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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

Comparative analysis of cooperative versus non-cooperative Ca2+ binding to CaM. Two mathematical models for Ca2+-Cam interactions are compared under the assumptions for the presence and absence of cooperative binding. The comparison between the two scenarios was performed under steady state conditions (a), (b) and in response to a step change in Ca2+ concentration (c), (d). The model predicts that the cooperativity influences the maximums of the concentrations for the intermediate forms (N1/LT, N2/LT and N3/LT) as well as the steady-state levels of apo- (N0/LT) and fully saturated forms (N4/LT). However, the difference observed in the distribution of the conformation species in the presence and absence of the cooperative binding is quantitative while the overall shape of the distributions remains unchanged. Due to this finding the following model analysis was performed without cooperative binding assumptions
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Fig7: Comparative analysis of cooperative versus non-cooperative Ca2+ binding to CaM. Two mathematical models for Ca2+-Cam interactions are compared under the assumptions for the presence and absence of cooperative binding. The comparison between the two scenarios was performed under steady state conditions (a), (b) and in response to a step change in Ca2+ concentration (c), (d). The model predicts that the cooperativity influences the maximums of the concentrations for the intermediate forms (N1/LT, N2/LT and N3/LT) as well as the steady-state levels of apo- (N0/LT) and fully saturated forms (N4/LT). However, the difference observed in the distribution of the conformation species in the presence and absence of the cooperative binding is quantitative while the overall shape of the distributions remains unchanged. Due to this finding the following model analysis was performed without cooperative binding assumptions

Mentions: In order to investigate the influence of cooperativity, we chose a well-characterized protein, CaM, as the model object. The CaM protein contains two independent EF-hand globular domains, with two binding sites [1, 3, 5, 16, 17]. The sites within each of the domains cooperatively influence each other. It has been reported that cooperative binding occurs between two neighbouring sites within the N- and C- terminal domains of CaM [22, 53, 54]. Figure 7 shows the model predictions for CaM where we assume that the molecule has two independent domains, with two identical cooperative sites. In the first domain the affinity of one site changes from K1 = 0.9 μM to K1c = 0.2 μM if the other site is occupied and in the second domain the affinity changes from K2 = 0.8 μM to K2c = 0.1 μM (Eq. (28) in Methods) [22]. Figure 7a and b show the influence of cooperativity on the steady-state concentrations of CaM with certain number of bound sites. The presence of cooperativity shifts the dose-response characteristics along the ligand concentration axis and changes the magnitude of intermediate conformations allowing more developed selective regulation of the activity of CaM. The investigation of the dynamic properties of co-operativity in CaM (Fig. 7c and d) for intermediate, apo- and saturated species revealed that the cooperativity influences the magnitudes of time-dependent characteristics. The proposed model predicts that the cooperative binding leads to more pronounced selective effects for intermediate conformations and higher differences between the initial and steady-state levels for the apo- and saturated forms.Fig. 7


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)

Comparative analysis of cooperative versus non-cooperative Ca2+ binding to CaM. Two mathematical models for Ca2+-Cam interactions are compared under the assumptions for the presence and absence of cooperative binding. The comparison between the two scenarios was performed under steady state conditions (a), (b) and in response to a step change in Ca2+ concentration (c), (d). The model predicts that the cooperativity influences the maximums of the concentrations for the intermediate forms (N1/LT, N2/LT and N3/LT) as well as the steady-state levels of apo- (N0/LT) and fully saturated forms (N4/LT). However, the difference observed in the distribution of the conformation species in the presence and absence of the cooperative binding is quantitative while the overall shape of the distributions remains unchanged. Due to this finding the following model analysis was performed without cooperative binding assumptions
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig7: Comparative analysis of cooperative versus non-cooperative Ca2+ binding to CaM. Two mathematical models for Ca2+-Cam interactions are compared under the assumptions for the presence and absence of cooperative binding. The comparison between the two scenarios was performed under steady state conditions (a), (b) and in response to a step change in Ca2+ concentration (c), (d). The model predicts that the cooperativity influences the maximums of the concentrations for the intermediate forms (N1/LT, N2/LT and N3/LT) as well as the steady-state levels of apo- (N0/LT) and fully saturated forms (N4/LT). However, the difference observed in the distribution of the conformation species in the presence and absence of the cooperative binding is quantitative while the overall shape of the distributions remains unchanged. Due to this finding the following model analysis was performed without cooperative binding assumptions
Mentions: In order to investigate the influence of cooperativity, we chose a well-characterized protein, CaM, as the model object. The CaM protein contains two independent EF-hand globular domains, with two binding sites [1, 3, 5, 16, 17]. The sites within each of the domains cooperatively influence each other. It has been reported that cooperative binding occurs between two neighbouring sites within the N- and C- terminal domains of CaM [22, 53, 54]. Figure 7 shows the model predictions for CaM where we assume that the molecule has two independent domains, with two identical cooperative sites. In the first domain the affinity of one site changes from K1 = 0.9 μM to K1c = 0.2 μM if the other site is occupied and in the second domain the affinity changes from K2 = 0.8 μM to K2c = 0.1 μM (Eq. (28) in Methods) [22]. Figure 7a and b show the influence of cooperativity on the steady-state concentrations of CaM with certain number of bound sites. The presence of cooperativity shifts the dose-response characteristics along the ligand concentration axis and changes the magnitude of intermediate conformations allowing more developed selective regulation of the activity of CaM. The investigation of the dynamic properties of co-operativity in CaM (Fig. 7c and d) for intermediate, apo- and saturated species revealed that the cooperativity influences the magnitudes of time-dependent characteristics. The proposed model predicts that the cooperative binding leads to more pronounced selective effects for intermediate conformations and higher differences between the initial and steady-state levels for the apo- and saturated forms.Fig. 7

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