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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

The comparison between the cases where the free ligand concentration is barely affected by interaction and exhausted as a result of buffering. The kinetics of multisite protein species alterations in response to step change in ligand concentration from UT0/K = 0.01 to UT1/K = 200 for two different ratios of the protein concentration to the affinities of the binding sites LT/K = 2 a for the intermediate species N1/LT, N2/LT and N3/LT, b for the apo- and fully bound species N0/LT and N4/LT respectively) and LT/K = 50 c for the intermediate species N1/LT, N2/LT and N3/LT, d for the apo- and fully bound species N0/LT and N4/LT respectively). The model predicts that due to the lack of available ligand and buffering by the multisite protein in the case of limited amount of ligand, the multisite protein is unable to become fully saturated after the step change in ligand, and the majority of the ligand becomes distributed among the intermediate species. e. The comparison of the dynamics of free ligand concentration U/K after step change in ligand. The amount of available ligand is barely altered for LT/K = 2, and exhausted when the ratio of total protein concentration to the binding constant is LT/K = 50
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Fig8: The comparison between the cases where the free ligand concentration is barely affected by interaction and exhausted as a result of buffering. The kinetics of multisite protein species alterations in response to step change in ligand concentration from UT0/K = 0.01 to UT1/K = 200 for two different ratios of the protein concentration to the affinities of the binding sites LT/K = 2 a for the intermediate species N1/LT, N2/LT and N3/LT, b for the apo- and fully bound species N0/LT and N4/LT respectively) and LT/K = 50 c for the intermediate species N1/LT, N2/LT and N3/LT, d for the apo- and fully bound species N0/LT and N4/LT respectively). The model predicts that due to the lack of available ligand and buffering by the multisite protein in the case of limited amount of ligand, the multisite protein is unable to become fully saturated after the step change in ligand, and the majority of the ligand becomes distributed among the intermediate species. e. The comparison of the dynamics of free ligand concentration U/K after step change in ligand. The amount of available ligand is barely altered for LT/K = 2, and exhausted when the ratio of total protein concentration to the binding constant is LT/K = 50

Mentions: The previous sections considered the physiological case where the ligand concentration was above saturation level meaning that the ligand-multisite protein interactions did not affect the availability of the ligand. Here the case when the amount of ligand is limited is considered. This can occur in cases when the ligand concentration level is comparable to the multisite protein availability. The model predictions show the relative redistribution of the ligand in the free and bound states. The responses of a multisite protein with four identical binding sites to ligand concentration step change (Eqs. (44) and (45) in Methods) for two different protein concentrations, LT/K = 2 and LT/K = 50, were studied (Fig. 8). Instead of considering absolute ligand concentrations, the approach considered ratios of the ligand concentration to the affinities of the binding sites. A borderline case where the free ligand concentration is barely affected by interaction was considered (Fig. 8a and b) as well as a smaller total ligand concentration where the free ligand is nearly exhausted as a result of buffering by the multisite protein (Fig. 8c and d). The comparison of the free ligand concentration (Eqs. (43) and (44) in Methods) for these two cases is shown in Fig. 8e. The model predicts that the strongest effect of the ligand availability can be observed for the multisite protein conformations with three and four (fully saturated) bound ligands. A possible explanation for this phenomenon may be that the multisite protein conformations, which form complexes with smaller number of ligand molecules by definition, do not require significant amount of ligand and as a result are not strongly affected under conditions when the free ligand is limited. Whereas the multisite protein interactions with the larger number of ions occur after the significant amount of ligand is “used up” to form the intermediate conformations, however is still required for conformations with larger number of ions. As a result the final levels of the conformations with three and four ions are affected. It can also be seen from Fig. 8 that the shapes of the intermediate conformations time lines are skewed.Fig. 8


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)

The comparison between the cases where the free ligand concentration is barely affected by interaction and exhausted as a result of buffering. The kinetics of multisite protein species alterations in response to step change in ligand concentration from UT0/K = 0.01 to UT1/K = 200 for two different ratios of the protein concentration to the affinities of the binding sites LT/K = 2 a for the intermediate species N1/LT, N2/LT and N3/LT, b for the apo- and fully bound species N0/LT and N4/LT respectively) and LT/K = 50 c for the intermediate species N1/LT, N2/LT and N3/LT, d for the apo- and fully bound species N0/LT and N4/LT respectively). The model predicts that due to the lack of available ligand and buffering by the multisite protein in the case of limited amount of ligand, the multisite protein is unable to become fully saturated after the step change in ligand, and the majority of the ligand becomes distributed among the intermediate species. e. The comparison of the dynamics of free ligand concentration U/K after step change in ligand. The amount of available ligand is barely altered for LT/K = 2, and exhausted when the ratio of total protein concentration to the binding constant is LT/K = 50
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig8: The comparison between the cases where the free ligand concentration is barely affected by interaction and exhausted as a result of buffering. The kinetics of multisite protein species alterations in response to step change in ligand concentration from UT0/K = 0.01 to UT1/K = 200 for two different ratios of the protein concentration to the affinities of the binding sites LT/K = 2 a for the intermediate species N1/LT, N2/LT and N3/LT, b for the apo- and fully bound species N0/LT and N4/LT respectively) and LT/K = 50 c for the intermediate species N1/LT, N2/LT and N3/LT, d for the apo- and fully bound species N0/LT and N4/LT respectively). The model predicts that due to the lack of available ligand and buffering by the multisite protein in the case of limited amount of ligand, the multisite protein is unable to become fully saturated after the step change in ligand, and the majority of the ligand becomes distributed among the intermediate species. e. The comparison of the dynamics of free ligand concentration U/K after step change in ligand. The amount of available ligand is barely altered for LT/K = 2, and exhausted when the ratio of total protein concentration to the binding constant is LT/K = 50
Mentions: The previous sections considered the physiological case where the ligand concentration was above saturation level meaning that the ligand-multisite protein interactions did not affect the availability of the ligand. Here the case when the amount of ligand is limited is considered. This can occur in cases when the ligand concentration level is comparable to the multisite protein availability. The model predictions show the relative redistribution of the ligand in the free and bound states. The responses of a multisite protein with four identical binding sites to ligand concentration step change (Eqs. (44) and (45) in Methods) for two different protein concentrations, LT/K = 2 and LT/K = 50, were studied (Fig. 8). Instead of considering absolute ligand concentrations, the approach considered ratios of the ligand concentration to the affinities of the binding sites. A borderline case where the free ligand concentration is barely affected by interaction was considered (Fig. 8a and b) as well as a smaller total ligand concentration where the free ligand is nearly exhausted as a result of buffering by the multisite protein (Fig. 8c and d). The comparison of the free ligand concentration (Eqs. (43) and (44) in Methods) for these two cases is shown in Fig. 8e. The model predicts that the strongest effect of the ligand availability can be observed for the multisite protein conformations with three and four (fully saturated) bound ligands. A possible explanation for this phenomenon may be that the multisite protein conformations, which form complexes with smaller number of ligand molecules by definition, do not require significant amount of ligand and as a result are not strongly affected under conditions when the free ligand is limited. Whereas the multisite protein interactions with the larger number of ions occur after the significant amount of ligand is “used up” to form the intermediate conformations, however is still required for conformations with larger number of ions. As a result the final levels of the conformations with three and four ions are affected. It can also be seen from Fig. 8 that the shapes of the intermediate conformations time lines are skewed.Fig. 8

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