Machine learning/molecular dynamic protein structure prediction approach to investigate the protein conformational ensemble

• Published in: Scientific reports 2022-06, Vol.12 (1), p.10018-10018, Article 10018
• Main Authors: Audagnotto, Martina, Czechtizky, Werngard, De Maria, Leonardo, Käck, Helena, Papoian, Garegin, Tornberg, Lars, Tyrchan, Christian, Ulander, Johan
• Format: Article
• Language: English
• Subjects: 631/114/2411; 631/535/1267; Deep learning; Humanities and Social Sciences; Learning algorithms; Machine learning; multidisciplinary; Predictions; Protein folding; Protein structure; Proteins; Residues; Science; Science (multidisciplinary); Sequence analysis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-13714-z

Proteins exist in several different conformations. These structural changes are often associated with fluctuations at the residue level. Recent findings show that co-evolutionary analysis coupled with machine-learning techniques improves the precision by providing quantitative distance predictions between pairs of residues. The predicted statistical distance distribution from Multi Sequence Analysis reveals the presence of different local maxima suggesting the flexibility of key residue pairs. Here we investigate the ability of the residue-residue distance prediction to provide insights into the protein conformational ensemble. We combine deep learning approaches with mechanistic modeling to a set of proteins that experimentally showed conformational changes. The predicted protein models were filtered based on energy scores, RMSD clustering, and the centroids selected as the lowest energy structure per cluster. These models were compared to the experimental-Molecular Dynamics (MD) relaxed structure by analyzing the backbone residue torsional distribution and the sidechain orientations. Our pipeline allows to retrieve the experimental structural dynamics experimentally represented by different X-ray conformations for the same sequence as well the conformational space observed with the MD simulations. We show the potential correlation between the experimental structure dynamics and the predicted model ensemble demonstrating the susceptibility of the current state-of-the-art methods in protein folding and dynamics prediction and pointing out the areas of improvement.