( I ) Previously resolved crystal structure of a FMN reductase with non-covalently bound FMN (PDB: 4PTZ ). ( J ) Structural alignments of FMN reductase proteins with and without covalent FMN binding. Dashed oval highlights a C-terminus extension that is lacking in 4PTZ (left). Right panel shows zoom-in view of non-covalent FMN molecule from 4PTZ and surrounding residues. Arrow indicates the serine residue in flavinylated FMN reductase responsible for covalent FMN binding. ( K ) Taxonomic distribution of FMN reductases. ( L ) SDS-PAGE gel image of purified flavinylated Flavodoxin_4 proteins from L. lactis and L. taiwanensis , visualized under UV. Covalent FMN moieties appear as bright bands on SDS-PAGE visualized under UV.

Article Snippet: AlphaFold models of the ApbE-associated Flavodoxin_4 proteins from Anaerocolumna xylanovorans ( ; National Center for Biotechnology Information [NCBI] accession SHO45324.1 ) and Desulfosporosinus lacus ( ; NCBI accession WP_073032509.1 ) resemble a crystal structure of a homologous non-covalent flavin-binding protein (PDB: 3KLB ) from Bacteroides fragilis ( ).

Techniques: Residue, Binding Assay, Bacteria, SDS Page, Purification