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In the Supporting Information, the solutions to Training Module 3, Questions 1, 3, and 4 have been revised to enhance clarity and include details that were omitted in the original submission.
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Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.
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In the original manuscript, the value of parameter c was not explicitly provided. We wish to clarify that c was refitted to the hydrogen atom exchange energy, using the updated value of κ. With the updated κ = 0.2501, the optimized value of the parameter is c = 0.391596228. These values supersede any implicit assumptions about c in the original manuscript, and readers are encouraged to use these parameters for reproducing the results presented therein.
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Dr. Laor Bar-Yosef was significantly involved in the introduction and use of the Raman microspectroscopy part of this project. She was a major contributor to the novel conceptual use of this technology for detecting and monitoring sphingolipids in vitro and in cells. As expected from her deep involvement, Dr. Laor Bar-Yosef took part in analyzing the corresponding results.
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No abstract provided.