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2 claims from 1 paper

1. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Assessing Structures and Conformational Ensembles of Apo and Holo Protein States Using Randomized Alanine Sequence Scanning Combined with Shallow Subsampling in AlphaFold2 : Insights and Lessons from Predictions of Functional Allosteric Conformations

   Raisinghani, Parikh, Foley and Verkhivker · bioRxiv (Cold Spring Harbor Laboratory) · 2024

   The authors used AlphaFold2 with randomised alanine masking and shallow sequence subsampling to predict apo and holo protein states, finding good accuracy for small shifts but limits for large hinge-like movements.

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   1. UncheckedAn AlphaFold2 method using alanine masking and shallow subsampling is reported to predict apo and holo protein structures and ensembles robustly, with similar dynamics.“Using several well-established datasets of structurally diverse apo-holo protein pairs, the proposed approach enables robust predictions of apo and holo structures and conformational ensembles, while also displaying notably similar dynamics distributions.”
   2. UncheckedFor large hinge-like domain movements, AlphaFold2 tends to predict the most stable domain orientation, typically the apo form, not the full holo range.“However, for large, hinge-like domain movements, AlphaFold2 tends to predict the most stable domain orientation which is typically the apo form rather than the full range of functional conformations characteristic of the holo ensemble.”