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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

Kinetics predictions for multisite protein species with marginally different association constants. The kinetics of multisite protein species was investigated for the intermediate (N1/LT, N2/LT and N3/LT in a as well as the apo- and fully bound conformations (N0/LT and N4/LT respectively in b in response to step change of ligand from U0/K = 0.001 to U1/K = 1.43 for marginally different association constants h1 = 1, h2 = 0.9, h3 = 0.8, h4 = 0.7 and the same dissociation constants h1− = h2− = h3− = h4− = 1. Similar analysis was also performed when step change was U0/K = 0.001, U1/K = 100 for apo- (c) and fully bound (d) forms. The calculations show that the final level of the multisite protein species are defined by the ligand concentration after the step change. It is very clear that the fully bound species are not saturated and most of the ligand is distributed among species bound to fewer ligands. However, step change application of ligand with much higher concentration from U0/K = 0.001 to U1/K = 100 for apo- (c) and fully bound (d) species demonstrate that the application of higher concentrations of ligand causes fully saturates the protein
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Fig5: Kinetics predictions for multisite protein species with marginally different association constants. The kinetics of multisite protein species was investigated for the intermediate (N1/LT, N2/LT and N3/LT in a as well as the apo- and fully bound conformations (N0/LT and N4/LT respectively in b in response to step change of ligand from U0/K = 0.001 to U1/K = 1.43 for marginally different association constants h1 = 1, h2 = 0.9, h3 = 0.8, h4 = 0.7 and the same dissociation constants h1− = h2− = h3− = h4− = 1. Similar analysis was also performed when step change was U0/K = 0.001, U1/K = 100 for apo- (c) and fully bound (d) forms. The calculations show that the final level of the multisite protein species are defined by the ligand concentration after the step change. It is very clear that the fully bound species are not saturated and most of the ligand is distributed among species bound to fewer ligands. However, step change application of ligand with much higher concentration from U0/K = 0.001 to U1/K = 100 for apo- (c) and fully bound (d) species demonstrate that the application of higher concentrations of ligand causes fully saturates the protein

Mentions: To investigate the impact of the dissociation constants of individual binding sites we employed the multisite protein model (please see subsection “Multisite proteins with four different ligand binding sites” in Methods) with marginally (Fig. 5) and significantly different association constants (Fig. 6). The main result that follows from the analysis of the intermediate conformation curves is that the affinities of the different binding sites mainly affect the magnitudes of corresponding protein conformation. For example, the conformation of a multisite protein corresponding to the one ligand bound state is present in lower concentration if the affinity of the binding centre is lower. However the overall shape of the concentration dependent profile has not changed. This property is very similar to the case of steady-state dependence on the ligand concentration. The only difference is that the bell shape dependence on time during the kinetic response is partially skewed. However, significant variation in affinities changes the magnitude, and also leads to the asynchronous kinetics of the intermediate conformations.Fig. 5


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)

Kinetics predictions for multisite protein species with marginally different association constants. The kinetics of multisite protein species was investigated for the intermediate (N1/LT, N2/LT and N3/LT in a as well as the apo- and fully bound conformations (N0/LT and N4/LT respectively in b in response to step change of ligand from U0/K = 0.001 to U1/K = 1.43 for marginally different association constants h1 = 1, h2 = 0.9, h3 = 0.8, h4 = 0.7 and the same dissociation constants h1− = h2− = h3− = h4− = 1. Similar analysis was also performed when step change was U0/K = 0.001, U1/K = 100 for apo- (c) and fully bound (d) forms. The calculations show that the final level of the multisite protein species are defined by the ligand concentration after the step change. It is very clear that the fully bound species are not saturated and most of the ligand is distributed among species bound to fewer ligands. However, step change application of ligand with much higher concentration from U0/K = 0.001 to U1/K = 100 for apo- (c) and fully bound (d) species demonstrate that the application of higher concentrations of ligand causes fully saturates the protein
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig5: Kinetics predictions for multisite protein species with marginally different association constants. The kinetics of multisite protein species was investigated for the intermediate (N1/LT, N2/LT and N3/LT in a as well as the apo- and fully bound conformations (N0/LT and N4/LT respectively in b in response to step change of ligand from U0/K = 0.001 to U1/K = 1.43 for marginally different association constants h1 = 1, h2 = 0.9, h3 = 0.8, h4 = 0.7 and the same dissociation constants h1− = h2− = h3− = h4− = 1. Similar analysis was also performed when step change was U0/K = 0.001, U1/K = 100 for apo- (c) and fully bound (d) forms. The calculations show that the final level of the multisite protein species are defined by the ligand concentration after the step change. It is very clear that the fully bound species are not saturated and most of the ligand is distributed among species bound to fewer ligands. However, step change application of ligand with much higher concentration from U0/K = 0.001 to U1/K = 100 for apo- (c) and fully bound (d) species demonstrate that the application of higher concentrations of ligand causes fully saturates the protein
Mentions: To investigate the impact of the dissociation constants of individual binding sites we employed the multisite protein model (please see subsection “Multisite proteins with four different ligand binding sites” in Methods) with marginally (Fig. 5) and significantly different association constants (Fig. 6). The main result that follows from the analysis of the intermediate conformation curves is that the affinities of the different binding sites mainly affect the magnitudes of corresponding protein conformation. For example, the conformation of a multisite protein corresponding to the one ligand bound state is present in lower concentration if the affinity of the binding centre is lower. However the overall shape of the concentration dependent profile has not changed. This property is very similar to the case of steady-state dependence on the ligand concentration. The only difference is that the bell shape dependence on time during the kinetic response is partially skewed. However, significant variation in affinities changes the magnitude, and also leads to the asynchronous kinetics of the intermediate conformations.Fig. 5

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