Abstract
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.
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- Christensen L. L. Theoretical analysis of protein concentration determination using biosensor technology under conditions of partial mass transport limitation. Anal Biochem. 1997 Jul 1;249(2):153–164. doi: 10.1006/abio.1997.2182. [DOI] [PubMed] [Google Scholar]
- Edwards D. A., Goldstein B., Cohen D. S. Transport effects on surface-volume biological reactions. J Math Biol. 1999 Dec;39(6):533–561. doi: 10.1007/s002850050177. [DOI] [PubMed] [Google Scholar]
- Edwards D. A. The effect of a receptor layer on the measurement of rate constants. Bull Math Biol. 2001 Mar;63(2):301–327. doi: 10.1006/bulm.2000.0224. [DOI] [PubMed] [Google Scholar]
- Glaser R. W. Antigen-antibody binding and mass transport by convection and diffusion to a surface: a two-dimensional computer model of binding and dissociation kinetics. Anal Biochem. 1993 Aug 15;213(1):152–161. doi: 10.1006/abio.1993.1399. [DOI] [PubMed] [Google Scholar]
- Goldstein B., Coombs D., He X., Pineda A. R., Wofsy C. The influence of transport on the kinetics of binding to surface receptors: application to cells and BIAcore. J Mol Recognit. 1999 Sep-Oct;12(5):293–299. doi: 10.1002/(SICI)1099-1352(199909/10)12:5<293::AID-JMR472>3.0.CO;2-M. [DOI] [PubMed] [Google Scholar]
- Goldstein B., Dembo M. Approximating the effects of diffusion on reversible reactions at the cell surface: ligand-receptor kinetics. Biophys J. 1995 Apr;68(4):1222–1230. doi: 10.1016/S0006-3495(95)80298-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Karlsson R., Fält A. Experimental design for kinetic analysis of protein-protein interactions with surface plasmon resonance biosensors. J Immunol Methods. 1997 Jan 15;200(1-2):121–133. doi: 10.1016/s0022-1759(96)00195-0. [DOI] [PubMed] [Google Scholar]
- Mason T., Pineda A. R., Wofsy C., Goldstein B. Effective rate models for the analysis of transport-dependent biosensor data. Math Biosci. 1999 Jul;159(2):123–144. doi: 10.1016/s0025-5564(99)00023-1. [DOI] [PubMed] [Google Scholar]
- Myszka D. G., He X., Dembo M., Morton T. A., Goldstein B. Extending the range of rate constants available from BIACORE: interpreting mass transport-influenced binding data. Biophys J. 1998 Aug;75(2):583–594. doi: 10.1016/S0006-3495(98)77549-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Myszka D. G., Morton T. A. CLAMP: a biosensor kinetic data analysis program. Trends Biochem Sci. 1998 Apr;23(4):149–150. doi: 10.1016/s0968-0004(98)01183-9. [DOI] [PubMed] [Google Scholar]
- Myszka D. G., Morton T. A., Doyle M. L., Chaiken I. M. Kinetic analysis of a protein antigen-antibody interaction limited by mass transport on an optical biosensor. Biophys Chem. 1997 Feb 28;64(1-3):127–137. doi: 10.1016/s0301-4622(96)02230-2. [DOI] [PubMed] [Google Scholar]
- Myszka DG. Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors. Curr Opin Biotechnol. 1997 Feb 1;8(1):50–57. doi: 10.1016/s0958-1669(97)80157-7. [DOI] [PubMed] [Google Scholar]
- Parsons I. D., Stockley P. G. Quantitation of the Escherichia coli methionine repressor-operator interaction by surface plasmon resonance is not affected by the presence of a dextran matrix. Anal Biochem. 1997 Dec 1;254(1):82–87. doi: 10.1006/abio.1997.2356. [DOI] [PubMed] [Google Scholar]
- Rich R. L., Myszka D. G. Advances in surface plasmon resonance biosensor analysis. Curr Opin Biotechnol. 2000 Feb;11(1):54–61. doi: 10.1016/s0958-1669(99)00054-3. [DOI] [PubMed] [Google Scholar]
- Schuck P. Kinetics of ligand binding to receptor immobilized in a polymer matrix, as detected with an evanescent wave biosensor. I. A computer simulation of the influence of mass transport. Biophys J. 1996 Mar;70(3):1230–1249. doi: 10.1016/S0006-3495(96)79681-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Witz J. Kinetic analysis of analyte binding by optical biosensors: hydrodynamic penetration of the analyte flow into the polymer matrix reduces the influence of mass transport. Anal Biochem. 1999 Jun 1;270(2):201–206. doi: 10.1006/abio.1999.4087. [DOI] [PubMed] [Google Scholar]
- Yarmush M. L., Patankar D. B., Yarmush D. M. An analysis of transport resistances in the operation of BIAcore; implications for kinetic studies of biospecific interactions. Mol Immunol. 1996 Oct;33(15):1203–1214. doi: 10.1016/s0161-5890(96)00075-2. [DOI] [PubMed] [Google Scholar]