Abortive Complex Formation

A number of enzymes may form abortive complexes that are nonproductive forms of the enzyme. Such complexes appear as a result of the adsorption of ligands under conditions where the enzyme may not carry out its usual chemistiy. For example, the binding of NAD and acetaldehyde to alcohol dehydrogenase leads to the formation of an enzyme-NAD -acetaldehyde complex, wWch cannot allow for hydrogen transfer because both ligands are already in their oxidized states. 

To detect the presence of abortive ternary complexes, the kinetidst may raise the concentration of dissimilar substrate-product pairs (such as glucose-ADP and ATP-glucose-6-P in the hexokinase reaction, or acetaldehyde-NAD and ethanol-NADH in alcohol dehydrogenase reaction). This wiU lead to the inhibition of all exchanges irrespective of the kinetic mechanism, and provide useful information about the abortive complex formation (Wong Hanes, 1964 Wedler Boyer, 1972 Punch Allison, 1980, 2000). Nevertheless, product inhibition is stiU unrivaled as the means for detecting abortive complex formation. 

(1975) Initial rate enzyme kinetics. Springer-Verlag, Berlin. 

Pearson, R.G. (1961) Kinetics and mechanism, 2nd ed., WUey, New York, de L Hopital, G.F. 1696) Analyse des Infiniment Petits, Paris. 

Allison, R.D. (2000) Handbook of biochemical kinetics, Academic Press, New York. Segel, I.H. (1975) Enzyme kinetics, Wiley, New York. 

---

Rudolph, F. B., Product inhibition and abortive complex formation. Methods Enzymol, 1979. 63 pp. 411-436. 

Selected entries from Methods in Enzymology [vol, page(s)] Abortive complex formation, 63, 432 adenylate cyclase assay,... 

Fromm and Rudolph have discussed the practical limitations on interpreting product inhibition experiments. The table below illustrates the distinctive kinetic patterns observed with bisubstrate enzymes in the absence or presence of abortive complex formation. It should also be noted that the random mechanisms in this table (and in similar tables in other texts) are usually for rapid equilibrium random mechanism schemes. Steady-state random mechanisms will contain squared terms in the product concentrations in the overall rate expression. The presence of these terms would predict nonhnearity in product inhibition studies. This nonlin-earity might not be obvious under standard initial rate protocols, but products that would be competitive in rapid equilibrium systems might appear to be noncompetitive in steady-state random schemes , depending on the relative magnitude of those squared terms. See Abortive Complex... 

ISOTOPE TRAPPING STICKY SUBSTRATES Substrate-induced conformational change, INDUCED FIT MODEL SUBSTRATE INHIBITION ABORTIVE COMPLEX FORMATION LACTATE DEHYDROGENASE LEE-WILSON EQUATION... 

Experiments designed to reach conclusions about an enzyme-catalyzed reaction by examining how one or more products of the reaction alter the kinetic behavior of the enzyme. The diagnostic value of these approaches can be limited by formation of E substrate product abortive complexes in multisubstrate mechanisms. 

GMP <2, 7> (<2> competitive inhibitor to dGMP [2] <7> non competitive with respect to MgATP because of the formation of an abortive complex guanylate kinase-MgATP "GMP [18]) [2, 18]... 

Pre-steady-state kinetic studies established that the appearance of the NADH chromophore on addition of substrate was a two-step process, and these steps can now be identified as closure of the active site and hydride transfer. This study indicated that the on-enzyme equilibrium for addition of water or homocysteine to the enone was close to unity (and the value in free solution), whereas the equilibrium for oxidation of NAD by bound adenosine was 10 times more favourable than in free solution. The focusing of the catalytic power of the enzyme on the oxidation step avoids the formation of abortive complexes by hydride transfer between enone and NADH, yielding 4,5-dehydroadenosine and NAD ". This happens about 10 " times faster than productive hydride transfer at the beginning and end of the catalytic cycle, with the slow rate (close to that of model reactions) apparently arising from a conformationally modulated increase in the distance the hydride has to be transferred. 

The formation of abortive complexes of the type EAQ and EPB, a common cause of substrate inhibition of dehydrogenases (Section II, F), can also be detected in isotope exchange experiments by inhibition of all exchanges when the concentrations of A and Q or P and B are increased together. The complexes E NADH malate (34) and E NAD(P)H glutamate (44), for example, were detected in this way, and are probably responsible for the substrate inhibition observed in initial rate studies of these enzymes (Section II,F,1). The latter complex, but not the former. 

The reaction is not compulsory. Dalziel and Dickinson 322) have proposed a more general mechanism based on the formation of abortive ternary E-NADH-alcohol complexes and binary E-alcohol complexes. Formation at high alcohol concentrations of this abortive ternary complex from which NADH can dissociate had previously been suggested 252). Evidence for this alternative pathway was furthermore adduced by Sil-verstein and Boyer 341) on the basis of isotope exchange experiments. 

Otvos and Armitage (46a) have observed Tj values similar to those presented here in their study of alkaline phosphatase. They attempted to apply simple models to their Tj data using rotational correlaton times for alkaline phosphatase. These models failed to explain the observed Ty and NOE, and their conclusion was that the relaxation was probably dominated by dipolar processes mediated by internal motions within the protein, This conclusion may also be consistent with the data presented here. For metalloproteins where one can "readily" exchange the metal(s) out of the protein, the "internal motions" may be the formation of "abortive" complexes similar to those described above. 

Once integrated into the host chromosome, the assembly of new viral particles necessitates the prodnction of viral RNA transcripts and proteins. Initiation of viral transcription is also an RNA independent process where host transcription promoters and enhancer elements such as NF-kB bind to the 5 -LTR. The host transcriptional complex is then recrnited and transcription commences.Once transcription has been initiated, RNA and RNA-RNA interactions play a critical role in mediating the production of viral transcripts. The multiprotein transcription complex has a recognition factor for nonhost DNA and quickly releases from viral DNA, creating short, abortive transcripts. Processing and nuclear export of these transcripts leads to the translation of the HIV Tat protein, a small early-phase viral protein (Figure 10.4) that plays a key role in the ultimate formation of fnll-length viral RNA transcripts. 

For multisubstrate enzymatic reactions, the rate equation can be expressed with respect to each substrate as an m function, where n and m are the highest order of the substrate for the numerator and denominator terms respectively (Bardsley and Childs, 1975). Thus the forward rate equation for the random bi bi derived according to the quasi-equilibrium assumption is a 1 1 function in both A and B (i.e., first order in both A and B). However, the rate equation for the random bi bi based on the steady-state assumption yields a 2 2 function (i.e., second order in both A and B). The 2 2 function rate equation results in nonlinear kinetics that should be differentiated from other nonlinear kinetics such as allosteric/cooperative kinetics (Chapter 6, Bardsley and Waight, 1978) and formation of the abortive substrate complex (Dalziel and Dickinson, 1966 Tsai, 1978). 

Inhibition of protein synthesis by aminoglycoside antibiotics, especially by streptomycin, is bactericidal (rev.46)). The antibiotic binds to the smaller ribosomal subunit and leads to the formation of abortive initiation complexes of ribosomes, streptomycin and amino acyl tRNA which progressively trap ribosomes in the form of such biologically irreversible complexes. When protein synthesis is prematurely terminated by puromycin and ribosomes are thus made available for reinitiation of de novo protein biosynthesis, the bactericidal action of streptomycin is accelerated47). Destruction of ribosomes under the influence of primaquine operationally also results in non-occurrence of protein synthesis and in a marked bactericidal effect48, 49 ... 

Dalziel and Dickinson (34 ) found that this pathway contributed significantly to the kinetic parameters when cyclohexanol was used as a substrate. Isotope exchange studies 343) have confirmed the partly random mechanism for this substrate. Shore and Theorell (344) have studied the substrate inhibition for several aliphatic alcohols resulting from the formation of abortive E-NADH> alcohol complexes. 

Various reasons for the advantages gained in the specialization of major LDH isozymes have been proposed (68,69,71-74) One possibility may be in the greater degree of pyruvate inhibition of the H4 isozyme (1,36,69) as a result of the formation of the abortive ternary LDH NAD-pyruvate complex (see Section III,C,3). 

The formation of abortive ternary complexes of enolpyruvate with... 

Subsequently, Cross et al. (SOI) demonstrated that formation of the E-NADPH binary complex, and the abortive ternary complexes E-NADPH-L-glutamate and E-NADP-a-ketoglutarate are all characterized by a red shift in the tryptophan absorption spectrum. It appears likely, therefore, that a tryptophan residue is located in or near the coenzyme binding site. 

---