Detailed Insight into the Chignolin Folding Process from Maximally Informative Low-Resolution Representations of Its Isocommittor Hypersurfaces

Abstract The synthetic miniprotein chignolin features a small size, a well-defined native structure, and a rather paradigmatic two-state folding transition. Nonetheless, this deceivingly simple molecule showcases a nontrivial folding pathway, whose detailed characterization has been the subject of several studies and still presents some open questions. In this work, we investigate chignolin by employing, for the first time in a combined and integrated pipeline, transition-path theory (TPT) and the mapping entropy optimization workflow (MEOW). The former describes the folding process in terms of its natural reaction coordinate, that is, the committor; the latter pinpoints, in an unsupervised and system-agnostic manner, those residues of a biomolecule that are most informative about the structural, mechanical, and energetic organization of the configurational ensemble. Through this joint framework, we characterize in great detail the entire transition of the peptide from the unfolded to the native state. The approach allows us to identify which residues entail the largest degree of information about a conformational ensemble at a given level of progress of the folding transition; comparison with data from the literature and validation against independent observables, including the outcomes of an in silico mutation analysis, show that these residues also bear functional significance. This work analyzes the folding process of chignolin from a new perspective and showcases the integration of the MEOW protocol with TPT into a pipeline that can complement existing approaches for the investigation of proteins.