TABLE 2.
Definitions for all states found in the equations and in Figs. 3 and 6, recurring prefixes used in state names, subscripts for SscFv production in the equations, all icons found in the aforementioned figures, and recurring prefixes and suffixes used in parameter subscript labels
| State name | State definition |
|---|---|
| BiP | BiP (binding protein). |
| BiP·PDI·UP | BiP- and PDI (protein disulfide isomerase)-bound generic unfolded protein. |
| BiP·PDI·UscFv | BiP- and PDI-bound unfolded scFv (single-chain 4-4-20 antibody fragment) protein. |
| BiP·UP | BiP-bound generic unfolded protein. |
| BiP·UscFv | BiP-bound unfolded scFv protein. |
| Cytoplasmic scFv mRNA | Cytoplasmic scFv mRNA. |
| Cytoplasmic UscFv | Cytoplasmic unfolded scFv protein. |
| MscFv | Misfolded scFv protein. |
| Nuclear scFv mRNA | Nuclear scFv mRNA. |
| PDI | PDI. |
| PDI·UP | PDI-bound generic unfolded protein. |
| PDI·UscFv | PDI-bound unfolded scFv protein. |
| ptt'ing UscFv | Post-translational translocating unfolded scFv protein. |
| scFv mRNA | scFv mRNA. |
| SscFv | Secreted scFv. |
| UscFv | Unfolded scFv protein. |
| UP | Generic unfolded protein within the ER, excluding scFv. |
| State prefix |
Significance |
| M- | Misfolded. |
| S- | Secreted. |
| U- | Unfolded. |
 |
Subscript definition |
| -nominal | No BiP or PDI overexpressed. |
| -O.BiP | BiP overexpressed. |
| -O.BiP+PDI | Both BiP and PDI overexpressed. |
| -O.PDI | PDI overexpressed. |
| -SS | Steady-state. |
| Icon description |
Icon definition |
| Double-headed arrow | Indicates reversible reaction. |
| k– | Rate constant defined in Table 3. |
| Multiplication sign | Indicates an additional reactant in a second-order reaction. |
| Orange sunburst | BiP. |
| Pink/turquoise banana-shape | PDI acting as a foldase. |
| Pink/turquoise tooth-shape | PDI acting as a chaperone. |
| Plus sign | Indicates additional products of a reaction. |
| Red box containing text “VscFv” | scFv mRNA input. |
| Red curved line bundle | Folded scFv destined for secretion (SscFv). |
| Red oval containing text | scFv state defined by text. |
| Red sun containing text “deg.” | Indicates degradation of the reactant. |
| Single-headed arrow | Indicates irreversible reaction. |
| Turquoise oval containing text | Generic unfolded protein state defined by text. |
| Rate constant subscript prefix/suffix |
Significance |
| -b | Specific to a three-state model. |
| -bit | BiP-independent translocation into the ER. |
| (-)d | Degradation. |
| m- | Misfolding rate. |
| r- | Reverse reaction rate. |