Fig 1.
Network diagram of the model of PD-1 signaling pathway.
Solid line represents a chemical reaction and dashed line represents catalytic effect on a reaction. Three types of chemical reactions are involved in the model: phosphorylation, dephosphorylation and association-dissociation. Lckactive (= Lckya+Lckyiya) is the total active form of Lck and similarly CPactive (= CP1+CP2) is the total Shp2 bound to PD-1. The model equations and parameters are given in Table 1 and Table 2. The description of model variables are listed in Table A in S1 File.
Table 1.
List of model equations.
Table 2.
Description of model parameters and their values.
Fig 2.
a) Time course of Shp2 (binding domain) recruitment for different concentrations of PD-1 receptor with 7.2 nM Lck and 100 nM Shp2. b) Time course of full length Shp2 recruitment by PD-1 receptor for different Lck concentrations with 300nM PD-1 and 50 nM Shp2. c) Time course of PI3K and Zap70 recruitment in absence of PD1 with 800 nM CD3ζ and CD28, 300nM Zap70 and PI3k, and 100nM Lck. d) Time course of PI3K and Zap70 disengagement in absence of Lck and PD1 with 300nMof Zap70i, 300nMof PI3Kb, and 200nMof CP2. e) and f) Effect of PD-1 on the time course of recruitment of PI3K and Zap70 respectively. For e and f the concentrations used were 50 nM CD3ζ, 300 nM Zap70, 250 nM CD28, 500 nM PI3K, 300 nM Lck, 100 nM PD-1 and Shp2.
Fig 3.
PD-1 dose response curves of various signaling molecules.
Concentrations of the components are as follows: 100nM Lck and CD3ζ; 200nM PI3K; 300nM CD28, Zap70, Shp2, LAT, Gads and SLP76. These concentrations are same as Hui et al [46]. Concentration of phosphorylated species is calculated as: Phosphorylated CD3ζ = CD3a+Zap70i+Zap70a1+Zap70a2, Phosphorylated CD28 = CD28a+PI3Kb, ZAP70 phosphorylated at Y315 = Zap70a1+Zap70a2, Zap70 phosphorylated at Y493 = Zap70a2, Lck phosphorylated at Y505 = Lckyi+Lckyiya+Lckpi, Lck phosphorylated at Y394 = Lckya+Lckyiya+Lckpi, Phosphorylated LAT = LATa+ Gadsa+Slp76i+Slp76a and Phosphorylated SLP76 = Slp76a.
Table 3.
Comparison of model calculated and experimental [46] IC50 values for PD-1 dose response curves.
Fig 4.
Recruitment of Shp2 after 30 min of simulation for various doses of Lck and PD-1 with 300 nM of Shp2 without (left) and with (right) self-dephosphorylation of PD-1 by Shp2.
Fig 5.
Effect of 300 nM PD-1 and Shp2 on (a) CD28 phosphorylation, (b) CD3ζ phosphorylation, (c) PI3K recruitment and (d) Zap70 recruitment for a range concentrations of Lck and CD28 or CD3ζ. Concentrations of other components are same as in Fig 3.
Fig 6.
Effect of PD-1 on (a) CD28 phosphorylation, (b) CD3ζ phosphorylation, (c) PI3K recruitment, (d)Zap70 recruitment, (e) activation of Zap70 (Zap70a2) and (f) activation of Slp76 (Slp76a) with 300 nM Shp2 and 100 nM Lck.
Fig 7.
(a) Time course of active and inactive Lck with and without PD-1. (b) Percentage of active Lck at 30 minutes for different PD-1 and Lck concentrations. (c) Effect of Lck dephosphorylation on Zap70 Y493 phosphorylation and (d) Slp76 phosphorylation. The concentrations used for a-d are 100nM CD3ζ and Lck, 300 nM Zap70, Shp2, LAT, SLP76 and Gads. Concentration of PD-1 was 300 nM for (a) and 500 nM for (c) and (d).
Fig 8.
Time course of free Shp2 in the absence of (a) Lck dephosphorylation and b) PD-1 dephosphorylation for different PD-1 concentrations with 100nM Lck and 300nM Shp2.
Fig 9.
Parameter sensitivity: Bar plot showing K-S Statistic measure of parameters tested for sensitivity of Shp2 recruitment (% of bound Shp2) (a), PI3K recruitment (% of bound PI3K) (b) and Slp76 activation (% of Slp76a) (c).