Intermediate population

REX-CPHMD simulations have also been applied to understand the mechanism of the formation of protein intermediate states. Recent solution NMR data revealed a sparsely populated intermediate in the villin headpiece domain, in which the N-terminal subdomain is largely random but the C-terminal subdomain adopts a nativelike fold [34], Interestingly, H41 in this intermediate state titrates at a pH value of... 

As mentioned in the introduction, there is not a single folding pathway. The flexible protein might choose from many different pathways via many different low populated intermediates or transition states, all leading eventually to the native state. Hence, there is not only one transition state, but instead a whole ensemble of states the transition state ensemble (TSE). To explore the... 

Stochastic theory and multistep ET via dynamically populated intermediate states. 

Theory of stochastic behaviour of the conformational and solvent dynamics, environmental relaxation, and multi-step processes via dynamically populated intermediate eleetronic states. 

Much larger alanine peptides have also been studied. Eor instance, Asher et al. (2004), using UV Raman spectroscopy, examined the melting of a 21-residue, mainly alanine peptide (containing three arginines to confer solubility). The peptide was mainly in an a-helix conformation at 0°C and melted to a PPII conformation as the temperature increased. Above room temperature the peptide existed mainly as a PPII helix. The authors did not observe evidence of any other significantly populated intermediates. 

Figure 39. Probabilities of significantly populated intermediate states for the folding of the X-repressor in the diffusion collision model as a function of time for 0 = 0.01. The states are labeled as described in the text.

The populated level begins to relax vibrationally after the first ET step, but the second step, i.e., electron transfer fix>m the populated intermediate level to the positively biased electrode, occurs before fiill relaxation. This pattern corresponds to coherent two-step ET, of n4iich strictly resonating three-level transfer would be a limiting case. 

N. Feiguson, A. P. Capaldi, R. James, C. Kleanthous, and S. E. Radford, Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9. J. Mol. Biol. 286, 1597-1608 (1999). 

One should now compare these DIFFERENCE CROSS-SECTION SPECTRA of the respective intermediates (Fig.3) with the TRANSIENT ABSORPTION SPECTRA of Fig. 2, which reflect the actual absorption of the sample at a certain delay time tj after excitation. According to eq. (2) the TRANSIENT ABSORPTION SPECTRA do not characterize the single intermediates, but show a mixture of the absorption properties of the intermediates populated at the specific delay time tj. As a consequence the mixture of states may hide a weakly populated intermediate, especially if the absorption of this intermediate overlaps with the bands of other intermediates populated at the same time. 

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