The Role of Mathematics in Core-Program Development

Alberty, Elsie J.

doi:10.1086/442336

Cited by 9 publications

(6 citation statements)

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“…The formation of a ternary complex starting with 30S, poly(U), and A-AcPhe-tRNA can be regarded as analogous to an enzymatic reaction involving one enzyme (30 S) and two substrates (poly(U) and TV-AcPhe-tRNA). In these reactions different pathways can lead to the formation of the ternary complex and the rate equations for the various mechanisms have been derived (Laedler and Socquet, 1950;Segal et al, 1952;Ingraham and Makower, 1954;Alberty, 1956;Fromm, 1975). In the case of the 30S initiation complex two different pathways have been proposed (Noll and Noll, 1974; Jay and Kaempfer, 1975;Benne et al, 1973;Vermeer et al, 1973).…”

Section: Resultsmentioning

confidence: 99%

Initial rate kinetic analysis of the mechanism of initiation complex formation and the role of initiation factor IF-3

Gualerzi¹,

Risuleo²,

Pon³

1977

Biochemistry

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Initial rate kinetics of the formation of ternary complexes of Escherichia coli 30S ribosomal subunits, poly(uridylic acid), and N-acetylphenylalanyl transfer ribonucleic acid in the presence and in the absence of IF-3 are consistent with the hypothesis that the ternary complex is formed through a random order of addition of polynucleotide and aminoacyl-tRNA to separate and independent binding sites on the 30S ribosomes. The transformation of an intermediate into a stable ternary complex which probably entails a rearrangement of the ribosome structure leading to a codon-anticodon interaction represents the rate-limiting step in the formation of the ternary complex. The rate constant of this transformation, as well as the association constants for the formation of the 30S-poly(U) and 30S-N-AcPhe-tRNA binary complexes, are enhanced by the presence of IF-3 which acts as a kinetic effector on reactions which are intrinsic properties of the 30S ribosome. The IF-3-induced modification of these kinetic parameters of the 30S ribosomal subunit can per se explain the effect of IF-3 on protein synthesis without invoking a specific action at the level of the mRNA-ribosome interaction. This seems to be confirmed by the finding that IF-3 can stimulate several-fold the formation of a ternary complex even if one by-passes the ribosome-template binding step by starting with a covalent 30S-polynucleotide binary complex. Furthermore, the above-mentioned changes induced by IF-3 appear to be compatible with the previously proposed idea that the binding of the factor modifies the conformation of the 30S subunit. The random order of addition of substrates determined for the 30S-N-AcPhe-tRNA-poly(U) model system was found to be valid also for the more physiological 30S initiation complex containing poly(A,U.G) and (fMet-tRNA formed at low Mg2+ concentration in the presence of GTP and all three initiation factors.

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Section: Resultsmentioning

confidence: 99%

Initial rate kinetic analysis of the mechanism of initiation complex formation and the role of initiation factor IF-3

Gualerzi¹,

Risuleo²,

Pon³

1977

Biochemistry

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“…By varying pH and [S] it is possible to determine the pK values of the functional groups that are involved in the binding and conversion of the substrate and it is also possible to distinguish between them (Dixon, 1953;Alberty, 1956;Laidler, 1958;Dixon & Webb, 1965;Ahlers et al, 1974). [Mg2+] = 1mM; temperature = 30°C; below 8.8, 32mM-Tris was adjusted 1 value with 1M-HCl; above pH18.8, 1…”

Section: Results and Discussion Pk Values Of The Functional Groupsmentioning

confidence: 99%

“…The rate equations were derived from the rapid-equilibrium reaction mechanism according to models presented by Botts & Morales (1953), Laidler (1956), Ohlenbusch (1962) and Cleland (1970). Methods used to interpret the results of varying pH have also been described ( (Dixon, 1953;Alberty, 1956;Laidler, 1958;Dixon & Webb, 1965;Ahlers et al, 1974).…”

Section: Mg2dmentioning

confidence: 99%

The mechanism of hydrolysis of β-glycerophosphate by kidney alkaline phosphatase

Ahlers

1975

Biochemical Journal

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1. To identify the functional groups that are involved in the conversion of beta-glycerophosphate by alkaline phosphatase (EC 3.1.3.1) from pig kidney, the kinetics of alkaline phosphatase were investigated in the pH range 6.6-10.3 at substrate concentrations of 3 muM-30 mM. From the plots of log VH+ against pH and log VH+/KH+m against pH one functional group with pK = 7.0 and two functional groups with pK = 9.1 were identified. These groups are involved in substrate binding. Another group with pK = 8.8 was found, which in its unprotonated form catalyses substrate conversion. 2. GSH inhibits the alkaline phosphatase reversibly and non-competitively by attacking the bound Zn(II). 3. The influence of the H+ concentration on the activation by Mg2+ ions of alkaline pig kidney phosphate was investigated between pH 8.4 and 10.0. The binding of substrate and activating Mg2+ ions occurs independently at all pH values between 8.4 and 10.0. The activation mechanism is not affected by the H+ concentration. The Mg2+ ions are bound by a functional group with a pK of 10.15. 4. A scheme is proposed for the reaction between enzyme, substrate, Mg2+ and H+ and the overall rate equation is derived. 5. The mechanism of substrate binding and splitting by the functional groups of the active centre is discussed on the basis of a model. Mg2+ seems to play a role as an autosteric effector.

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“…In order to determine the kinetic parameters, concentrations of L-aspartate and 2-oxoglutarate were varied over the ranges 15 to 2.5 mm and 0.75 to 0.075 mM respectively. The data were then analysed by primary (double-reciprocal) plots and secondary plots in which the ordinate intercepts of the primary plots were plotted against the reciprocal of the concentration of the second substrate (Alberty, 1956;Price & Stevens, 1982).…”

Section: Methodsmentioning

confidence: 99%

The unfolding and refolding of cytoplasmic aspartate aminotransferase from pig heart

West

Price

1989

Biochemical Journal

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The unfolding of cytoplasmic aspartate aminotransferase from pig heart in solutions of guanidinium chloride (GdnHCl) was studied. Data from protein fluorescence, c.d. and thiol-group reactivity indicated that the enzyme was unfolded in 6 M-GdnHCl. Spectroscopic studies showed that this unfolding was accompanied by dissociation of the pyridoxal 5'-phosphate cofactor. On dilution of the GdnHCl, re-activation of the enzyme occurred in reasonable yield, provided that dithiothreitol and pyridoxal 5'-phosphate were present. The regain of activity obeyed second-order kinetics. In the absence of added dithiothreitol and pyridoxal 5'-phosphate, substantial formation of high-Mr aggregates occurred.

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The Role of Mathematics in Core-Program Development

Cited by 9 publications

References 0 publications

Initial rate kinetic analysis of the mechanism of initiation complex formation and the role of initiation factor IF-3

Initial rate kinetic analysis of the mechanism of initiation complex formation and the role of initiation factor IF-3

The mechanism of hydrolysis of β-glycerophosphate by kidney alkaline phosphatase

The unfolding and refolding of cytoplasmic aspartate aminotransferase from pig heart

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