ON THE NEED TO CONSIDER KINETIC AS WELL AS THERMODYNAMIC CONSEQUENCESOF THE PARKING PROBLEM IN QUANTITATIVE STUDIES OF NONSPECIFIC-BINDINGBETWEEN PROTEINS AND LINEAR POLYMER-CHAINS
Pd. Munro et al., ON THE NEED TO CONSIDER KINETIC AS WELL AS THERMODYNAMIC CONSEQUENCESOF THE PARKING PROBLEM IN QUANTITATIVE STUDIES OF NONSPECIFIC-BINDINGBETWEEN PROTEINS AND LINEAR POLYMER-CHAINS, Biophysical chemistry, 71(2-3), 1998, pp. 185-198
Attention is drawn to a need for caution in the thermodynamic characte
rization of nonspecific binding of a large ligand to a linear acceptor
such as a polynucleotide or a polysaccharide-because of the potential
for misidentification of a transient (pseudoequilibrium) state as tru
e equilibrium. The time course of equilibrium attainment during the bi
nding of a large ligand to nonspecific three-residue sequences of a li
near acceptor lattice has been simulated, either by numerical integrat
ion of the system of ordinary differential equations or by a Monte Car
lo procedure, to identify the circumstances under which the kinetics o
f elimination of suboptimal ligand attachment (called the parking prob
lem) create such difficulties. These simulations have demonstrated tha
t the potential for the existence of a transient plateau in the time c
ourse of equilibrium attainment increases greatly (i) with increasing
extent of acceptor saturation (i.e., with increasing ligand concentrat
ion), (ii) with increasing magnitude of the binding constant, and (iii
) with increasing length of the acceptor lattice. Because the capacity
of the polymer lattice for ligand is most readily determined under co
nditions conducive to essentially stoichiometric interaction, the para
meter so obtained is thus likely to reflect the transient (irreversibl
e) rather than equilibrium binding capacity. A procedure is described
for evaluating the equilibrium capacity from that irreversible paramet
er; and illustrated by application to published results [M. Nesheim, M
.N. Blackburn, C.M. Lawler, K.G. Mann, J. Biol. Chem. 261 (1986) 3214-
3221] for the stoichiometric titration of heparin with thrombin. (C) 1
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