Fitted rate constants

Using contaminant sources and reaction rate constants as fitting parameters, while constraining reaction rates to literature values, the authors calibrated the model to the data and obtained good agreement. In addition, for the most part, the fitted rate constants were close to field and/or laboratory measured values. The authors were careful to note, however, that the model was not used in a predictive mode. 

Table 1. Fitted rate constants from the work of Heidner et al. ...

In a similar way, Atkinson [52-54] claims to have fitted rate constants to within a factor of 2 between 250 and 1000 K by consideration of CH3—, CH2—, and >CH— as groups attacked and functioning as near-neighbour groups. For OH + alkane,... 

With [Co(phen)3] + as oxidant for PCu(I), rate constants determined by the stopped-flow method approach zero at low pH, consistent with zero reactivity of the trigonally coordinated Cu(I) form. However, with [FelCNlel as oxidant there is sometimes difficulty in fitting rate constants to the relevant [H ] dependence, which leaves open the question as to whether the rates actually become zero (57). Whereas [Co(phen)3l + is believed to react with PCu(I) at both the remote (acidic) and the adjacent (hydrophobic) patches, [FefCNleP reacts predominantly at the latter. The instability of PCu(I) in solution at pH < 4.5 makes it difficult to settle this issue conclusively. The range of studies has been extended using the pH-jump method in which protein, at high pH (with relatively small concentration of buffer), is stopped-flow mixed with the redox reagent at low pH (with excess buffer), and this approach has been used more extensively in recent studies. 

Because we have been thorough in our sampling across time, these simple models are easily fit. This was done separately for each time profile from each experimental run. The quality of the fits was reasonable (fit diagnostics not shown), although some lack of fit was exhibited, particularly for C and E. Note that at this stage we choose not to include a degradation path for C in the model. The model will require further refining, but nevertheless the model explained much of the variation in the data. Table 11 contains the fitted rate constants. 

Figure 11.14. Distributions of (logarithmsof)the apparent open time (left)and apparent shut time (right) for wild-type human receptors (top) and for mutant eL221F receptors (bottom). The histogram shows the experimental observations. The continuous lines were not fitted directly to the data in the histograms, but were calculated from the rate constants for the mechanism that was fitted (Fig. 11.10, scheme B, with the two sites constrained to be independent). The distributions were calculated with appropriate allowance for missed events (HJC distributions) (65, 66). The fact that they superimpose well on the histograms shows that the mechanism was a good description of the observations. The dashed lines show the distributions calculated from the fitted rate constants in the conventional way (45), without allowance for missed events, so they are our estimate of the true distributions cf open and shut times (296). See color insert.

Fig. 7. Dynein ATPase burst kinetics. The kinetics of a presteady-state burst of ATP binding (o) and hydrolysis ( ) were determined at two ATP concentrations (A) 30 and (B) 50 /xAf. The data fit rate constants of k = 4.7 juAf sec", ki = 55 sec, k-2 = 10 see", and ks = 8 see" according to Scheme IV. Reproduced with permission from (J9).

Figure 4. Correhtion between experimental and calculated best-fit rate constants of LRET, k y for cis (open data points) and trans (filled data points) isomers of H-Trp-(Pro)j -Tyr-OH peptides (inverted triangles) and H-Tyr-(Pro)j -Trp-OH peptides (squares). The best agreement between the experimental and calculated rates has been obtained for the following values of the parameters sought = (10 2) X 10 s, = 2.5 0.1 nm y and...

Fitting rate constants in hepatitis B varus model. 545... 

Figure 20-2 PCTox3raionosulfate yield versus average energy dissipation during reaction. The lines give micromixing predictions [with the E-model of Baldyga and Bourne (1989) using fitted rate constants].

---