alphafold2 protein structure prediction software version 2.2.1  (Deepmind Technologies Ltd)

Journal: Microorganisms

Article Title: Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages

doi: 10.3390/microorganisms9102151

Figure Lengend Snippet: AlphaFold2 structure predictions for OE33PA Dit, Tal, and RBP. ( A – G ) Dit of OE33PA. ( A ) Dit domain organization. Domains with structural homologs are shown in salmon, while domains with unknown folds are shown in grey. The domain boundaries predicted by AlphaFold2 are indicated. ( B ) Ribbon representations of the predicted belt and putative ‘arm’ structure (rainbow) and of the phage p2 Dit belt–arm domain (steel blue). ( C ) Comparison of the Dit dimeric assembly predicted by AlphaFold2 (rainbow) and a p2 Dit dimeric assembly determined by X-ray crystallography (steel bleu). Dotted ovals highlight intermolecular contacts. ( D ) Ribbon representation of the predicted β -domain (rainbow). This structure did not return significant hits with Dali. ( E ) Ribbon representations of the predicted CBM (rainbow) and the C-terminal domain of a phage tail spike (gold). ( F ) Ribbon representation of the predicted β -domain (rainbow). This structure did not return significant hits with Dali. ( G ) Ribbon representations of the predicted galectin structure (rainbow) and the phage SPP1 Dit galectin domain (red). ( H ) (Top) Tal domain organization. (Bottom) Ribbon representations of the predicted Tal structure (rainbow) and the phage p2 Tal structural domain (purple). ( I ) (Top) RBP domain organization. (Bottom) Ribbon representations of the predicted RBP structure (rainbow), the phage Bil170 RBP head domain (pink), and the phage 1358 RBP shoulder domain (light blue). ( J ) Ribbon representations of the AlphaFold2 RBP trimeric assembly. The dotted oval highlights shoulder domain swapping.

Article Snippet: However, in the last few weeks, the structure prediction software AlphaFold2 developed by the DeepMind company has become publicly available and may change the landscape of phage structural studies [ , , ].

Techniques: Comparison

Journal: Microorganisms

Article Title: Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages

doi: 10.3390/microorganisms9102151

Figure Lengend Snippet: AlphaFold2 structure predictions of Vinitor162 Dit and Tal. ( A ) Dit domain organization (top). Ribbon representations of the predicted belt and galectin domains (rainbow) and the phage p2 Dit belt–arm and galectin domains (pink). ( B ) Tal domain organization in the N-terminal region (top). Ribbon representations of the Tal and CBM_1 predicted structure s(rainbow) and their Dali hits, the listerial phage EGD-e Tal structural domain (light blue), and a CAZy CBM15 (light green), respectively. ( C ) Tal domain organization in the middle of the protein (top). Ribbon representations of the predicted CBM_2 to CBM_5 (rainbow) and their Dali hits. Besides CBM_2, the three other CBMs correspond to CAZy CBM22, CBM4, and CBM22. ( D ) Tal domain organization in the C-terminal region (top). Ribbon representations of the predicted Tal C-terminal domain (rainbow) compared to Dali hits, a R2 pyocin spike (orange), and a T5 fiber chaperone (pink) at each extremity.

Article Snippet: However, in the last few weeks, the structure prediction software AlphaFold2 developed by the DeepMind company has become publicly available and may change the landscape of phage structural studies [ , , ].

Techniques: