Computation suggests that the cell adhesion sub-proteome is enriched for sites of pH-dependence and charge burial.

ABSTRACT: Prediction of protein pH-dependence is generally made for individual proteins or pathways, and is also increasingly being used to aid protein functional design. Combining high-throughput pKa prediction methods with AlphaFold models allows pH-dependence to be studied across a proteome. Here, two methods and a variety of features for detecting pH-dependence and charge burial that is physiologically relevant, have been applied to human proteins. Predictions are effective for a small benchmark subset of well-characterised proteins and, more broadly, identify an overlap between features associated with pH-dependence and enzymes and transporters. The most informative filters are those describing relatively buried ionisable groups, with pKas close to neutral pH and/or involvement in highly-couple

SUBMITTER: Sallah S 

PROVIDER: S-EPMC12688153 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature