Jeremy Gunawardena

TL;DR: This work frames central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today, and uses this framework to assess existing data and ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?"

TL;DR: High-accuracy species-specific phosphorylation and acetylation site predictors, trained on the modification sites contained in PHOSIDA, allow the in silico determination of modified sites on any protein on the basis of the primary sequence.

TL;DR: The ‘mod‐form distribution’—the relative stoichiometries of each mod‐form—is introduced as the most informative measure of a protein's state as well as a quantitative framework in which to interpret ideas of ‘PTM codes’ that are emerging in several areas of biology.

TL;DR: It is pointed out that conventional measures of ultrasensitivity must be modified to discriminate between thresholding and switching; additional factors that influence switching efficiency are discussed and new directions for experimental investigation are suggested.

TL;DR: It is shown that, when kinase and phosphatase act in opposition on a multisite substrate, the system can exhibit distinct stable phospho-form distributions at steady state and that the maximum number of such distributions increases with n, reducing the complexity of calculating steady states from simulating 3 × 2n differential equations to solving two algebraic equations, while treating parameters symbolically.