Strength of binding

The functional reaction center contains two quinone molecules. One of these, Qb (Figure 12.15), is loosely bound and can be lost during purification. The reason for the difference in the strength of binding between Qa and Qb is unknown, but as we will see later, it probably reflects a functional asymmetry in the molecule as a whole. Qa is positioned between the Fe atom and one of the pheophytin molecules (Figure 12.15). The polar-head group is outside the membrane, bound to a loop region, whereas the hydrophobic tail is... 

Figure 3.13 shows the thermal stability of immobilized ODN and PNA. The signal for the Thy- and Cyt-bases obtained with temperature-programmed (TP) SIMS starts to decrease at approximately 150 °C for ODN and 200 °C for PNA. This variance is caused by the different strengths of binding between the bases and the sugar-phosphate and peptide backbones, respectively. 

Affinity is the strength of binding of a drag to a receptor. It is quantified by an equilibrium dissociation constant. 

Some microbial exopolysaccharides contain the inorganic substituents phosphate and sulphate. Phosphate has been found in exopolysaccharide from bacteria of medical importance, including Escherichia coli. Sulphate is far less common than phosphate and has only been found in spedes of cyanobaderia. In addition to these inorganic components, which form part of the structure of some exopolysaccharides, all polyanionic polymers will bind a mixture of cations. Exopolysaccharides are, therefore, purified in the salt form. The strength of binding of the various cations depend on the exopolysaccharide some bind the divalent cations calrium, barium and strontium very strongly, whereas others prefer certain monovalent cations, eg Na ... 

A number of workers have observed that the strength of binding of monovalent counterions depends on ionic radius. However, the effect of ionic radius is somewhat obscure as it depends on hydration phenomena and whether the size of the bare ion or that of the hydrated ion is the significant parameter (Wilson Crisp, 1977). 

Hunt I think that E—Q mutant you discovered inadvertently could have differential effects on the binding of cyclin, because that helix is a major point of cyclin/Cdc2 contact. We certainly have mutants which map in different places that affect the relative strength of binding of cyclins A and B. 

Values of /c2 and Kd for the reactions of the cycloamyloses with a variety of phenyl acetates are presented in Table IV. The rate constants are normalized in the fourth column of this table to show the maximum accelerations imposed by the cycloamyloses. These accelerations vary from 10% for p-f-butylphenyl acetate to 260-fold for m-f-butylphenyl acetate, again showing the clear specificity of the cycloamyloses for meta-substituted esters. Moreover, these data reveal that the rate accelerations and consequent specificity are unrelated to the strength of binding. For example, although p-nitrophenyl acetate forms a more stable complex with cyclohexa-amylose than does m-nitrophenyl acetate, the maximal rate acceleration, h/kan, is much greater for the meta isomer. 

Values of /c2, the maximal rate constant for disappearance of penicillin at pH 10.24 and 31.5°, and Ka, the cycloheptaamylose-penicillin dissociation constant are presented in Table VII. Two features of these data are noteworthy. In the first place, there is no correlation between the magnitude of the cycloheptaamylose induced rate accelerations and the strength of binding specificity is again manifested in a rate process rather than in the stability of the inclusion complex. Second, the selectivity of cycloheptaamylose toward the various penicillins is somewhat less than the selectivity of the cycloamyloses toward phenyl esters—rate accelerations differ by no more than fivefold throughout the series. As noted by Tutt and Schwartz (1971), selectivity can be correlated with the distance of the reactive center from the nonpolar side chain. Whereas the carbonyl carbon of phenyl acetates is only two atoms removed from the phenyl ring, the reactive center... 

More recently, Kaiser and coworkers reported enantiomeric specificity in the reaction of cyclohexaamylose with 3-carboxy-2,2,5,5-tetramethyl-pyrrolidin-l-oxy m-nitrophenyl ester (1), a spin label useful for identifying enzyme-substrate interactions (Flohr et al., 1971). In this case, the catalytic mechanism is identical to the scheme derived for the reactions of the cycloamyloses with phenyl acetates. In fact, the covalent intermediate, an acyl-cyclohexaamylose, was isolated. Maximal rate constants for appearance of m-nitrophenol at pH 8.62 (fc2), rate constants for hydrolysis of the covalent intermediate (fc3), and substrate binding constants (Kd) for the two enantiomers are presented in Table VIII. Significantly, specificity appears in the rates of acylation (fc2) rather than in either the strength of binding or the rate of deacylation. 

Kinetic aspects of the use of alkali metals as templates for the formation of other crowns have been studied in some depth (Mandolini Masci, 1984). The results of such investigations parallel the previous observations - namely, that the catalytic efficiency of such ions in promoting cyclization shows a strong tendency to parallel their strength of binding with the crown products (this in turn often correlates with the fit of the metal ion for the macrocyclic cavity in the product). 

The affect of Li+ on the metabolism of serotonin (5-hydroxytryp-tamine, 5-HT) is equivocal. A number of studies consistently find a Li+-induced increase in the levels of the major metabolite, 5-hydroxyin-doleacetic acid (5-HIAA), in rat brain and in human CSF [155], which appears to reflect an increase in the rate of synthesis of 5-HT [156]. Li+-induced increases in the level of the amino acid precursor, tryptophan, and in the uptake of tryptophan by brain have also been reported [157], implying elevated tryptophan availability during Li+ treatment. In rat brain, chronic Li+ decreases the activity of tryptophan hydroxylase, the enzyme which, when activated by a Ca2+ and calmodulin-dependent protein kinase, leads to the synthesis of 5-HT [158]. Ca2+ increases the strength of binding of tryptophan to the enzyme, whereas Li+ has the opposite effect [159]. Tryptophan uptake is coupled to 5-HT utilization by a negative feedback mechanism and, therefore, the Li+-induced inhibition of tryptophan hydroxylase with a resultant decrease in 5-HT utilization could produce the observed increase in tryptophan uptake. 

Antibody affinity from the Latin, affinis = connected with, having things in common. In immunohistochemistry, antibody affinity determines the strength of binding of a monovalent antibody, such as Fab fragment, to one epitope, i.e., how tightly an antibody binds to its particular antigen. 

Therefore, km (in mol dm-3) is equal to the concentration of the substrate at which the initial rate is half of its maximum value. The value of km for an enzyme depends on the particular substrate and also on experimental conditions like pH, temperature, solvent, ionic strength etc. km gives an idea of strength of binding and saturation of enzyme and substrate. 

In just the way that Km defines the dissociation of an enzyme from its substrate, K (the inhibitor constant) defines the strength of binding of a reversible inhibitor to the enzyme. 

There are two components to consider in the interaction of a drug with a protein. One is the capacity of the protein for binding drug molecules and this is related to the number of binding sites (n). The other is the affinity, or strength of binding, which is usually expressed as an apparent association constant (fc). 

The internal rotational relaxation times of 1-pyrene carboxaldehyde in sulfonate systems may offer some indication of the extent of probe binding to the inverted micelle. In the absence of any background fluorescence interference to the time-dependent anisotropy decay profile, the internal rotational relaxation time should correlate with the strength of binding with the polar material in the polar core. However, spectral interference from the aromatic moieties of sulfonates is substantial, so that the values of internal rotational relaxation time can only be used for qualitative comparison. 

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