Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves

Federico Sevlever, Juan Pablo Di Bella and Alejandra C Ventura

PLOS Computational Biology, 2020, vol. 16, issue 6, 1-21

Abstract: Negative cooperativity is a phenomenon in which the binding of a first ligand or substrate molecule decreases the rate of subsequent binding. This definition is not exclusive to ligand-receptor binding, it holds whenever two or more molecules undergo two successive binding events. Negative cooperativity turns the binding curve more graded and cannot be distinguished from two independent and different binding events based on equilibrium measurements only. The need of kinetic data for this purpose was already reported. Here, we study the binding response as a function of the amount of ligand, at different times, from very early times since ligand is added and until equilibrium is reached. Over those binding curves measured at different times, we compute the dynamic range: the fold change required in input to elicit a change from 10 to 90% of maximum output, finding that it evolves in time differently and controlled by different parameters in the two situations that are identical in equilibrium. Deciphering which is the microscopic model that leads to a given binding curve adds understanding on the molecular mechanisms at play, and thus, is a valuable tool. The methods developed in this article were tested both with simulated and experimental data, showing to be robust to noise and experimental constraints.Author summary: When two successive events occur, it may make sense to know if they affect somehow each other, particularly if the properties of the second event are modified by the occurrence of the first one. Two scenarios lead to the same overall outcome: first, the two events are identical but they interfere with each other, and second, the two events are independent but non identical. The interference caused in the first scenario produces the same result as having a second event with different properties. Now, let’s name these events as bindings, the interference as negative cooperativity, and the non-identical events as independent binding. In this work we focus on the dynamic process by which the two scenarios produce the same result. We selected a relevant but not characterized before property of the binding process, called its dynamic range, and found it behaves differently in these two scenarios and controlled by different parameters of interest. Based on this feature, we developed and algorithm to distinguish between negative cooperativity and independent binding based on the time evolution of the dynamic range. This tool allows to discover the microscopic model behind the data and may be useful in other similar problems in cell signaling.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1007929

DOI: 10.1371/journal.pcbi.1007929

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