Rate constant protein folding

There does, however, appear to be a statistically significant correlation between the rate constants for folding of single domain proteins and the average sequence separation between contacting residues in the native state. Proteins that have primarily local contacts (i.e., have a low contact order) tend to fold more rapidly than those that have more non-local interactions (i.e., have a high contact order).81,82... 

There is a severe practical problem in looking for correlations between the rate constants for folding of small proteins and their structural or thermodynamic properties—specific structural features can dominate the rate of folding. For example, we know from the protein engineering studies on barnase and CI2 that specific mutations can slow down the rate of folding by several orders of... 

Fig. 6. Acceleration of refolding of different proteins as a function of PPI activity. The acceleration factor is given as the ratio hlk of the observed rate constants for folding in the presence of PPI, k, and in the absence of PPI, ki,. The PPI activity is given as /f/ml. The K values are defined as described in footnote b to Table I. The following protein concentrations were used in the refolding experiments ( ) 2 /iM immunoglobulin light chain, ( ) 11 juAf porcine pancreatic RNase, and ( ) 17 fiM S-protein fragment of bovine RNase A. The final conditions for refolding were 0.25 M urea (0.30 M urea for porcine RNase), 0.1 Af Tris-HCl, pH 8.0, 10°C. Based on data from Lang el at. (1987).

Here, U, M, and M refer to unfolded, collapsed, and folded monomers, A to aggregates, and, k2 to the first- and second-order rate constants of folding and association, respectively. If the side reactions win, the protein will be degraded or precipitated, or chaperones will take care of Each step along the sequen-... 

Chung et al. have used this technique to measure rate constants for folding and unfolding of several proteins [51-54]. They also explore how quickly individual transitimis between U and N states can occur, as measured by the minimum time between detection of photons with wavelengths indicative of different states. The transitimi time is much less than the macroscopic time constant for folding and unfolding. 

Protein B from M. capsulatus (Bath) not only increases the product yields, but also influences the rate constant for the single turnover reaction of Hred with nitrobenzene (51,67). The pseudo-first-order rate constant increases up to 33-fold when Hred is titrated with protein B. Neither addition of reductase to Hox or Hred, nor addition of protein B and reductase to Hred, could similarly affect the rate constant. These... 

Figure 19.22 The gatekeeping or filtering activity of the GroEL ATPase. The turnover number for the ATPase reaction (0.05-0.1 s-"1) is far slower than the refolding rate constant of 2-2.5 s-1 for GroEL-bound bamase. Only slowly folding proteins bind long enough to enter the chaperoning cycles of Figure 19.23.

For 02 and some other small proteins, but not in general, the folding rate constant, kf, follows a similar relationship for [denaturant] < [denaturant] 50% ... 

Under conditions that strongly favor folding, the rate constant of refolding is considerably faster than that of unfolding, so that K > o, and k0 can be ignored. Equation 18.27 has two extreme limits. When kc > fcint, as is usual for most globular proteins under most conditions, the observed rate constant of exchange reduces to... 

This case is particularly relevant in regard to the formation of inclusion bodies (see Section 17.6 below) as overexpression of a target protein is a mode of obtaining the protein. With the assumption that folding and aggregation behave as in case 1, and nascent protein is expressed with a zerofh-order rate constant k0 with respect to the... 

The reductive nitrosylation of a synthetic iron porphyrin by HNO (193) proceeds with a reported rate constant of 1 x 107 A/-1 s However, this value was estimated based on a HNO dimerization rate constant of 8 x 109 M-1 s-1 (210), which is now considered to be 1000-fold lower [(8 x 106 A/-1 s-1 (106)]. The recalculated constant for the reaction of HNO with the porphyrin (3 x 10s AT V1) is similar to the estimated value of HNO addition to metMb. Synthetic porphyrins generally react 30-fold faster with NO (1 x 109M 1 s-1) than ferrous Mb [for a recent, thorough review see (44)] due to rate-limiting diffusion of NO through the protein. The similarity in rate constants for HNO with metMb and the ferric porphyrin suggests that the rate-limiting step in reductive nitrosylation is likely addition of HNO to the ferric metal, with little influence from the protein structure. 

The ability of modern HPLC techniques to yield quantitative data on rate constants for polypeptide or protein folding and unfolding transitions as well as to detect conformational intermediates with relaxation half-times of similar (or larger) magnitude to the mass transport time (i.e., rconf rmasstransfer, where Tmasstransfer > 10 sec) also has important ramifications in the selection... 

Although copper binds tighter than zinc to aU forms of the enzyme tested, zinc stabilizes the protein fold better as judged by solvent-induced denaturation experiments. In addition the dissociation rate constant for zinc is about 100 times slower than copper suggesting the zinc is kinetically trapped once folding has occurred. This may thus be a physiological means by which metal ion specificity is achieved. ... 

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