Kinetic binding affinity

Kinetics is the branch of science concerned with the rates of chemical reactions. The study of enzyme kinetics addresses the biological roles of enzymatic catalysts and how they accomplish their remarkable feats. In enzyme kinetics, we seek to determine the maximum reaction velocity that the enzyme can attain and its binding affinities for substrates and inhibitors. Coupled with studies on the structure and chemistry of the enzyme, analysis of the enzymatic rate under different reaction conditions yields insights regarding the enzyme s mechanism of catalytic action. Such information is essential to an overall understanding of metabolism. 

To evaluate the influence of structural parameters governed by the cyclophosphazene core concerning the valency and the spatial orientation of epitopes, as well as the nature of linkers directly related to the ligation technique used for the mannoside incorporation, the authors performed preliminary kinetic turbidimetric assays with Con A. Insoluble cross-linked complexes formed rapidly for all compounds, without marked difference for the hexavalent analogues. On the other hand, the incorporation of additional mannosyl units led merely to statistical binding-affinity enhancements, notably for the less-dense decamer 194, which presents favorable extended intersugar distances. 

Van Dort, H.M., Moriyama, R. and Low, P.S., 1998, Effect ofband 3 subunit equilibrium on the kinetics and affinity of ankyrin binding to erythrocyte membrane vesicles. J. Biol. Chem., 273 14819-14826. 

Two-dimensional heteronuclear ( H- N) nuclear magnetic relaxation studies indicate that the dihydrofolate reductase-folate complex exhibits a diverse range of backbone fluctuations on the time-scale of picoseconds to nanoseconds To assess whether these dynamical features influence Michaelis complex formation, Miller et al used mutagenesis and kinetic measurements to assess the role of a strictly conserved residue, namely Gly-121, which displays large-amplitude backbone motions on the nanosecond time scale. Deletion of Gly-121 dramatically reduces the hydride transfer rate by 550 times there is also a 20-times decrease in NADPH cofactor binding affinity and a 7-fold decrease for NADP+ relative to wild-type. Insertion mutations significantly decreased both... 

Since then, a considerable amount of structural and mechanistic information has been collected and yeast enolase is probably the best understood sequential enzyme to date. It is a homodimer and requires two Mg + ions per active site for catalytic activity under physiological conditions, although magnesium can be replaced with a variety of divalent metal ions in vitro. During a catalytic turnover, the metal ions bind to the active site in a kinetically ordered, sequential manner with differential binding affinities. The mode of action of yeast enolase is illustrated in Figure 26 and is unusually well understood since several solid-state structures for each intermediate identified with kinetic methods have been determined. 

The issue of bioavailability is further clouded by the physical characteristics of soil and the role of a possible mass transfer limitation. Soil constituents are not simply flat surfaces with free and equal access to all bacterial species. The formation of aggregates from sand-, silt-, and clay-sized particles results in stable structures which control microbial contact with the substrate (Figure 2.7). Discussion of sorption mechanisms and binding affinities must include the possible impact of intra-aggregate transport of the substrate. If the substrate is physically inaccessible to the microorganism then both desorption from soil constituents and diffusion to an accessible site are necessary. The impact of intra-aggregate diffusion on degradation kinetics has been modeled for y-hexachlorocyclohexane (Rijnaarts et al., 1990) and naphthalene (Mihelcic Luthy, 1991). 

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