Model parameters used in this study
| Parameter | Unit, symbol | Value | References |
| GEF, Sec3, v-SNARE, Cdc42 copy numbers | 1,000 (bem1Δ: 350), 377, 1,000, 3,000 | Saccharomyces Genome Database; M&M | |
| Maximal number of endocytic coats/early endocytic proteins (simplified endocytic pathway) | 200/1,000 | Saccharomyces Genome Database; M&M; Agrawal et al., 2010 | |
| Diffusion constant, Cdc42, GEF complex, and early endocytic patches | μm2s−1, Dm | 0.036 | M&M; Marco et al., 2007; Slaughter et al., 2009 |
| Diffusion constant, v-SNARES | μm2s−1, Dmslow | 0.0025 | Valdez-Taubas and Pelham, 2003; Marco et al., 2007 |
| Radius of the cell | μm, Rc | 3 | Layton et al., 2011; Savage et al., 2012 |
| GEF complex membrane-binding rate | s−1, k1 | 1 | From Bem1 FRAP (Layton et al., 2011; Savage et al., 2012) |
| GEF complex unbinding rate | s−1, k−1 | 1 | // |
| Bimolecular and trimolecular GEF complex–mediated Cdc42 activation rate | μM−1s−1, k2, k3 | 0.16, 0.63 | Layton et al., 2011; Savage et al., 2012 |
| Cdc42 inactivation rate | s−1, k−2 | 0.35 | // |
| Trimolecular complex dissociation rate | s−1, k−4 | 10 | // |
| Trimolecular complex assembly rates (from cytosol and membrane) | μM−1s−1, k4, k7 | 10, 10 | // |
| Cdc42-GDP binding and unbinding rates | s−1, kb, ku | 10, 0.02, rdi1Δ: 0.5, 0.001 | M&M |
| Actin cables detachment rate | s−1, kdet | 10 | M&M; Yang and Pon, 2002 |
| Cdc42-mediated cable nucleation rate | s−1, knuc | 0.1 | // |
| Coefficient for negative feedback on cable nucleation | unitless, β | 1.5 | // |
| Cable growth duration | s, dnuc | 6 | // |
| Coefficient for negative feedback on cable detachment | unitless, βtot | 2 | M&M; Marco et al., 2007; Slaughter et al., 2009 |
| Vesicle secretion rate from the internal buffer to actin cables | s−1, Kex | 3, LatA treated cells: 0 | Layton et al., 2011; Savage et al., 2012 |
| Rate of exocyst complex assembly per Sec3 protein | s−1, kexocyst | 10 | Liu et al., 2005; Domanska et al., 2009; Karatekin et al., 2010 |
| Rate of SNARE complex assembly | s−1, ksnare | 64 | // |
| Fusion rate | s−1, kfus | 40 | // |
| Maximal number of Cdc42-GTP per exocytic vesicle | 8 | From SV2 protein count in rat brain synaptic vesicles (Mutch et al., 2011) | |
| Maximal number of Cdc42-GDP per exocytic vesicle | 8 | // | |
| Maximal number of v-SNARES per vesicle | 8 | In vitro study (Liu et al., 2005; Domanska et al., 2009; Karatekin et al., 2010) | |
| Maximal number of endocytic coat proteins per exocytic vesicle | 1 complete coat | M&M | |
| Rate of early endocytic patch transition to coat recruitment phase (complete model) | s−1, kcoat | WT: 0.0103, sla2Δ,sla1Δ/bbc1Δ: 0.0025, LatA-treated cells: 0 | M&M |
| Duration of coat recruitment phase | s, dcoat | 5 | // |
| Rate of coated patch transition to Cdc42/v-SNARE loading phase | s−1, kgrowth | WT: 1, sla2Δ: 0.25 | // |
| Duration of Cdc42/v-SNARE loading phase and actin-driven growth | s, dgrowth | 10 | This study (Fig. 2 B); Liu et al., 2009; Carroll et al., 2012 |
| Endocytic scission rate | s−1, ksc | WT: 10, rvsΔ: 0.1, sla1Δ/bbc1Δ: 0.5 | Scission is not rate limiting in WT cells (Liu et al., 2009; Carroll et al., 2012). We chose ksc >> 1 |
| Cdc42-GDP endocytic loading rate | s−1, kload | 0.4 | Chosen to allow continuous cycling of cargo proteins |
| Cdc42-GTP endocytic loading rate | s−1, | 0.4 | // |
| v-SNARE endocytic loading rate | s−1, kloadv | 40 | // |
| Parameter | Unit, symbol | Value | References |
| GEF, Sec3, v-SNARE, Cdc42 copy numbers | 1,000 (bem1Δ: 350), 377, 1,000, 3,000 | Saccharomyces Genome Database; M&M | |
| Maximal number of endocytic coats/early endocytic proteins (simplified endocytic pathway) | 200/1,000 | Saccharomyces Genome Database; M&M; Agrawal et al., 2010 | |
| Diffusion constant, Cdc42, GEF complex, and early endocytic patches | μm2s−1, Dm | 0.036 | M&M; Marco et al., 2007; Slaughter et al., 2009 |
| Diffusion constant, v-SNARES | μm2s−1, Dmslow | 0.0025 | Valdez-Taubas and Pelham, 2003; Marco et al., 2007 |
| Radius of the cell | μm, Rc | 3 | Layton et al., 2011; Savage et al., 2012 |
| GEF complex membrane-binding rate | s−1, k1 | 1 | From Bem1 FRAP (Layton et al., 2011; Savage et al., 2012) |
| GEF complex unbinding rate | s−1, k−1 | 1 | // |
| Bimolecular and trimolecular GEF complex–mediated Cdc42 activation rate | μM−1s−1, k2, k3 | 0.16, 0.63 | Layton et al., 2011; Savage et al., 2012 |
| Cdc42 inactivation rate | s−1, k−2 | 0.35 | // |
| Trimolecular complex dissociation rate | s−1, k−4 | 10 | // |
| Trimolecular complex assembly rates (from cytosol and membrane) | μM−1s−1, k4, k7 | 10, 10 | // |
| Cdc42-GDP binding and unbinding rates | s−1, kb, ku | 10, 0.02, rdi1Δ: 0.5, 0.001 | M&M |
| Actin cables detachment rate | s−1, kdet | 10 | M&M; Yang and Pon, 2002 |
| Cdc42-mediated cable nucleation rate | s−1, knuc | 0.1 | // |
| Coefficient for negative feedback on cable nucleation | unitless, β | 1.5 | // |
| Cable growth duration | s, dnuc | 6 | // |
| Coefficient for negative feedback on cable detachment | unitless, βtot | 2 | M&M; Marco et al., 2007; Slaughter et al., 2009 |
| Vesicle secretion rate from the internal buffer to actin cables | s−1, Kex | 3, LatA treated cells: 0 | Layton et al., 2011; Savage et al., 2012 |
| Rate of exocyst complex assembly per Sec3 protein | s−1, kexocyst | 10 | Liu et al., 2005; Domanska et al., 2009; Karatekin et al., 2010 |
| Rate of SNARE complex assembly | s−1, ksnare | 64 | // |
| Fusion rate | s−1, kfus | 40 | // |
| Maximal number of Cdc42-GTP per exocytic vesicle | 8 | From SV2 protein count in rat brain synaptic vesicles (Mutch et al., 2011) | |
| Maximal number of Cdc42-GDP per exocytic vesicle | 8 | // | |
| Maximal number of v-SNARES per vesicle | 8 | In vitro study (Liu et al., 2005; Domanska et al., 2009; Karatekin et al., 2010) | |
| Maximal number of endocytic coat proteins per exocytic vesicle | 1 complete coat | M&M | |
| Rate of early endocytic patch transition to coat recruitment phase (complete model) | s−1, kcoat | WT: 0.0103, sla2Δ,sla1Δ/bbc1Δ: 0.0025, LatA-treated cells: 0 | M&M |
| Duration of coat recruitment phase | s, dcoat | 5 | // |
| Rate of coated patch transition to Cdc42/v-SNARE loading phase | s−1, kgrowth | WT: 1, sla2Δ: 0.25 | // |
| Duration of Cdc42/v-SNARE loading phase and actin-driven growth | s, dgrowth | 10 | This study (Fig. 2 B); Liu et al., 2009; Carroll et al., 2012 |
| Endocytic scission rate | s−1, ksc | WT: 10, rvsΔ: 0.1, sla1Δ/bbc1Δ: 0.5 | Scission is not rate limiting in WT cells (Liu et al., 2009; Carroll et al., 2012). We chose ksc >> 1 |
| Cdc42-GDP endocytic loading rate | s−1, kload | 0.4 | Chosen to allow continuous cycling of cargo proteins |
| Cdc42-GTP endocytic loading rate | s−1, | 0.4 | // |
| v-SNARE endocytic loading rate | s−1, kloadv | 40 | // |
// indicates same as previous row.