Ordered binding

Sometimes the binding site for one substrate does not exist until the other substrate binds to the enzyme. This creates a specific binding order in which A must bind before B can bind (or vice versa). 

Kanner, B. I. and Bendahan, A. (1982) Binding order of substrates to the sodium and potassium ion coupled L-glutamic acid transporter from rat brain. Biochemistry 21,6327-6330. 

A potential limitation encountered when one seeks to characterize the kinetic binding order of certain rapid equilibrium enzyme-catalyzed reactions containing specific abortive complexes. Frieden pointed out that initial rate kinetics alone were limited in the ability to distinguish a rapid equilibrium random Bi Bi mechanism from a rapid equilibrium ordered Bi Bi mechanism if the ordered mechanism could also form the EB and EP abortive complexes. Isotope exchange at equilibrium experiments would also be ineffective. However, such a dilemma would be a problem only for those rapid equilibrium enzymes having fccat values less than 30-50 sec h For those rapid equilibrium systems in which kcat is small, Frieden s dilemma necessitates the use of procedures other than standard initial rate kinetics. 

INFLUENCE OF OTHER STEPS ON THE MAGNITUDE OF OBSERVED ISOTOPE EFFECTS. As noted earlier, nonenzymatic reaction mechanisms do not involve those complexities imposed by substrate binding order, rates of substrate binding/release, as well as conformational changes that attend enzyme catalysis. As a result, the opportunity for detecting isotope effects is... 

Sorption energies in silicalite were found to be spread over a relatively small range, 18 and 9 kJ/mol, for full- and reduced-charge models, respectively. In each case, the preferential binding order was the same 1-butanol adsorbs the most strongly, then 2-butanol, and finally butyl alcohol. The locations of adsorption were also found to be similar for all isomers 1-butanol prefers to adsorb in the sinusoidal channels, whereas 2-butanol... 

HG Vinnicombe, JP Derrick. Dihydropteroate synthase from Streptococcus pneumoniae. characterization of substrate binding order and sulfonamide inhibition. Bio-chem Biophys Res Commun 258 752-757, 1999. 

Overview of other bimolecular mechanisms The random bi-uni mechanism (random bi-substrate binding order with single product) has the form ... 

This means that he could also give binding orders in individual cases, and these orders had the force of law. This was expressly confirmed by the Reichstag in its well-known decision of April 26, 1942.141 In other words, in deviation from the principle of the separation of powers, Hitler as head of state could give an individual order which required the same obedience as does a law in a democratic state. 

S-Adenosyl-L-homocysteine (10) (Fig. 17.12), the product of the reaction, and 2-(2,5-dichlorophenyDcyclopropylamine (1 l)are analogs of S-adenosyl-L-methionine and norepinephrine, respectively. Using these inhibitors it was possible to ascertain the binding order of the two substrates (75). Kinetic analyses showed that SAH was a competitive inhibitor of SAM and a noncompetitive inhibitor of norepinephrine, whereas (1 l)was a competitive inhibitor of norepinephrine and an uncompetitive inhibitor of SAM. This indicates that the binding of substrates is ordered, with SAM binding first. If norepinephrine bound first, it would be expected that SAH would be an uncompetitive inhibitor and (1 l)would be noncompetitive with respect to SAM. If a random... 

The differences in binding orders between TBPA and TBG suggest that different structural features may play a key role in receptor interactions. It has been shown (4,28) that TBG also preferentially binds to a tetraiodo-4 -phenoxide ion, but since Ti is the strongest binder, this suggests a different side chain stereochemistry. Here we can assume that it is the twist-skewed diphenyl ether conformation which orients the Tside chain for optimal receptor-hormone interactions. In the case of the nuclear proteins optimal binding is observed for a distally oriented 3 -I and a 4 -hydroxyl. Side chain requirements appear to be similar to those of TBG (28,31). 

It is relevant to this discussion that membrane equilibrium measurements have shown that under certain conditions the lithium ion is bound more strongly to long-chain phosphates than the sodium ion (46), as this reversal of the normal binding order implies penetration of the phosphate groups through the hydration shell of the alkali metal ions, and thus site binding. 

This binding order was also observed by electrophoresis (47),... 

Figure 11.8 HDX patterns for various Ca binding sites (obtained as peptides by peptic digestion) indicated the binding orders. Each column represents deuterium distribution of the peptic peptides for each EF hand III, IV, II, and I (left to right). Each row represents various Ca bound states 0, 1, 2, 3, and 4 Ca bound (top to bottom). Redrawn from data in Ref [31]...

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