Unfolding events

This very simple and rather unphysical model [143] is intended to illustrate the basic limiting process. An initial stem is laid down one segment at a time, such that the probability of continuing is ac, and at each level the chain may also bend, that is, fold, with probability ab. It does not take any detaching or unfolding events into account. Hence ... 

In this study the perspective of unfolding events, leading to an ineffective control, is obtained. The considerations which made sense at the moment of occurrence, but led to an ineffective control, are retrieved by collecting the answers to the five steps from Dekker. To derive the answers to the five steps from Dekker, Figure 23 is used. Steps 1 and 2 can be seen as the ineffective control element in Figure 23. An event from the tunnel (as depicted in Figure 24) can be seen as an ineffective control element. 

That peptidyl-proline isomerization is a post-unfolding event is readily demonstrated by double-jump experiments.17 The protein is denatured for several milliseconds and then restored to renaturing conditions before the peptidyl prolines have had time to isomerize. The proline-related phases are then no longer seen. 

Other measures of protein flexibility have been found to correlate with thermal stability. One is resistance to proteolysis (Daniel et al., 1982 Fontana, 1988). Another is the quenching of buried tryptophan fluorescence by acrylamide, used in a study by Varley and Pain (1991). Both these processes are mediated by the same combination of local and global unfolding events that determine rates of hydrogen exchange. Their rates will depend on the ability of another molecule, acrylamide or a proteolytic enzyme, to penetrate into normally buried regions of the protein in order to either quench fluorescence or cleave peptide bonds. 

To see to what extent these unfolding events of secondary structural elements depend on the temperature, force extension curves were recorded at 8°C... 

Besides the continuous improvements of FTIR-VCD instruments described above, some exciting new developments related to VCD measurements have been reported in recent years. These include the developments of matrix isolation FTIR-VCD instruments and of laser based real time VCD spectrometers. These new developments are associated with brand new applications and research directions, such as combining the matrix isolation technique with VCD spectroscopy to probe conformationally flexible chiral molecules and H-bonded chiral molecular complexes, and using femtosecond laser VCD instruments to record time resolved VCD spectra for monitoring fast chemical reactions or folding and unfolding events of peptides and proteins in solution. These will be discussed in more detail in Sects. 4.5 and 4.6. 

Distinguishing unfolding events from local fluctuations -hydrogen exchange with dilute denaturant... 

In general, unfolding events are known to be promoted by denaturant. Although there are many models for this dependence of unfolding free energy on denaturant (Pace, 1986), the simplest is a linear model where... 

Fig. 17.12. Unfolding data obtained from ubiquitin, Ubig, polyproteins at a constant pulling force of 110 pN. (a) The length versus time traces show 20 nm stepwise increases in length each time a single protein domain unfolds. The time of occurrence of the unfolding events (At) is probabilistic, (b) Histogram of unfolding dwell times is measured at 110 pN. The dashed line is a single exponential fit with an unfolding rate, fc, of 0.6 s [10,18]. The solid line is a stretched exponential fit with p(t) = exp[—(fct) ] with b = 0.7...

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