Receptor–ligand kinetics

In biochemistry, receptor–ligand kinetics is a branch of chemical kinetics in which the kinetic species are defined by different non-covalent bindings and/or conformations of the molecules involved, which are denoted as receptor(s) and ligand(s). Receptor–ligand binding kinetics also involves the on- and off-rates of binding.[1]

A main goal of receptor–ligand kinetics is to determine the concentrations of the various kinetic species (i.e., the states of the receptor and ligand) at all times, from a given set of initial concentrations and a given set of rate constants. In a few cases, an analytical solution of the rate equations may be determined, but this is relatively rare. However, most rate equations can be integrated numerically, or approximately, using the steady-state approximation.[1] A less ambitious goal is to determine the final equilibrium concentrations of the kinetic species, which is adequate for the interpretation of equilibrium binding data.

A converse goal of receptor–ligand kinetics is to estimate the rate constants and/or dissociation constants of the receptors and ligands from experimental kinetic or equilibrium data. The total concentrations of receptor and ligands are sometimes varied systematically to estimate these constants.

Binding kinetics

The binding constant is a special case of the equilibrium constant ${\displaystyle K}$. It is associated with the binding and unbinding reaction of receptor (R) and ligand (L) molecules, which is formalized as:

${\displaystyle {\ce {{R}+ {L}<=> {RL}}}}$.

The reaction is characterized by the on-rate constant ${\displaystyle k_{\rm {on}}}$ and the off-rate constant ${\displaystyle k_{\rm {off}}}$, which have units of 1/(concentration time) and 1/time, respectively. In equilibrium, the forward binding transition ${\displaystyle {\ce {{R}+ {L}-> {RL}}}}$ should be balanced by the backward unbinding transition ${\displaystyle {\ce {{RL}-> {R}+ {L}}}}$. That is,

${\displaystyle k_{{\ce {on}}}\,[{\ce {R}}]\,[{\ce {L}}]=k_{{\ce {off}}}\,[{\ce {RL}}]}$,

where ${\displaystyle {\ce {[{R}]}}}$, ${\displaystyle {\ce {[{L}]}}}$ and ${\displaystyle {\ce {[{RL}]}}}$ represent the concentration of unbound free receptors, the concentration of unbound free ligand and the concentration of receptor-ligand complexes. The binding constant, or the association constant ${\displaystyle K_{\rm {a}}}$ is defined by

${\displaystyle K_{\rm {a}}={k_{\ce {on}} \over k_{\ce {off}}}={\ce {[{RL}] \over {[{R}]\,[{L}]}}}}$.

Simplest case: single receptor and single ligand bind to form a complex

The simplest example of receptor–ligand kinetics is that of a single ligand L binding to a single receptor R to form a single complex C

${\displaystyle {\ce {{R}+ {L}<-> {C}}}}$

The equilibrium concentrations are related by the dissociation constant K_d

${\displaystyle K_{d}\ {\stackrel {\mathrm {def} }{=}}\ {\frac {k_{-1}}{k_{1}}}={\frac {[{\ce {R}}]_{eq}[{\ce {L}}]_{eq}}{[{\ce {C}}]_{eq}}}}$

where k₁ and k₋₁ are the forward and backward rate constants, respectively. The total concentrations of receptor and ligand in the system are constant

${\displaystyle R_{tot}\ {\stackrel {\mathrm {def} }{=}}\ [{\ce {R}}]+[{\ce {C}}]}$

${\displaystyle L_{tot}\ {\stackrel {\mathrm {def} }{=}}\ [{\ce {L}}]+[{\ce {C}}]}$

Thus, only one concentration of the three ([R], [L] and [C]) is independent; the other two concentrations may be determined from R_tot, L_tot and the independent concentration.

This system is one of the few systems whose kinetics can be determined analytically. Choosing [R] as the independent concentration and representing the concentrations by italic variables for brevity (e.g., ${\displaystyle R\ {\stackrel {\mathrm {def} }{=}}\ [{\ce {R}}]}$), the kinetic rate equation can be written

${\displaystyle {\frac {dR}{dt}}=-k_{1}RL+k_{-1}C=-k_{1}R(L_{tot}-R_{tot}+R)+k_{-1}(R_{tot}-R)}$

Dividing both sides by k₁ and introducing the constant 2E = R_tot - L_tot - K_d, the rate equation becomes

${\displaystyle {\frac {1}{k_{1}}}{\frac {dR}{dt}}=-R^{2}+2ER+K_{d}R_{tot}=-\left(R-R_{+}\right)\left(R-R_{-}\right)}$

where the two equilibrium concentrations ${\displaystyle R_{\pm }\ {\stackrel {\mathrm {def} }{=}}\ E\pm D}$ are given by the quadratic formula and D is defined

${\displaystyle D\ {\stackrel {\mathrm {def} }{=}}\ {\sqrt {E^{2}+R_{tot}K_{d}}}}$

However, only the ${\displaystyle R_{+}}$ equilibrium has a positive concentration, corresponding to the equilibrium observed experimentally.

Separation of variables and a partial-fraction expansion yield the integrable ordinary differential equation

${\displaystyle \left\{{\frac {1}{R-R_{+}}}-{\frac {1}{R-R_{-}}}\right\}dR=-2Dk_{1}dt}$

whose solution is

${\displaystyle \log \left|R-R_{+}\right|-\log \left|R-R_{-}\right|=-2Dk_{1}t+\phi _{0}}$

or, equivalently,

${\displaystyle g=exp(-2Dk_{1}t+\phi _{0})}$

${\displaystyle R(t)={\frac {R_{+}-gR_{-}}{1-g}}}$

for association, and

${\displaystyle R(t)={\frac {R_{+}+gR_{-}}{1+g}}}$

for dissociation, respectively; where the integration constant φ₀ is defined

${\displaystyle \phi _{0}\ {\stackrel {\mathrm {def} }{=}}\ \log \left|R(t=0)-R_{+}\right|-\log \left|R(t=0)-R_{-}\right|}$

From this solution, the corresponding solutions for the other concentrations ${\displaystyle C(t)}$ and ${\displaystyle L(t)}$ can be obtained.

See also

• Binding potential
• Patlak plot
• Scatchard plot

References

1. Srinivasan, Bharath (2020-09-27). "Words of advice: teaching enzyme kinetics". The FEBS Journal. doi:10.1111/febs.15537. ISSN 1742-464X.

Further reading

• D.A. Lauffenburger and J.J. Linderman (1993) Receptors: Models for Binding, Trafficking, and Signaling, Oxford University Press. ISBN 0-19-506466-6 (hardcover) and 0-19-510663-6 (paperback)