AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes.

Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2, which combines randomized alanine sequence masking with shallow multiple sequence alignment subsampling to expand the conformational diversity of the predicted structural ensembles and capture conformational changes between apo and holo protein forms. 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. These observations are consistent with the view that the intrinsic dynamics of allosteric proteins are defined by the structural topology of the fold and favor conserved conformational motions driven by soft modes. Our findings provide evidence that AlphaFold2 combined with randomized alanine sequence masking can yield accurate and consistent results in predicting moderate conformational adjustments between apo and holo states, especially for proteins with localized changes upon ligand binding. For large hinge-like domain movements, the proposed approach can predict functional conformations characteristic of both apo and ligand-bound holo ensembles in the absence of ligand information. These results are relevant for using this AlphaFold adaptation for probing conformational selection mechanisms according to which proteins can adopt multiple conformations, including those that are competent for ligand binding. The results of this study indicate that robust modeling of functional protein states may require more accurate characterization of flexible regions in functional conformations and the detection of high-energy conformations. By incorporating a wider variety of protein structures in training datasets, including both apo and holo forms, the model can learn to recognize and predict the structural changes that occur upon ligand binding.