Fitness conformation-dependent value

Conformation-dependent Value Functions and Fitness Landscapes... 

The NO dissociation rate constants are summarized in Table HI (50) and are smaller than those seen with NO-metmyoglobin complexes. NP2 and NP3 (A ofr 0.1 s ) release NO approximately 10 times more slowly than NPl and NP4 kofs 2-3 s ) at pH 8.0, and the NO release rate for all nitrophorins decreases as the pH is lowered to 5.0. The NO release curves cannot be fit with a single exponential, indicating two off rates at each pH, as previously noted for both recombinant and insect-derived NPl (46), and which has also been recently reported for recombinant NP2 (145). The biphasic kinetics suggest the presence of slowly interconverting conformations. The values obtained are pH and protein dependent, ranging from 2.6 to 0.05 (Table HI) (50), values that are considerably slower than found for sperm whale metmyoglobin... 

As can be seen from Eq. (77), the quantity Aa is definitely not a constant but diould grow with an increase in chain flexibility (Le. decrease of 0). Thus, if both the SB relationship and our Eq. (76) are correct, the plot of Aa against 0 Aa should be a straight line with a slope of unity. And, indeed, Aa actually tends to increase with decrease of 0, but this behavior cannot be quantitatively accounted for by Eq. (77), as the deviations of the experimental points from the theoretical line become steadily more pronounced as Aa decreases. The best fit of experimental values of Aa is observed only for those polymers which exactly conform to the SB rule (polyvinylchloride, polyvinylacetate, etc.). This result emphasizes once more that the value of fg as defined earlier is not a constant, at least for the many varieties of polymers. To gain a deeper insight into the expected relationship between Aaand 0, we plotted lg Aa against 0 Aa. In this case much better linear dependence clearly results, with the experimental points fluctuating around the theoretical line even for those polymers which do not obey the SB rule. 

Lines in Figure 30.12 were drawn with parameters obtained when fitting data with Equation 30.3. It is fairly obvious that, outside the experimental window, data would not necessarily conform to such a simple model, which in addition cannot meet the inflection at 100% strain. All results were nevertheless fitted with the model essentially because correlation coefficient were excellent, thus meaning that the essential features of G versus strain dependence are conveniently captured through fit parameters. Furthermore any data can be recalculated with confidence within the experimental strain range with an implicit correction for experimental scatter. Results are given in Table 30.1 note that 1/A values are given instead of A. 

The accuracy of PHMD methods and their feasibility for studying pH-dependent conformational phenomena of proteins can be assessed by pKa calculations. In this case, PHMD simulations are performed with several pH values. The resulting occupancy values for deprotonated states (.S dc prot) are plotted against pH (Figure 10-3). A titration curve and pATa values (Figure 10-3) can be obtained by fitting the data to the generalized HH equation (Eq. 10-5). 

The contribution of the poly(Pro)II conformation to the ensemble of unordered peptides has been considered.1158 The temperature dependence of [0]222 for the peptide Ac-YEAAAKEAPAKEAAAKA-NH2 in 8 M guanidinium chloride and of poly(Lys) in water and in ethylene glycol/water (2 1) mixtures 156 was fitted to a two-state equation for a poly(Pro)II-unordered equilibrium with a temperature-independent AH and temperature-independent molar ellipticities for the two components. The peptide with a Pro at the central position is an unordered peptide, the spectrum of which has pronounced poly(Pro)II-like features at low temperatures. This fit yielded [0]222=- -9580 deg-cm2dmol 1 for the poly (Pro)II component and —5560 deg-cm2-dmol 1 for the unordered component. These values provide a method for roughly estimating the poly(Pro)II content, /Pn, of an unordered peptide from [0]222 ... 

Moha et al. (54) considered that polypeptides in helicogenic solvents can assume intact helices but that the resulting rods can be weakly bent, and proposed to represent such a flexible rod by a wormlike chain. It was shown that the nonlinear dependence of 1/2 on N as depicted in Fig. 21 can be fitted by a suitable choice of the two parameters characterizing the wormlike-chain model. However, the necessary value for the length per monomeric unit forces us to accept the conclusion that the helical conformation is not of the a-type but of the 310-type. This is at variance with the ample experimental evidence now available for many synthetic polypeptides. 

Specificity, in the sense of discrimination between competing substrates, is independent of the above three effects. The reasons are discussed in detail in Chapter 13. The basic reason is that specificity depends on kcal/KM, and strain and nonproductive binding do not affect the value of kcJKM because it is independent of interactions in the ES complex (equations 12.10 and 3.36). Equation 12.16 shows that induced fit does alter kcal/KM for the active conformation, but equally for all substrates (i.e., by a factor of K). 

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