Random order of binding

ATP + (d)CMP = ADP + (d)CDP (<4> formation of a ternary complex, addition of substrates is random [5] <1> reaction proceeds by a sequential mechanism, a ternary complex of the enzyme with both substrates is formed as the central intermediate in the reaction [12] <3> reaction mechanism is sequential and nonequilibrium in nature, substrates bind to the enzyme in a random order, substrate binding is cooperative [14] <7> the mechanism is analogous to the phosphoryl transfer mechanism in cAMP-dependent protein kinase that phosphorylates the hydroxyl groups of serine residues [16] <8> random bi-bi mechanism [17])... 

The sequential mechanisms can be subdivided in those which have a compulsory order and those which have a random order of S binding. These mechanisms are often described with the popular shorthand notation given by Cleland (1963), in which uni, bi, ter, etc, denote the number of S and P species. The /Cm values of the various reactants are concentration values at which half of the maxi-... 

Another possibility is the random sequentiual reaction with no obligatory order of binding and release (Figure 6.9). 

Analysis of the reaction mechanism, using CoA substrate analogues indicates that the reaction mechanism proceeds sequentially through a ternary complex, probably by a random order of substrate binding. This proposal requires verification using the in vivo, acyl-ACP, substrates. 

Protrusion may be due to growth of new actin filaments, which requires net polymerisation of new filaments, and also by the organisation of actin-binding proteins into higher-order structures. Random movements of flexible membranes away from the filaments may result in gross distortion of actin polymerisation at the barbed ends. Thus, once a critical size is reached, ion pumping (i.e. of Ca2+) may occur at the tip of a pseudopod, which further aids directional changes in the network. 

Figure 8. The most common enzyme mechanisms, represented by their corresponding Cleland plots The order in which substrates and products bind and dissociate from the enzyme is indicated by arrows, (a) The Random Bi Bi Mechanism-. Both substrates bind in random order, (b) The Ordered Sequential Bi Bi Mechanism-. The substrates bind sequentially, (c) The Ping Pong Mechanism-. The enzyme exists in different states E and E. A substrate may transfer a chemical group to the enzyme. Only upon release of the first substrate, the chemical group is transferred to the second substrate.

Along these fines, Liebermeister and Klipp [161] suggested the use of a rapid-equilibrium random-order binding scheme as a generic mechanism for all enzymes, independent of the actual reaction stoichiometry. While there will be deviations from the (unknown) actual kinetics, such a choice, still outperforms power-law or lin-log approximations [161]. 

Fig. 6 (a) Schematic illustration of a flow cytometer used in a suspension array. The sample microspheres are hydrodynamically focused in a fluidic system and read-out by two laser beams. Laser 1 excites the encoding dyes and the fluorescence is detected at two wavelengths. Laser 2 is used to quantify the analyte, (b) Scheme of randomly ordered bead array concept. Beads are pooled and adsorbed into the etched wells of an optical fiber, (c) Scheme of randomly-ordered sedimentation array. A set of encoded microspheres is added to the analyte solution. Subsequent to binding of the analyte, microparticles sediment and assemble at the transparent bottom of a sample tube generating a randomly ordered array. This array is evaluated by microscope optics and a CCD-camera. Reproduced with permission from Refs. [85] and [101]. Copyright 1999, 2008 American Chemical Society... 

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. 

An enzyme reaction mechanism involving A binding before B and followed with the random release of products. In the absence of products and abortive complexes, the steady-state rate expression is identical to the rate expression for the ordered Bi Bi mechanism . A random on-ordered off Bi Bi mechanism has been proposed for a mutant form of alcohol dehydrogenase. ... 

A procedure that assists in the characterization of binding mechanisms for sequential (/.e., non-ping pong) reactions . The same general initial rate expression applies to the steady-state ordered Bi Bi reaction, the rapid-equilibrium random Bi Bi reaction, and the Theorell-... 

Bimolecular reactions of two molecules, A and B, to give two products, P and Q, are catalyzed by many enzymes. For some enzymes the substrates A and B bind into the active site in an ordered sequence while for others, bindingmay be iii a random order. The scheme shown here is described as random Bi Bi in a classification introduced by Cleland. Eighteen rate constants, some second order and some first order, describe the reversible system. Determination of these kinetic parameters is often accomplished using a series of double reciprocal plots (Lineweaver-Burk plots), such as those at the right. 

Reactions in which all the substrates bind to the enzyme before the first product is formed are called sequential. Reactions in which one or more products are released before all the substrates are added are called ping-pong. Sequential mechanisms are called ordered if the substrates combine with the enzyme and the products dissociate in an obligatory order. A random mechanism implies no obligatory order of combination or release. The term rapid equilibrium is applied when the chemical steps are slower than those for the binding of reagents. Some examples follow. 

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