Effective rate models for receptors distributed in a layer above a surface: application to cells and Biacore.
In the Biacore biosensor, a widely used tool for studying the kinetics of ligand/receptor binding, receptors are commonly localized to the sensor surface through attachment to polymers that extend from the surface to form a layer. The importance of the polymeric layer in analyzing data is controversial. The question of the effect of a binding layer also arises in the case of ligands interacting with binding sites distributed in the extracellular matrix of cells. To identify and quantify the effects of a binding layer on the estimation of association and dissociation rate constants, we derived effective rate coefficients. The expressions show that rate constants determined under the standard assumption that binding takes place on a two-dimensional surface underestimate the true reaction rate constants by a factor that depends on the ratio of the height of the layer to the mean free path of the ligand within the layer. We show that, for typical biological ligands, receptors, cells, and Biacore conditions, the binding layer will affect the interpretation of data only if transport of the ligand in the layer is slowed substantially--by one or two orders of magnitude--relative to transport outside the layer. From existing experiments and theory, it is not clear which Biacore experiments, if any, have transport within the dextran layer reduced to such an extent. We propose a method, based on the effective rate coefficients we have derived, for the experimental determination of ligand diffusion coefficients in a polymeric matrix.
Wofsy
Carla
C
Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico 87131, USA.
Goldstein
Byron
B
D001665:Binding Sites; D001703:Biophysics / Q000379:methods*; D003911:Dextrans / Q000737:chemistry; D004058:Diffusion; D007700:Kinetics; D008024:Ligands; D008962:Models, Theoretical; D011108:Polymers / Q000737:chemistry; D011485:Protein Binding; D013997:Time Factors
D003911:Dextrans; D008024:Ligands; D011108:Polymers