Kinases, Phosphatases & Phosphorylation Cascades

CED focus: Topics 4.2 and 4.3: protein modification and phosphorylation cascades; relaying and amplifying a signal; changes in cell function; effects of pathway inhibitors. Enzyme identities and reaction rates are not a memorisation list.

Close-up: each example protein has one regulatory phosphorylation site. Kinases transfer phosphate from ATP, producing ADP. Phosphatases catalyse hydrolysis, releasing inorganic phosphate (Pᵢ); this does not regenerate ATP. Proteins A and B are generic examples of activation and inhibition by phosphorylation, not two states of one protein whose regulatory effect changes. Selecting an example resets the close-up only. Enzymes bind the target during catalysis and separate afterward. The close-up shows water entering the phosphatase reaction and being consumed in hydrolysis; it is not a released product. One H₂O is used per phosphate removed. Enzyme shapes, docking positions and animation times are illustrative. Enzymes are reused.

Receptor conditions: a normal receptor undergoes an activating conformational change when the signal binds. The constitutively active condition supplies activation without ligand. The selected loss-of-function mutant retains ligand binding but cannot undergo the activating shape change. These are defined hypothetical conditions, not features of every receptor mutation. Pulses last 10 or 20 model seconds and preserve the chosen receptor, phosphatase and kinase-2 settings. Reset also preserves those conditions. Changing receptor condition during a run does not instantly remove existing downstream phosphates.

Pathway: the activated receptor is linked to an upstream kinase that directly contacts and phosphorylates K1 using ATP. No separate second messenger carries this first activation step. Each receptor activation illustrates one K1 encounter: approach, binding, ATP-to-protein phosphate transfer, then separation. This illustration follows model time and pauses with the simulation. The population kinetics continue independently of the representative encounter; subsequent encounters are not drawn individually. Reduced-motion mode shows the contact without movement. Three protein pools are represented by continuous phosphorylated fractions. The illustrative pools contain 4 kinase-1, 12 kinase-2 and 36 target equivalents; the drawings sample these populations. Phosphorylation activates all three selected proteins. A kinase can catalyse multiple phosphorylation events and is not consumed. Each event uses a fresh ATP from an assumed available supply. Kinase 2 inhibition blocks catalysis even if kinase 2 is phosphorylated.

After the signal ends: the normal receptor returns to its inactive conformation and new receptor-driven activation stops. A constitutively active receptor continues providing activation. Existing active kinases can still modify downstream substrates until phosphatases reset them, so the response may persist or briefly keep rising. Phosphatases work before, during and after the signal; their setting is independent of the signal here. Blocking them prevents this model's reset. This is signal termination, not a model of negative feedback.

Predict / explain: a normal pulse produces delayed downstream activation followed by gradual recovery. A phosphatase block allows phosphorylation to persist after signal withdrawal. A kinase-2 block allows upstream signalling and kinase-2 phosphorylation, but prevents target phosphorylation. Faster phosphatase activity lowers the response during signalling and accelerates reset.

Limits: generic schematic shapes, one phosphorylation site per protein, and relative model units. Real proteins may have multiple sites; phosphorylation can alter activity, interactions, location or stability. Phosphatases can themselves be regulated. ATP production, protein turnover, receptor desensitisation, second messengers and other termination mechanisms are omitted. The model conserves terminal-phosphate equivalents across ATP use, bound phosphate and free Pᵢ; these are explanatory bookkeeping values, not measured cellular inventories.

Biology references: Primary research: ligand-independent receptor activation; IUBMB: protein phosphatase uses H₂O; RCSB PDB-101: protein kinase action; RCSB PDB-101: phosphorylation can inhibit a protein; RCSB PDB: protein phosphatase. Curriculum alignment uses the supplied AP Biology Course and Exam Description (2025).