Kinetics zippering

FIGURE 13.16 Diagram illustrating the kinetic zipper effect of a polymeric additive in CMP slurry that functions to stabilize the adsorption from removal under certain applied forces. 

DA d Avignon, GL Bretthorst, ME Holtzer, A Holtzer. Thermodynamics and kinetics of a folded-folded transition at vahne-9 of a GCN4-hke leucine zipper. Biophys I 76 2752-2759, 1999. 

Girvin DC, Sklarew DS, Scott AJ, Zipperer JP (1990) Release and attenuation of PCB congeners, measurements of desorption kinetics and equilibrium sorption partition coefficients. GS6875, Electric Power Research Institute, Palo Alto, CA 94304... 

However, active uptake mechanisms have now been found in some bacteria for various xenobiotic organic anions. These include 4-chlorobenzoate (Groenewegen et al., 1990), 4-toluene sulfonate (Locher et al., 1993), 2,4-D (Leveau et al., 1998), mecoprop and dichlorprop (Zipper et al., 1998), and even aminopolycarboxylates (Egli, 2001). Such active uptake appears to be driven by the proton motive force (i.e., accumulation of protons in bacterial cytoplasm). These transport mechanisms exhibit saturation kinetics (e.g., Zipper et al., 1998), and so their quantitative treatment is the same as other enzyme-limited metabolic processes (discussed below as Michaelis-Menten cases). 

Girvin, D. C., Skalrew, D. S., Scott, A.J. Zipperer, J. P. (1990). Release and Attenuation of PCB Congeners Measurement of Desorption Kinetics and Equilibrium Sorption Partition Coefficients. Palo Alto, CA. Electric Power Research Institute, EPRI GS-6875. 

Kinetic analysis indicates that renaturation is a two-step process. In the slow step effective contact is made between two complementary regions of DNA originated from separate strands. This rate-limiting step called nucleation is a function of the concentration of complementary strands. Nucleation is followed by a relatively rapid zippering up of adjoining base residues into a duplex structure. The steps involved in denaturation and renaturation are depicted in figure 25.14. 

Table XVI gives a partial list of native proteins that have been hydrolyzed with proteolytic enzymes. A discussion of the interpretation of each example listed is beyond the scope of this review, but a few comments concerning certain features of proteolysis are ivarranted. The mechanism of enzymatic hydrolysis of native proteins was studied in detail by Tiselius and Eriksson-Quensel (1939), who examined the action of pepsin on ovalbumin. Two mechanisms of proteolysis were considered by these workers. In the first mechanism the enzyme hydrolyzes all susceptible peptide bonds in one substrate molecule before hydrolysis of a second molecule begins. This type of mechanism has been described by Lmderstrpm-Lang (1952) as the all or none type. In the second mechanism, the enzyme hydrolyzes the single, most susceptible bond in all substrate molecules before hydrolysis of other bonds occurs. This mechanism is called the zipper type. Hydrolysis of a protein can proceed by either of the two mechanisms or by a mechanism which has features of both types. General aspects of the problem have been reviewed and theoretical equations which describe the kinetics of ea( h mechanism have been derived (Linderstr0m-Lang, 1952, 1953).

In other studies it appears that the kinetics of digestion of human serum albumin by pepsin and chymotrypsin follow the all or none mechanism, whereas tryptic action is of the zipper type (Kaminski and Tanner,... 

Computer programs have been used to correlate the degradation kinetics of poly(vinyl halides) assuming a kinetic model that is based on the zipper mechanism. Best fit values of the parameters of the kinetic model allow reproduction of a degradation with an error that is usually less than 0.6% per point. 

The two kinetic models that effectively correlate data for the degradation of vinyl polymers were developed on the basis of the zipper mechanism and differ only in the approximations used to account for the premature termination of zip chains. Although the equations are complex in appearance (3), they are based on the relatively simple assumptions of the zipper mechanism. Chains are initiated as a certain fraction of chains per second, k., and unzip at a certain fraction of a started chain per second, R.. 

Thus, first order kinetics and zero order kinetics appear as special cases of the more general kinetics which have been derived on the basis of the zipper mechanism. The zipper model does not invoke the steady state assumption but allows the number of producing sites to increase during the acceleratory period as more zip chains start production and to decrease during the de-celeratory period as more chains are terminating than are starting. 

The crystal structure of both ribonuclease A and S have been determined and residues 2-13 form two-three turns of a-helix (4,). In the dissociated state, S-peptide contains little detectable helix either by circular dichroism (5) or by NMR (6,7). Either the S-protein induces the bound conformation during the association or a conformer too limited in concentration to be detected by spectroscopy is preferentially bound. It has been argued (3) on kinetic grounds that the induced-fit or "zipper" hypothesis is more likely, but no relevant experimental data exists on this or other systems to our knowledge. 

It is now apparent that difficult reproducibility is a built-in characteristic of zipper kinetics. Even though reproducibility is a recognized problem, the values of the parameters k and kz have theoretical and practical significance and can be directly related to the processes that occur in any specific degradation. 

This reaction is believed to involve a number of complex processes, by which four alkynes coordinate to a metal center to undergo either a stepwise coupling or a concerted zipper-type cyclization. However, the Ni2(COT)2-catalyzed reaction involves the formation of a bis(cyclopentadienylnickel) complex, a homobimetallic center,as supported by the actual determination of the structure from X-ray crystallography by the fast initiation of the reaction without an induction period when used directly for alkynes compared to other types of catalysts,and by kinetic studies and labeling experiments. An illustrative mechanism catalyzed by Ni2(COT)2 is given here. 

The dehydrohalogenation of poly(vinylhalides) is important because of its presumed relationship to thermal stability. Most reports agree that PVC and PVDC dehydro-chlorinate by a Zipper Mechanism but kinetic studies have not followed the implications of that mechanism. The rate of PVC dehydrochlorination has been reported to increase, decrease, and remain constant with time and the catalytic effect of hydrogen chloride has not always been observed. PVDC has been reported to follow first order kinetics, but the acceleratory phase of the dehydrochlorination was not adequately accounted for. 

PVC, PVDC, and PVF follow acceleratory dehydrohalo-genations and a kinetic model based on the Zipper Mechanism gives excellent correlation of data over the entire ranges of decomposition for all three polymers. The time for a PVC chain to unzip depended upon the length of the chain and an initiation mechanism at a site at or near a chain end seemed reasonable. 

Hauser, K., Krejtschi, C., Huang, R., Wu, L., Keiderling, T.A. Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using tanpaature-jump IR spectroscopy and isotopic labeling. J. Am. Chem. Soc. 130,2984—2992 (2008)... 

PAA brushes were prepared on flat silicon wafers coated with polystyrene using the LB technique as described earlier in this chapter. Adsorption and desorption were monitored using fixed-angle optical reflectometry [58]. The kinetics and reversibility of the formation of a zipper brush are demonstrated in Figure 7.9, representing a typical reflectometry experiment of the adsorption and desorption of P2MVP-PEO to a PAA brush. 

Structure of the Zipper Brush and the Kinetic Barrier in Its Formation... 

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