A danger of low copy numbers for inferring incorrect cooperativity degree
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RESEARCH
Open Access
A danger of low copy numbers for inferring incorrect cooperativity degree Zoran Konkoli Correspondence: zorank@chalmers. se Chalmers University of Technology, Department of Microtechnology and Nanoscience, Bionano Systems Laboratory, Sweden
Abstract Background: A dose-response curve depicts the fraction of bound proteins as a function of unbound ligands. Dose-response curves are used to measure the cooperativity degree of a ligand binding process. Frequently, the Hill function is used to fit the experimental data. The Hill function is parameterized by the value of the dissociation constant and the Hill coefficient, which describes the cooperativity degree. The use of Hill’s model and the Hill function has been heavily criticised in this context, predominantly the assumption that all ligands bind at once, which resulted in further refinements of the model. In this work, the validity of the Hill function has been studied from an entirely different point of view. In the limit of low copy numbers the dynamics of the system becomes noisy. The goal was to asses the validity of the Hill function in this limit, and to see in what ways the effects of the fluctuations change the form of the dose-response curves. Results: Dose-response curves were computed taking into account effects of fluctuations. The effects of fluctuations were described at the lowest order (the second moment of the particle number distribution) by using the previously developed Pair Approach Reaction Noise EStimator (PARNES) method. The stationary state of the system is described by nine equations with nine unknowns. To obtain fluctuation-corrected dose-response curves the equations have been investigated numerically. Conclusions: The Hill function cannot describe dose-response curves in a low particle limit. First, dose-response curves are not solely parameterized by the dissociation constant and the Hill coefficient. In general, the shape of a doseresponse curve depends on the variables that describe how an experiment (ensemble) is designed. Second, dose-response curves are multi-valued in a rather non-trivial way.
Background The Hill function is frequently used to infer the degree of cooperativity of the chemical reaction in which ligand molecules bind to a protein [1]. Often, the binding of a ligand increases the association rate for the binding of the next ligand. Such reactions are said to be (positively) cooperative. There are examples of cooperative reactions in cell biology. The classical example is the binding of oxygen molecules by hemoglobin [1]. Other perhaps less well-known examples would be parts of the Notch signaling and 30 S ribosome assembly processes [2], as well as the assembly of cholesterol-sphingomyelin complexes [3]. Also, the noise characteristics of various ligand binding reactions © 2010 Konkoli; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use
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