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

Biophysical Journal

Volumn 70, Issue 3, 1996, Pages 1230-1249

  Schuck, Peter ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEXTRAN; POLYMER;

ARTICLE; BINDING KINETICS; BIOSENSOR; COMPUTER MODEL; COMPUTER SIMULATION; DIFFUSION COEFFICIENT; GEL; LIGAND BINDING; PARTITION COEFFICIENT; REACTION TIME; RECEPTOR BINDING; REFRACTION INDEX; TRANSPORT KINETICS;

EID: 0030070499     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79681-9     Document Type: Article

References (74)

1. Balgi, G., D. E. Leckband, and J. M. Nitsche. 1995. Transport effects on the kinetics of protein-surface binding. Biophys. J. 68:2251-2260.
2. Borrebaeck, C. A. K., A.-C. Malmborg, C. Furebring, A. Michaelsson, S. Ward, L. Danielsson, and M. Ohlin. 1992. Kinetic analysis of recombinant antibody-antigen interactions: relation between structural domains and antigen binding. BioTechnology. 10:697-698.
3. Buckle, P. E., R. J. Davies, T. Kinning, D. Yeung, P, R. Edwards. D. Pollard-Knight, and C. R. Lowe. 1993. The resonant mirror: a novel optical sensor for direct sensing of biomolecular interactions. Part II: Applications. Biosens. Bioelectron. 8:355-363.
4. Calakos, N., M. K. Bennett, K. E. Peterson, and R. H. Scheller. 1994. Protein-protein interactions contributing to the specifity of intracellular vesicular trafficking. Science. 263:1146-1149.
5. Chaiken, I., S. Rosé, and R. Karlsson. 1992. Analysis of macromolecular interactions using immobilized lieands. Anal. Biochem. 201: 197-210
6. Cooper, L. J. N. D. Robertson, R. Granzow, and N. S. Greenspan. 1994. Variable domain-identical antibodies exhibit IgG subclass-related differences in affinity and kinetic constants as determined by surface plasmon resonance. Mol. Immunol 31:577-584.
7. Corti, A., C. Poiesi, S. Merli, and G. Cassani. 1994. Tumor necrosis factor (TNF)α quantification by ELISA and bioassay: effects of TNFα-soluble TNF receptor (p55) complex dissociation during assay incubations. J. Immunol. Methods. 177:191-198.
8. Crank, J. 1975. The Mathematics of Diffusion, 2nd ed. Clarendon Press, Oxford.
9. Crank, J., and P Nicholson. 1947. A practical method for numerical evaluation of solutions of partial differential equations of the heat-conduction type. Proc. Cambridge Phil. Soc. 43:50-67.
10. Cush, R., J. M. Cronin, W. J. Steward. C. H. Maule, J. Molloy, and N. J. Goddard. 1993 The resonant mirror: a novel optical biosensor for direct sensing of biomolecular interactions. Part I: Principle of operation and associated instrumentation. Biosens. Bioelectron. 8:347-353.
11. DeLisi, C. 1980 The biophysics of ligand-receptor interactions. Q. Rev. Biophys. 13:201-230.
12. de Gennes, P. G 1980. Conformation of polymers attached to an interface. Macromolecules. 13:1069-1075.
13. Fàgerstam, L. G., Å. Frostell-Karlsson, R. Karlsson, B. Persson, and I. Rönnberg. 1992. Biospecific interaction analysis using surface plasmon resonance detection applied to kinetic, binding site and concentration analysis. J. Chromatogr. 597:397-410.
14. Felder, S , M. Zhou, P Hu, J. Ureña. A. Ullrich. M. Chaudhuri, M. White, S. E. Shoelson, and J. Schlesinger 1993. SH2 domains exhibit high-affinity binding to tyrosine-phosphorylated peptides yet also exhibit rapid dissociation and exchange Mol. Cell. Biol. 13: 1449-1455.
15. Fisher, R J., and M. Fivash. 1994. Surface plasmon resonance based methods for measuring the kinetics and binding affinities of biomolecular interactions. Curr. Opin. Biotechnol. 5:389-395
16. Fisher, R. J., M. Fivash, J. Casas-Finet, S. Bladen, and K. L. McNitt. 1994. Real-time BIAcore measurement of Escherichia coli single-stranded DNA binding (SSB) protein to polydeoxythymidylic acid reveals single-state kinetics with steric cooperatrvity. Methods. A Companion to Methods Enzymol. 6:121-133.
17. Foote, J., and C. Milstein. 1991. Kinetic maturation of an immune response. Nature. 352:530-532.
18. Foote, J., and C. Milstein. 1994. Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA. 91:10370-10374.
19. George, A. J. T., R R. French, and M. J. Glennie 1995. Measurement of kinetic binding constants of a panel of anti-saporin antibodies using a resonant mirror biosensor. J. Immunol. Methods. 183:51-63.
20. Gershon, P. D., and S. Khiko. 1995. Stable chelating linkage for reversible immobilization of oligohistidine tagged proteins in the BIAcore surface plasmon resonance detector. J. Immunol. Methods. 183:65-76.
21. Giddings, J. C., E. Kucera, C. P. Russell, and M. N. Myers. 1968. Statistical theory for the equilibrium distribution of rigid molecules in inert porous networks. Exclusion chromatosraphy. J. Phys. Chem. 72: 4397-4408.
22. Glaser, R. W. 1993. 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. 213: 152-161.
23. Goldstein, B., and M. Dembo. 1995. Approximating the effects of diffusion on reversible reactions at the cell surface: ligand-receptor kinetics. Biophys. J. 68:1222-1230.
24. Gorti, S., and B. R. Ware. 1985. Probe diffusion in an aqueous polyelectrolyte solution. J. Chem. Phys. 83:6449-6456.
25. Guichard, G., N. Benkirane, G. Zeder-Lutz, M. H. V. Van Regenmortel, J.-P. Briand, and S. Muller. 1994. Antigenic mimicry of natural L-peptides with retro-inverso-peptidomimetics. Proc. Natl. Acad. Sci. USA. 91:9765-9769.
26. Haschemeyer, R. H., and W. F. Bowers. 1970. Exponential analysis of concentration or concentration difference data for discrete molecular weight distributions in sedimentation equilibrium. Biochemistry. 9:435-445.
27. Horenstein, A. L., C. Poiesi, L. DeMonte, M. Camagna, M. Mariani, A. Albertini, and F. Malavasi. 1993. Real-time kinetic analysis applied to the production of bispecific monoclonal antibodies for radioimmunodetection of cancer. Int. J. Clin. Lab. Res. 23:199-205.
28. Hsieh, H. V., and N. L. Thompson. 1994. Theory for measuring bivalent surface binding kinetics using total internal reflection with fluorescence photobleaching recovery. Biophys. J. 66:898-911.
29. Ito, W., and Y. Kurosawa, 1993. Development of an artificial antibody system with multiple valency using an Fv fragment fused to a fragment of protein A. J. Biol. Chem. 268:20668-20675.
30. Johne, B., M. Gadnell, and K. Hansen 1993. Epitope mapping and binding kinetics of monoclonal antibodies studied by real time biospecific interaction analysis using surface plasmon resonance. J. Immunol. Methods. 160:191-198.
31. Johnsson, B., S. Löfås, G. Lindquist, Å. Edstrom, R.-M. Müller Hillgren, and A. Hansson. 1995. Comparison of methods for immobilization to carboxymethyl dextran sensor surfaces by analysis of the specific activity of monoclonal antibodies. J. Mol. Recogn. 8:125-131.
32. Jönsson, U., L. Fägerstam, B. Ivarsson, B. Johnsson, R. Karlsson, K. Lundh, S. Lofås, B. Persson, H. Roos, I. Rönnberg, S. Sjolander, E. Stenberg, R. Ståhlberg, C. Urbaniczky, H. Östlin, and M. Malmqvist. 1991. Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technolosy. BioTechniques. 11: 620-627.
33. Jönsson, U., L. Fägerstam, S Löfås, E. Stenberg, R. Karlsson, Å. Frostell, F. Markey, and F. Schindler. 1993. Introducing a biosensor based technology for real-time biospecific interaction analysis. Ann. Biol. Clin. 51:19-26.
34. Karlsson, R., A. Michaelsson, and L. Mattson. 1991. Kinetic analysis of monoclonal antibody-antigen interactions with a new biosensor based analytical system. J. Immunol. Methods 145:229-240.
35. Karlsson, R., H. Roos, L. Fagerstam, and B. Persson. 1994. Kinetic and concentration analysis using BIA technology. Methods: A Companion to Methods Enzymol. 6:99-110.
36. Kelley, R. F. 1994. Thermodynamics of protein-protein interaction studied by using BIAcore and single-site mutagenesis. Methods: A Companion to Methods Enzymol. 6:111-120.
37. Kooyman, R. P. H., H. Kolkman, J. Van Gent, and J. Greve. 1988. Surface plasmon resonance immunosensors: sensitivity considerations. Anal. Chim. Acta. 213.35-45.
38. Langevin, D., and F. Rondelez. 1978. Sedimentation of large colloidal particles through semidilute polymer solutions. Polymer. 19:875-882.
39. Liedberg, B., I. Lundstrom. and E. Stenberg. 1993. Principles of biosensing with an extended coupling matrix and surface plasmon resonance. Sensors Actuators B. 11:63-72.
40. Löfås, S., and B. Johnsson. 1990. A novel hydrogel matrix on gold surfaces in surface plasmon resonance sensors for fast and efficient covalent immobilization of ligands. J. Chem. Soc. Chem. Commun 21: 1526-1528.
41. Löfås, S., M. Malmqvist, I. Rönnberg, E. Stenberg, B. Liedberg, and I. Lundström. 1991. Bioanalysis with surface plasmon resonance. Sensors Actuators B. 5:79-84.
42. Malmborg, A.-C., and C. A. K. Borrebaeck. 1995. BIAcore as a tool in antibody engineering. J. Immunol. Methods. 183:7-13.
43. Malmborg, A.-C., A. Michaëlsson, M. Ohlin, B. Jansson, and C A. K. Borrebaeck. 1992. Real time analysis of antibody-antigen reaction kinetics. Scand. J. Immunol. 35:643-650.
44. Mani, J.-C., V. Marchi, and C. Cucurou. 1994. Effect of HlV-I peptide presentation on the affinity constants of two monoclonal antibodies determined by BIAcore technology. Mol. Immunol. 31:439-444.
45. Morton, T. A., D. B. Bennett, E. R. Appelbaum, D. M. Cusimano, K. O. Johanson, R. E. Matico, P. R. Young, M. Doyle, and I. M. Chaiken. 1994. Analysis of the interaction between human interleukin-5 and the soluble domain of its receptor using a surface plasmon resonance biosensor. J. Mol. Recogn. 7:47-55.
46. Natsume, T., T. Koide, S.-i. Yokota, K. Hirayoshi, and K. Nagata 1994. Interactions between collagen-binding stress protein HSP47 and collagen. J. Biol. Chem. 269:31224-31228.
47. O'Shannessy, D. J. 1994. Determination of kinetic rate and equilibrium binding constants for macromolecular interactions: a critique of the surface plasmon resonance literature. Curr. Opin. Biotechnol. 5:65-71.
48. O'Shannessy, D. J., M. Brigham-Burke, K. K. Soneson, P. Hensley. and I. Brooks. 1993. Determination of rate and equilibrium binding constants for macromolecular interactions using surface plasmon resonance: use of nonlinear least squares analysis methods. Anal. Biochem. 212:457-468.
49. Pack, P., K. Müller, R. Zahn, and A. Plückthun. 1995. Tetravalent mini-antibodies with high avidity assembling in Escherichia coli. J. Mol. Biol. 246:28-34.
50. Panayotou, G., G. Gish, P. End, O. Truong, I. Gout, R. Dhand, M. J Fry. I. Hiles, T. Pawson, and M. D. Waterfield. 1993. Interactions between SH2 domains and tyrosine-phosphorylated platelet-derived growth factor β-receptor sequences: analysis of kinetic parameters by a novel biosensor-based approach. Mol. Cell. Biol. 13:3567-3576.
51. Parsons, I. D., B. Persson, A. Mekhalfia, G. M. Blackburn, and P. G. Stockley. 1995. Probing the molecular mechanism of action of corepressor in the E. coli methionine repressor-operator complex using surface plasmon resonance (SPR). Nucleic Acids Res. 23:211-216
52. src Src homology 2 domain binding to tyrosine-phosphorylated peptides determined by a competition assay or surface plasmon resonance. Proc. Natl. Acad. Sci USA. 90:4902-4906.
53. Phillies, G. D. J 1985. Diffusion of bovine serum albumin in a neutral polymer solution. Biopolymers 24.379-386.
54. Phillips, D. L. 1962. A technique for the numerical solution of certain integral equations of the first kind. J. Assist. Comput. Mach. 9:84-97.
55. Plant, A. L., M. Brigham-Burke, E. C. Petrella, and D. J. O'Shannesy. 1995. Phosphoupid/alkanethiol bilayers for cell-surface receptor studies by surface plasmon resonance. Anal. Biochem. 226:342-348.
56. Poiesi, C , A. Albertini, S. Ghielmi. G Cassani. and A. Corti. 1993. Kinetic analysis of the TNF-α oligomer-monomer transition by surface plasmon resonance and immunochemical methods. Cytokine. 5:539-545.
57. Press, W. H., S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery 1992. Numerical Recipes in C, 2nd ed (corrected 1994). Cambridge University Press, Cambridge.
58. Provencher, S. W. 1979. Inverse problems in polymer characterization: direct analysis of polydispersity with photon correlation spectroscopy. Makromol. Chem. 180:201-209.
59. Raether, H. 1977. Surface plasma oscillations and their applications. In Physics of Thin Films. G. Hass, M. H. Francombe. and R. W. Hoffman, editors. Academic Press. New York. 9:145-261.
60. Ramsdale, T E., P. R. Andrews, and E. C Nice. 1993. Verification of the interaction between peptide T and CD4 using surface plasmon resonance. FEBS Lett. 333:217-222.
61. Richalet-Sécordel, P. M., G. Zeder-Lutz, S. Plaue, G. Sommermeyer-Leroux, and M H V. Van Regenmortel. 1994. Cross-reactivity of monoclonal antibodies to a chimeric V3 peptide of HIV-1 with peptide analogues studied by biosensor technology and ELISA. J. Immunol. Methods. 176:221-234.
62. Silhavy, T. J., S. Szmelcman, W. Boos, and M. Schwartz. 1975. On the significance of the retention of ligand by protein. Proc. Natl. Acad. Sci. USA. 72:2120-2124.
63. Sjolander, S., and C. Urbaniczky. 1991. Integrated fluid handling system for biomolecular interaction analysis. Anal. Chem. 63:2338-2345.
64. Stenberg, E., B. Persson, H. Roos, C. Urbaniczky. 1991. Quantitative determination of surface concentration of protein with surface plasmon resonance using radiolabeled proteins. J. Colloid Interface Sci. 143: 513-526.
65. Takano, E., M. Hatanaka, and M, Maki. 1994. Real-time analysis of the calcium-dependent interaction between caimodulin and a synthetic oligopeptide of calcineurin by a surface plasmon resonance biosensor. FEBS Lett. 352:247-250.
66. Takano, E., H. Ma, H. Q. Yang, M. Maki, and M. Hatanaka. 1995. Preference of calcium-dependent interactions between calmodulin-like domains of calpain and calpastatin subdomains FEBS Lett. 362:93-97.
67. Tosser, G., T. Delaunay, E. Kohli, J. Grosclaude, P. Pothier, and J. Cohen. 1994. Topology of bovine rotavirus (RF strain) VP6 epitopes by real-time biospecific interaction analysis. Virology. 204:8-16.
68. van der Merwe, P. A., M. H. Brown, S. J. Davis, and A. N. Barclay. 1993. Affinity and kinetic analysis of the interaction of the cell adhesion molecules rat CD2 and CD48. EMBO J. 12:4945-4954.
69. Varan, J. M. 1985. On fitting exponentials by nonlinear least squares. Siam J. Sci. Stat. Comput. 6:30-44.
70. Watts, H. J., C. R. Lowe, and D. V. Pollard-Knight. 1994. Optical biosensor for monitoring microbial cells. Anal. Chem. 66:2465-2470.
71. Wohlhueter, R. M., K. Parekh, V. Udhayakumar, S. Fang, and A. A. Lal. 1994. Analysis of binding of monoclonal antibody to a malarial peptide by surface plasmon resonance biosensor and integrated rate equations. J. Immunol. 153:181-189.
72. Yang, H. Q., H. Ma, E. Takano, M. Hatanaka, and M. Maki. 1994. Analysis of calcium-dependent interaction between amino-terminal conserved region of calpastatin functional domain and calmodulin-like domain of μ-calpain large subunit. J. Biol. Chem. 269:18977-18984.
73. Zahn, R , S. E. Axmann, K.-P. Rücknagel, E. Jaeger, A. A. Laminet. and A. Plückthun. 1994. Thermodynamic partitioning model for hydrophobic binding of polypeptides by GroEL. J. Mol. Biol. 242:150-164.
74. Zwanzig, R., and A. Szabo. 1991. Time dependent rate of diffusion-influenced ligand binding to receptors on cell surfaces. Biophys. J. 60:671-678.