Limits...
Cooperativity in Binding Processes: New Insights from Phenomenological Modeling.

Cattoni DI, Chara O, Kaufman SB, González Flecha FL - PLoS ONE (2015)

Bottom Line: Here we analyze the simplest phenomenological model that can account for cooperativity (i.e. ligand binding to a macromolecule with two binding sites) by generating equilibrium binding isotherms from deterministically simulated binding time courses.We show that the Hill coefficients determined for cooperative binding, provide a good measure of the Gibbs free energy of interaction among binding sites, and that their values are independent of the free energy of association for empty sites.We also conclude that although negative cooperativity and different classes of binding sites cannot be distinguished at equilibrium, they can be kinetically differentiated.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina.

ABSTRACT
Cooperative binding is one of the most interesting and not fully understood phenomena involved in control and regulation of biological processes. Here we analyze the simplest phenomenological model that can account for cooperativity (i.e. ligand binding to a macromolecule with two binding sites) by generating equilibrium binding isotherms from deterministically simulated binding time courses. We show that the Hill coefficients determined for cooperative binding, provide a good measure of the Gibbs free energy of interaction among binding sites, and that their values are independent of the free energy of association for empty sites. We also conclude that although negative cooperativity and different classes of binding sites cannot be distinguished at equilibrium, they can be kinetically differentiated. This feature highlights the usefulness of pre-equilibrium time-resolved strategies to explore binding models as a key complement of equilibrium experiments. Furthermore, our analysis shows that under conditions of strong negative cooperativity, the existence of some binding sites can be overlooked, and experiments at very high ligand concentrations can be a valuable tool to unmask such sites.

Show MeSH

Related in: MedlinePlus

Saturation curves for the three characteristic types of interactions between sites.The fractional saturation of a macromolecule by a ligand was simulated using Eq 1 for identical and independent sites (green line), positive cooperativity (orange line) and negative cooperativity (blue line). Panel A shows a detail of the curves at low ligand concentrations, whereas Panel B includes saturation values for a wide range of ligand concentration in a logarithmic scale
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4696654&req=5

pone.0146043.g001: Saturation curves for the three characteristic types of interactions between sites.The fractional saturation of a macromolecule by a ligand was simulated using Eq 1 for identical and independent sites (green line), positive cooperativity (orange line) and negative cooperativity (blue line). Panel A shows a detail of the curves at low ligand concentrations, whereas Panel B includes saturation values for a wide range of ligand concentration in a logarithmic scale

Mentions: Fig 1 exemplifies the three types of binding interactions between sites, showing the fractional saturation of binding sites in a macromolecule as a function of the free ligand concentration.


Cooperativity in Binding Processes: New Insights from Phenomenological Modeling.

Cattoni DI, Chara O, Kaufman SB, González Flecha FL - PLoS ONE (2015)

Saturation curves for the three characteristic types of interactions between sites.The fractional saturation of a macromolecule by a ligand was simulated using Eq 1 for identical and independent sites (green line), positive cooperativity (orange line) and negative cooperativity (blue line). Panel A shows a detail of the curves at low ligand concentrations, whereas Panel B includes saturation values for a wide range of ligand concentration in a logarithmic scale
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4696654&req=5

pone.0146043.g001: Saturation curves for the three characteristic types of interactions between sites.The fractional saturation of a macromolecule by a ligand was simulated using Eq 1 for identical and independent sites (green line), positive cooperativity (orange line) and negative cooperativity (blue line). Panel A shows a detail of the curves at low ligand concentrations, whereas Panel B includes saturation values for a wide range of ligand concentration in a logarithmic scale
Mentions: Fig 1 exemplifies the three types of binding interactions between sites, showing the fractional saturation of binding sites in a macromolecule as a function of the free ligand concentration.

Bottom Line: Here we analyze the simplest phenomenological model that can account for cooperativity (i.e. ligand binding to a macromolecule with two binding sites) by generating equilibrium binding isotherms from deterministically simulated binding time courses.We show that the Hill coefficients determined for cooperative binding, provide a good measure of the Gibbs free energy of interaction among binding sites, and that their values are independent of the free energy of association for empty sites.We also conclude that although negative cooperativity and different classes of binding sites cannot be distinguished at equilibrium, they can be kinetically differentiated.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina.

ABSTRACT
Cooperative binding is one of the most interesting and not fully understood phenomena involved in control and regulation of biological processes. Here we analyze the simplest phenomenological model that can account for cooperativity (i.e. ligand binding to a macromolecule with two binding sites) by generating equilibrium binding isotherms from deterministically simulated binding time courses. We show that the Hill coefficients determined for cooperative binding, provide a good measure of the Gibbs free energy of interaction among binding sites, and that their values are independent of the free energy of association for empty sites. We also conclude that although negative cooperativity and different classes of binding sites cannot be distinguished at equilibrium, they can be kinetically differentiated. This feature highlights the usefulness of pre-equilibrium time-resolved strategies to explore binding models as a key complement of equilibrium experiments. Furthermore, our analysis shows that under conditions of strong negative cooperativity, the existence of some binding sites can be overlooked, and experiments at very high ligand concentrations can be a valuable tool to unmask such sites.

Show MeSH
Related in: MedlinePlus