Academic Journal
When B2 is Not Enough: Evaluating Simple Metrics for Predicting Phase Separation of Intrinsically Disordered Proteins
| Title: | When B2 is Not Enough: Evaluating Simple Metrics for Predicting Phase Separation of Intrinsically Disordered Proteins |
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| Authors: | Wesley W. Oliver, William M. Jacobs, Michael A. Webb |
| Source: | The Journal of Physical Chemistry B. 129:9551-9565 |
| Publication Status: | Preprint |
| Publisher Information: | American Chemical Society (ACS), 2025. |
| Publication Year: | 2025 |
| Subject Terms: | Soft Condensed Matter, Statistical Mechanics (cond-mat.stat-mech), FOS: Biological sciences, Soft Condensed Matter (cond-mat.soft), FOS: Physical sciences, Quantitative Methods, Quantitative Methods (q-bio.QM), Statistical Mechanics |
| Description: | Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex dependence on protein primary sequence remains challenging. In this study, we evaluate the efficacy of several simple computational metrics to quantify the propensity of single-component IDP solutions to phase separate; specific metrics considered include the single-chain radius of gyration, the second virial coefficient, and a newly proposed quantity termed the expenditure density. Each metric is computed using coarse-grained molecular dynamics simulations for 2,034 IDP sequences. Using machine learning, we analyze this data to understand how sequence features correlate with the predictive performance of each metric and to develop insight into their respective strengths and limitations. The expenditure density is determined to be a broadly useful metric that combines simplicity, low computational cost, and accuracy; it also provides a continuous measure that remains informative across both phase-separating and non-phase-separating sequences. Additionally, this metric shows promise in its ability to improve predictions of other properties for IDP systems. This work extends existing literature by advancing beyond binary classification, which can be useful for rapidly screening phase behavior or predicting other properties of IDP-related systems. 46 pages, 7 figures, supporting information |
| Document Type: | Article |
| Language: | English |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/acs.jpcb.5c04955 |
| DOI: | 10.48550/arxiv.2507.12312 |
| Access URL: | http://arxiv.org/abs/2507.12312 |
| Rights: | STM Policy #29 CC BY |
| Accession Number: | edsair.doi.dedup.....acfef81be058429ee059ce3072a2682c |
| Database: | OpenAIRE |
| ISSN: | 15205207 15206106 |
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| DOI: | 10.1021/acs.jpcb.5c04955 |