Sequential folding

Quadruplexes could also act purely as a structural feature, enabling easy recognition by proteins or other species. This model has been proposed for telomeric repeats, perhaps as a beads-on-a-string model of sequential folded quadruplexes. Other regions could also have such structural behaviours. 

P. Chen, C.-L. Evans, J. D. Hirst, and M. S. Searle, Biochemistry, 50,125 (2011). Structural Insights into the Two Sequential Folding Transition States of the PBl Domain of NBRl from Value Analysis and Biased Molecular Dynamics Simulations. 

V (the potential) is identified with the enthalpy, i.e. the number n of base pairings (contacts), and T corresponds to the entropy. At each stage in the folding process, as many as possible new favourable intramolecular interactions are fonned, while minimizing the loss of confonnational freedom (the principle of sequential minimization of entropy loss, SMEL). The entropy loss associated with loop closure is (and the rate of loop closure exp... 

Fernandez A and Cendra H 1996 in vitro RNA folding the principle of sequential minimization of entropy loss at work Biophys. Chem. 58 335-9... 

All peptidases within a family will have a similar tertiary structure, and it is not uncommon for peptidases in one family to have a similar structure to peptidases in another family, even though there is no significant sequence similarity. Families of peptidases with similar structures and the same order of active site residues are included in the same clan. A clan name consists of two letters, the first representing the catalytic type as before, but with the extra letter P , and the second assigned sequentially. Unlike families, a clan may contain peptidases of more than one catalytic type. So far this has only been seen for peptidases with protein nucleophiles, and these clans are named with an initial P . Only three such clans are known. Clan PA includes peptidases with a chymotrypsin-like fold, which besides serine peptidases such as chymotrypsin... 

In conclusion, it seems more likely that the folds go into the crystal sequentially as it is being formed, rather than forming through equilibrium considerations — this idea is used as a basis for kinetic theories. 

This is a problem that has been reported by several researchers in other cya-nation methods on heteroaromatic halides. (Hetero)aryl chlorides have also been tackled via in situ halogen exchange to (hetero)aryl bromides followed by sequential cyanation (Scheme 71). For this microwave-assisted process an equimolar amount of NiBr2 and a two-fold excess of NaCN were used. The only heteroaromatic chloride tested was 2-chloropyridine. Although the procedures described involve the use of significant amounts of nickel salts, a clear advantage is that the reactions can be performed in air. Moreover, the cyanat-ing reagents are easily removed since they are water soluble. 

No sequence homologies can be detected. This is, perhaps, not surprising. The X-ray structure analysis of lysozyme by Phillips has shown that the polypeptide chain is folded in a way which puts none of the amino acids in sequential vicinity of the catalytic Asp-52 and Glu-37 that are near to the bound substrate. Comparable folding patterns can probably be realized with widely differing arrangements of amino acids, and thus the apparent lack of homologies. 

Ptitsyn OB (1973) Sequential mechanism of protein folding. Dokl Phys 210 1213 (in Russian)... 

Figure 4- Response of an lead-selective electrode based on a calix[6]arene hexaphosphene oxide to sequential 10-fold dilutions of a sample solution demonstrating a very rapid Nernstian response down to sub-nanomolar concentrations of lead. The inset shows a linear Nernstian plot is obtained with almost theoretical slope (25.7 mV per decade) down to 10-10 M.

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