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Steric hindrance effects on surface reactions: applications to bIAcore. (English) Zbl 1128.35307

The author presents some general mathematical principles for handling steric hindrance effect and a surface reaction model using mathematical model. The model developed has been experimented by a number of numerical experiments for illustration.

MSC:

35C15 Integral representations of solutions to PDEs
35B20 Perturbations in context of PDEs
92C45 Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.)
35K05 Heat equation
Full Text: DOI

References:

[1] Basmadjian D. (1990). The effect of flow and mass transport in thrombogenesis. Ann. Biomed. Eng. 18: 685–709 · doi:10.1007/BF02368455
[2] BIAcore, Inc. BIAcoreSystem Manual Version 1.1. BIAcore, Inc., Uppsala, undated
[3] Curto L.M., Caramelo J.J. and Delfino J.M. (2005). {\(\Delta\)}98{\(\Delta\)}, a functional all-{\(\beta\)}-sheet abridged form of intestinal fatty acid binding protein. Biochemistry 44: 13847–13857 · doi:10.1021/bi051080s
[4] Dionne K.E., Cain B.M., Li R.H., Bell W.J., Doherty E.J., Rein D.H., Lysaght M.J. and Gentile F.T. (1996). Transport characterization of membranes for immunoisolation. Biomaterials 17: 257–266 · doi:10.1016/0142-9612(96)85563-3
[5] Edwards D.A. (1999). Estimating rate constants in a convection-diffusion system with a boundary reaction. IMA J. Appl. Math. 63: 89–112 · Zbl 0939.92036 · doi:10.1093/imamat/63.1.89
[6] Edwards D.A. (2001). The effect of a receptor layer on the measurement of rate constants. Bull. Math. Biol. 63: 301–327 · Zbl 1323.92095 · doi:10.1006/bulm.2000.0224
[7] Edwards D.A. (2006). Convection effects in the BIAcore dextran layer: surface reaction model. Bull. Math. Biol. 68: 627–654 · Zbl 1334.92171 · doi:10.1007/s11538-005-9023-2
[8] Edwards D.A., Goldstein B. and Cohen D.S. (1999). Transport effects on surface-volume biological reactions. J. Math. Biol. 39: 533–561 · Zbl 0945.92004
[9] Edwards D.A. and Jackson S.A. (2002). Testing the validity of the effective rate constant approximation for surface reaction with transport. Appl. Math. Lett. 15: 547–552 · Zbl 0994.92041 · doi:10.1016/S0893-9659(02)80005-2
[10] Edwards D.A. and Swaminathan S. (2005). The effect of receptor site nonuniformity on the measurement of rate constants. Appl. Math. Lett. 18: 1101–1107 · Zbl 1125.80326 · doi:10.1016/j.aml.2004.10.007
[11] Garland P.B. (1996). Optical evanescent wave methods for the study of biomolecular reactions. Q. Rev. Biophys. 29: 91–117 · doi:10.1017/S0033583500005758
[12] Gherardi E., Youles M.E., Miguel R.N., Blundell T.L., Iamele L., Gough J., Bandyopadhyay A., Hartmann G. and Butler P.J.G. (2003). Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor scatter factor. PNAS 100: 12039–12044 · doi:10.1073/pnas.2034936100
[13] Grabowski E.F., Friedman L.I. and Leonard E.F. (1972). Effects of shear rate on the diffusion and adhesion of blood platelets to a foreign surface. Ind. Eng. Chem. Fund. 11: 224–232 · doi:10.1021/i160042a013
[14] He X.Y., Li N. and Goldstein B. (2000). Lattice boltzmann simulation of diffusion-convection systems with surface chemical reaction. Mol. Sim. 25: 145–156 · Zbl 0991.76063 · doi:10.1080/08927020008044120
[15] Hoffman T.L., Canziani G., Jia L., Rucker J. and Doms R.W. (2000). A biosensor assay for studying ligand-membrane receptor interactions: binding of antibodies and HIV-1 env to chemokine receptors. Proc. NAS 97: 11215–11220 · doi:10.1073/pnas.190274097
[16] Joss L., Morton T.A., Doyle M.L. and Myszka D.G. (1998). Interpreting kinetic rate constants from optical biosensor data recorded on a decaying surface. Anal. Biochem. 261: 203–210 · doi:10.1006/abio.1998.2744
[17] Karlsson R. and Fält A. (1997). Experimental design for kinetic analysis of protein-protein interactions with surface plasmon resonance biosensors. J. Immunol. Methods 200: 121–133 · doi:10.1016/S0022-1759(96)00195-0
[18] Karlsson R., Michaelson A. and Mattson L. (1991). Kinetic analysis of monoclonal antibody–antigen interactions with a new biosensor based analytical system. J. Immunol. Methods 145: 229–240 · doi:10.1016/0022-1759(91)90331-9
[19] Kleene S.J. (1999). Both external and internal calcium reduce the sensitivity of the olfactory cyclic-nucleotide-gated channel to cAMP. J. Neurophys. 81: 2675–2682
[20] Lee M., Rhodes A.L., Wyatt M.D., Forrow S. and Hartley J.A. (1993). GC-base sequence recognition by oligo (imidazolecarboxamide) and C-terminus-modified analogs of distamycin deduced from circular dichroism, proton nuclear magnetic resonance, and methidiumpropylethylenediaminetetraacetate-iron(II) footprinting studies. Biochemistry 32: 4237–4245 · doi:10.1021/bi00067a011
[21] Liedberg B., Lundstrom I. and Stenberg E. (1993). Principles of biosensing with an extended coupling matrix and surface-plasmon resonance. Sens. Actuators B 11: 63–72 · doi:10.1016/0925-4005(93)85239-7
[22] Long W.M. and Kalachev L.V. (2000). Asymptotic analysis of dissolution of a spherical bubble (case of fast reaction outside the bubble). Rocky Mt. J. Math. 30: 293–313 · Zbl 0986.76089 · doi:10.1216/rmjm/1022008992
[23] Marshall C.B., Chakrabartty A. and Davies P.L. (2005). Hyperactive antifreeze protein from winter flounder is a very long rod-like dimer of {\(\alpha\)}-helices. J. Biol. Chem. 280: 17920–17929 · doi:10.1074/jbc.M500622200
[24] O’Shannessy D.J., Brigham-Burke M. and Peck K. (1992). Immobilization chemistries suitable for use in the BIAcore surface plasmon resonance detector. Anal. Biochem. 205: 132–136 · doi:10.1016/0003-2697(92)90589-Y
[25] Raghavan M., Chen M.Y., Gastinel L.N. and Bjorkman P.J. (1994). Investigation of the interaction between the class I MHC-related Fc receptor and its immunoglobulin G ligand. Immunity 1: 303–315 · doi:10.1016/1074-7613(94)90082-5
[26] Staszak K. and Prochaska K. (2005). Estimation of diffusion coefficients based on adsorption measurements in model extraction systems. Chem. Eng. Tech. 28: 985–990 · doi:10.1002/ceat.200500095
[27] Sutovsky H. and Gazit E. (2004). The von Hippel-Lindau tumor suppressor protein is a molten globule under native conditions: implications for its physiological activities. J. Biol. Chem. 279: 17190–17196 · doi:10.1074/jbc.M311225200
[28] Szabo A., Stolz L. and Granzow R. (1995). Surface plasmon resonance and its use in bio-molecular interaction analysis (BIA). Curr. Opin. Struct. Biol. 5: 699–705 · doi:10.1016/0959-440X(95)80064-6
[29] Ward A.F.H. and Tordai L. (1946). Time-dependence of boundary tensions of solutions i. the role of diffusion in time-effects. J. Chem. Phys. 14: 453–461 · doi:10.1063/1.1724167
[30] Yarmush M.L., Patankar D.B. and Yarmush D.M. (1996). An analysis of transport resistance in the operation of BIAcoreTM; implications for kinetic studies of biospecific interactions. Mol. Immunol. 33: 1203–1214 · doi:10.1016/S0161-5890(96)00075-2
[31] Zheng Y. and Rundell A. (2003). Biosensor immunosurface engineering inspired by B-cell membrane-bound antibodies: modeling and analysis of multivalent antigen capture by immobilized antibodies. IEEE Trans. Nanobiosci. 2: 14–25 · doi:10.1109/TNB.2003.810158
[32] Zhou J. and Low P.S. (2001). Characterization of the reversible conformational equilibrium in the cytoplasmic domain of human erythrocyte membrane band 3. J. Biol. Chem. 276: 38147–38151
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