| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
Biophys J, August 1998, p. 583-594, Vol. 75, No. 2
*Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112-5330 USA; #Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 USA; §Department of Bioengineering, Boston University, Boston, Massachusetts 02215 USA; and ¶Division of Biochemistry and Molecular Biology, John Curtin School of Medical Research, Australian National University, Camberra, ACT 0200, Australia
Surface-based binding assays are often influenced by the
transport of analyte to the sensor surface. Using simulated data sets,
we test a simple two-compartment model to see if its description of
transport and binding is sufficient to accurately analyze BIACORE data.
First we present a computer model that can generate realistic BIACORE
data. This model calculates the laminar flow of analyte within the flow
cell, its diffusion both perpendicular and parallel to the sensor
surface, and the reversible chemical reaction between analyte and
immobilized reactant. We use this computer model to generate binding
data under a variety of conditions. An analysis of these data sets with
the two-compartment model demonstrates that good estimates of the
intrinsic reaction rate constants are recovered even when mass
transport influences the binding reaction. We also discuss the
conditions under which the two-compartment model can be used to
determine the diffusion coefficient of the analyte. Our results
illustrate that this model can significantly extend the range of
association rate constants that can be accurately determined from
BIACORE.
Biophys J, August 1998, p. 583-594, Vol. 75, No. 2
© 1998 by the Biophysical Society 0006-3495/98/08/583/12 $2.00
This article has been cited by other articles:
 |
|
 |
|
  S. J. Greive, S. E. Weitzel, J. P. Goodarzi, L. J. Main, Z. Pasman, and P. H. von Hippel Monitoring RNA transcription in real time by using surface plasmon resonance PNAS, March 4, 2008; 105(9): 3315 - 3320. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Bishop, A. M. Chagovetz, and S. Blair Kinetics of Multiplex Hybridization: Mechanisms and Implications Biophys. J., March 1, 2008; 94(5): 1726 - 1734. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Svitel, H. Boukari, D. Van Ryk, R. C. Willson, and P. Schuck Probing the Functional Heterogeneity of Surface Binding Sites by Analysis of Experimental Binding Traces and the Effect of Mass Transport Limitation Biophys. J., March 1, 2007; 92(5): 1742 - 1758. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. R. Geonnotti and D. F. Katz Dynamics of HIV Neutralization by a Microbicide Formulation Layer: Biophysical Fundamentals and Transport Theory Biophys. J., September 15, 2006; 91(6): 2121 - 2130. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Kusnezow, Y. V. Syagailo, S. Ruffer, N. Baudenstiel, C. Gauer, J. D. Hoheisel, D. Wild, and I. Goychuk Optimal Design of Microarray Immunoassays to Compensate for Kinetic Limitations: Theory and Experiment Mol. Cell. Proteomics, September 1, 2006; 5(9): 1681 - 1696. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Bishop, S. Blair, and A. M. Chagovetz A Competitive Kinetic Model of Nucleic Acid Surface Hybridization in the Presence of Point Mutants Biophys. J., February 1, 2006; 90(3): 831 - 840. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kubetzko, C. A. Sarkar, and A. Pluckthun Protein PEGylation Decreases Observed Target Association Rates via a Dual Blocking Mechanism Mol. Pharmacol., November 1, 2005; 68(5): 1439 - 1454. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Yan, B. E. Forbes, K. A. McNeil, R. C. Baxter, and S. M. Firth Role of N- and C-terminal Residues of Insulin-like Growth Factor (IGF)-binding Protein-3 in Regulating IGF Complex Formation and Receptor Activation J. Biol. Chem., December 17, 2004; 279(51): 53232 - 53240. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M. Gakamsky, I. F. Luescher, and I. Pecht T cell receptor-ligand interactions: A conformational preequilibrium or an induced fit PNAS, June 15, 2004; 101(24): 9063 - 9066. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Nguyen, D. Hamelberg, C. Bailly, P. Colson, J. Stanek, R. Brun, S. Neidle, and W. D. Wilson Characterization of a Novel DNA Minor-Groove Complex Biophys. J., February 1, 2004; 86(2): 1028 - 1041. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Svitel, A. Balbo, R. A. Mariuzza, N. R. Gonzales, and P. Schuck Combined Affinity and Rate Constant Distributions of Ligand Populations from Experimental Surface Binding Kinetics and Equilibria Biophys. J., June 1, 2003; 84(6): 4062 - 4077. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhang and S. Neelamegham Estimating the Efficiency of Cell Capture and Arrest in Flow Chambers: Study of Neutrophil Binding via E-selectin and ICAM-1 Biophys. J., October 1, 2002; 83(4): 1934 - 1952. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. S. Katsamba, M. Bayramyan, I. S. Haworth, D. G. Myszka, and I. A. Laird-Offringa Complex role of the beta 2-beta 3 Loop in the Interaction of U1A with U1 Hairpin II RNA J. Biol. Chem., August 30, 2002; 277(36): 33267 - 33274. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. L. Rich, L. R. Hoth, K. F. Geoghegan, T. A. Brown, P. K. LeMotte, S. P. Simons, P. Hensley, and D. G. Myszka Kinetic analysis of estrogen receptor/ligand interactions PNAS, June 25, 2002; 99(13): 8562 - 8567. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Roy, G. De Crescenzo, K. Khaleghpour, A. Kahvejian, M. O'Connor-McCourt, and N. Sonenberg Paip1 Interacts with Poly(A) Binding Protein through Two Independent Binding Motifs Mol. Cell. Biol., June 1, 2002; 22(11): 3769 - 3782. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. S.N. Day, C. L. Baird, R. L. Rich, and D. G. Myszka Direct comparison of binding equilibrium, thermodynamic, and rate constants determined by surface- and solution-based biophysical methods Protein Sci., May 1, 2002; 11(5): 1017 - 1025. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Khaleghpour, A. Kahvejian, G. De Crescenzo, G. Roy, Y. V. Svitkin, H. Imataka, M. O'Connor-McCourt, and N. Sonenberg Dual Interactions of the Translational Repressor Paip2 with Poly(A) Binding Protein Mol. Cell. Biol., August 1, 2001; 21(15): 5200 - 5213. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Park, D. G. Myszka, M. Yu, S. J. Littler, and I. A. Laird-Offringa HuD RNA Recognition Motifs Play Distinct Roles in the Formation of a Stable Complex with AU-Rich RNA Mol. Cell. Biol., July 1, 2000; 20(13): 4765 - 4772. [Abstract] [Full Text]
|
|
|
|
|
|
P. S. Katsamba, D. G. Myszka, and I. A. Laird-Offringa Two Functionally Distinct Steps Mediate High Affinity Binding of U1A Protein to U1 Hairpin II RNA J. Biol. Chem., June 8, 2001; 276(24): 21476 - 21481. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
