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Kinetic regulation of multi-ligand binding proteins.

Salakhieva DV, Sadreev II, Chen MZ, Umezawa Y, Evstifeev AI, Welsh GI, Kotov NV - BMC Syst Biol (2016)

Bottom Line: Therefore, buffering effects significantly influence the amounts of free ligands.The presented model makes predictions for the temporal distribution of multisite protein conformations in complex with variable numbers of ligands.Furthermore, it derives the characteristic time and the dynamics for the kinetic responses elicited by a ligand concentration change as a function of ligand concentration and the number of ligand binding sites.

View Article: PubMed Central - PubMed

Affiliation: Kazan (Volga Region) Federal University, 18 Kremlyovskaya St., 420008, Kazan, Russia.

ABSTRACT

Background: Second messengers, such as calcium, regulate the activity of multisite binding proteins in a concentration-dependent manner. For example, calcium binding has been shown to induce conformational transitions in the calcium-dependent protein calmodulin, under steady state conditions. However, intracellular concentrations of these second messengers are often subject to rapid change. The mechanisms underlying dynamic ligand-dependent regulation of multisite proteins require further elucidation.

Results: In this study, a computational analysis of multisite protein kinetics in response to rapid changes in ligand concentrations is presented. Two major physiological scenarios are investigated: i) Ligand concentration is abundant and the ligand-multisite protein binding does not affect free ligand concentration, ii) Ligand concentration is of the same order of magnitude as the interacting multisite protein concentration and does not change. Therefore, buffering effects significantly influence the amounts of free ligands. For each of these scenarios the influence of the number of binding sites, the temporal effects on intermediate apo- and fully saturated conformations and the multisite regulatory effects on target proteins are investigated.

Conclusions: The developed models allow for a novel and accurate interpretation of concentration and pressure jump-dependent kinetic experiments. The presented model makes predictions for the temporal distribution of multisite protein conformations in complex with variable numbers of ligands. Furthermore, it derives the characteristic time and the dynamics for the kinetic responses elicited by a ligand concentration change as a function of ligand concentration and the number of ligand binding sites. Effector proteins regulated by multisite ligand binding are shown to depend on ligand concentration in a highly nonlinear fashion.

No MeSH data available.


Related in: MedlinePlus

Model predictions for the half-maximal effective ligand concentrations as a function of the number of binding sites and ligand concentration. a. The dependence of the half-maximal effective ligand concentration, U00.5/K and Un0.5/K, for the apo- and saturated multisite protein conformations respectively, on the number of binding sites. The effect of the increasing of the amount of binding sites is negligible for the fully bound conformation. b. Calculations for the half-width between the half-maximal effective ligand concentrations as a function of the ligand concentration for proteins with two, three, four and five binding sites. c. The difference between ligand concentrations for the saturated multisite protein conformations when the protein species equal to 90 % and 10 % of the total concentration as a function of the ligand concentration for the proteins with one to six binding sites. d. The difference between ligand concentrations for the saturated multisite protein conformations when the protein species equal to 90 % and 10 % of the total concentration as a function of the number of binding sites up to six
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Fig2: Model predictions for the half-maximal effective ligand concentrations as a function of the number of binding sites and ligand concentration. a. The dependence of the half-maximal effective ligand concentration, U00.5/K and Un0.5/K, for the apo- and saturated multisite protein conformations respectively, on the number of binding sites. The effect of the increasing of the amount of binding sites is negligible for the fully bound conformation. b. Calculations for the half-width between the half-maximal effective ligand concentrations as a function of the ligand concentration for proteins with two, three, four and five binding sites. c. The difference between ligand concentrations for the saturated multisite protein conformations when the protein species equal to 90 % and 10 % of the total concentration as a function of the ligand concentration for the proteins with one to six binding sites. d. The difference between ligand concentrations for the saturated multisite protein conformations when the protein species equal to 90 % and 10 % of the total concentration as a function of the number of binding sites up to six

Mentions: Next, the ligand concentrations for half maximum effective ligand concentrations, U00.5 and Un0.5, for the apo- and saturated multisite protein conformations when the protein species equals 50 % of the total concentration were estimated (Eqs. (15) in Methods). This solution shows that the ligand concentration for the half maximal protein activity, known as EC50, would be equal to the equilibrium dissociation constant K (EC50 = K) for proteins with one binding site only (n = 1). Figure 2a shows the dependence of U00.5/K and Un0.5/K, on the number of binding sites. The model predicts that there is a significant change in the required ligand concentration Un0.5/K for the fully bound conformation, while U00.5/K does not change with time.Fig. 2


Kinetic regulation of multi-ligand binding proteins.

Salakhieva DV, Sadreev II, Chen MZ, Umezawa Y, Evstifeev AI, Welsh GI, Kotov NV - BMC Syst Biol (2016)

Model predictions for the half-maximal effective ligand concentrations as a function of the number of binding sites and ligand concentration. a. The dependence of the half-maximal effective ligand concentration, U00.5/K and Un0.5/K, for the apo- and saturated multisite protein conformations respectively, on the number of binding sites. The effect of the increasing of the amount of binding sites is negligible for the fully bound conformation. b. Calculations for the half-width between the half-maximal effective ligand concentrations as a function of the ligand concentration for proteins with two, three, four and five binding sites. c. The difference between ligand concentrations for the saturated multisite protein conformations when the protein species equal to 90 % and 10 % of the total concentration as a function of the ligand concentration for the proteins with one to six binding sites. d. The difference between ligand concentrations for the saturated multisite protein conformations when the protein species equal to 90 % and 10 % of the total concentration as a function of the number of binding sites up to six
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4835871&req=5

Fig2: Model predictions for the half-maximal effective ligand concentrations as a function of the number of binding sites and ligand concentration. a. The dependence of the half-maximal effective ligand concentration, U00.5/K and Un0.5/K, for the apo- and saturated multisite protein conformations respectively, on the number of binding sites. The effect of the increasing of the amount of binding sites is negligible for the fully bound conformation. b. Calculations for the half-width between the half-maximal effective ligand concentrations as a function of the ligand concentration for proteins with two, three, four and five binding sites. c. The difference between ligand concentrations for the saturated multisite protein conformations when the protein species equal to 90 % and 10 % of the total concentration as a function of the ligand concentration for the proteins with one to six binding sites. d. The difference between ligand concentrations for the saturated multisite protein conformations when the protein species equal to 90 % and 10 % of the total concentration as a function of the number of binding sites up to six
Mentions: Next, the ligand concentrations for half maximum effective ligand concentrations, U00.5 and Un0.5, for the apo- and saturated multisite protein conformations when the protein species equals 50 % of the total concentration were estimated (Eqs. (15) in Methods). This solution shows that the ligand concentration for the half maximal protein activity, known as EC50, would be equal to the equilibrium dissociation constant K (EC50 = K) for proteins with one binding site only (n = 1). Figure 2a shows the dependence of U00.5/K and Un0.5/K, on the number of binding sites. The model predicts that there is a significant change in the required ligand concentration Un0.5/K for the fully bound conformation, while U00.5/K does not change with time.Fig. 2

Bottom Line: Therefore, buffering effects significantly influence the amounts of free ligands.The presented model makes predictions for the temporal distribution of multisite protein conformations in complex with variable numbers of ligands.Furthermore, it derives the characteristic time and the dynamics for the kinetic responses elicited by a ligand concentration change as a function of ligand concentration and the number of ligand binding sites.

View Article: PubMed Central - PubMed

Affiliation: Kazan (Volga Region) Federal University, 18 Kremlyovskaya St., 420008, Kazan, Russia.

ABSTRACT

Background: Second messengers, such as calcium, regulate the activity of multisite binding proteins in a concentration-dependent manner. For example, calcium binding has been shown to induce conformational transitions in the calcium-dependent protein calmodulin, under steady state conditions. However, intracellular concentrations of these second messengers are often subject to rapid change. The mechanisms underlying dynamic ligand-dependent regulation of multisite proteins require further elucidation.

Results: In this study, a computational analysis of multisite protein kinetics in response to rapid changes in ligand concentrations is presented. Two major physiological scenarios are investigated: i) Ligand concentration is abundant and the ligand-multisite protein binding does not affect free ligand concentration, ii) Ligand concentration is of the same order of magnitude as the interacting multisite protein concentration and does not change. Therefore, buffering effects significantly influence the amounts of free ligands. For each of these scenarios the influence of the number of binding sites, the temporal effects on intermediate apo- and fully saturated conformations and the multisite regulatory effects on target proteins are investigated.

Conclusions: The developed models allow for a novel and accurate interpretation of concentration and pressure jump-dependent kinetic experiments. The presented model makes predictions for the temporal distribution of multisite protein conformations in complex with variable numbers of ligands. Furthermore, it derives the characteristic time and the dynamics for the kinetic responses elicited by a ligand concentration change as a function of ligand concentration and the number of ligand binding sites. Effector proteins regulated by multisite ligand binding are shown to depend on ligand concentration in a highly nonlinear fashion.

No MeSH data available.


Related in: MedlinePlus