Folding up conformation

Apart from any stabilisation effected with respect to the keto form, such intramolecular hydrogen-bonding will lead to a decrease in the polar character of the enol, and to a more compact, folded-up conformation of the molecule, compared with the more extended conformation of the keto form. This has the rather surprising result that where keto... 

Another example of a quantal repeat—but with considerable variation in sequence—is seen in the keratin-associated proteins (KAPs). In sheep, these display pentapeptide and decapeptide consensus repeats of the form G—G—Q—P—S/T and C-C-Q/R—P—S/T—C/S/T—C—Q—P/T—S, respectively (Parry et al., 1979). Some of the positions, as indicated by the presence of a consensus sequence, contain residues that occur much more frequently than others, but the absolute conservation of a residue in any position is not observed. The decapeptide consists of a pair of five-residue repeats closely related, but different to that displayed by the pentapeptide. Although the repeats have an undetermined structure, the similarity of the repeat to a sequence in snake neurotoxin suggests that the pentapeptides will adopt a closed loop conformation stabilized by a disulphide bond between cysteine residues four apart (Fig. 5 Fraser et al., 1988 Parry et al, 1979). Relative freedom of rotation about the single bond connecting disulphide-bonded knots would give rise to the concept of a linear array of knots that can fold up to form a variety of tertiary structures. The KAPS display imperfect disulphide stabilization of knots and have interacting... 

Five-membered ring formation is very favourable as the conformation needed 4 is reasonable and transition state and product are unstrained. If you make a molecular model of a long chain and fold it round you will find that the atoms that approach each other have a 1,5-relationship. Folding a chain 12 to form a six-membered ring takes the nucleophile past the electrophile 12a and only when the chain folds up in a chair-like fashion can cyclisation 13 occur. 

The polypeptide chain folds up to form a specific shape (conformation) in the protein. This conformation is the three-dimensional arrangement of atoms in the structure and is determined by the amino acid sequence. There are four levels of structure in proteins primary, secondary, tertiary and, sometimes but not always, quaternary. 

Double-stranded right-handed B-DNA has a highly repetitive, negatively charged polyphosphate surface, single-stranded nucleic acids that do not fold up to compact structures are much more flexible than the double-stranded nucleic acids and the predominantly hydrophobic bases are much more exposed. A common feature of all the A-, B- and Z-DNA conformations is that the two chains are antiparallel. 

The answer to the first point, as you may already have guessed, is that the assumption that the rings arc planar is simply not correct. It is easy to see how large rings can fold up into many different conformations as easily as acyclic compounds do. It is less clear to predict what happens in six-membered rings. 

This reaction happens only because it is intramolecular. There is no conjugating group attached to the dienophile and so there are no orbitals to overlap with the back of the diene. The molecule simply folds up in the sterically most favourable way (as shown in the margin, with the linking chain adopting a chair-like conformation) and this leads to the trans ring junction. 

When the transition state for a ring closure forms a chair then a trans relationship results. This is the case for the black Me and brown Me. When a boat is formed a cis relationship results. This is the case for the green Me and black H. Squalene folds up in a chair-boat-chair conformation and that leads to the observed stereochemistry. 

The conformation of the molecule in the moment of cyclization can be seen easily by working backwards from the product. The green dashed lines show new bonds that are being formed. All the six-membered rings in the transition state are chairs and all the ring junctions tram. This is an impressive result as there is no enzyme to help the molecule fold up in this way. 

The Lewis acid BF3) opens the epoxide to give the tertiary cation, which cyclizes on to the ally silane to give a 3-silyl cation that loses the Me3Si group in the usual way. It is clear from the product what the stereochemistry of this intermediate must be and it looks as though cyclization gives the more stable di-equatorial product (margin). Probably the cation folds up in this conformation. The alcohol controls the new centre and is then removed by oxidation to a ketone. 

Before proteins can actively function in the living cell they must fold up into a specific 3-dimensional structure, the so-called native state (see Fig. 1). Already in the 1960 s it was recognized that the long linear polypeptides chains can adopt their native structure starting from the random coil state in a surprisingly short time. The famous Levinthal paradox states that if a peptide bond between amino acids can only adopt two conformations a relatively short protein of a hundred residues can have around 2 10 possible... 

Proteins make up more than 50% of the dry weight of animals and bacteria. They perform many important functions in living organisms, a few of which are indicated in Table 28-7. Each protein carries out a specific biochemical function. Each is a polypeptide with its own unique sequence of amino acids. The amino acid sequence of a protein determines exactly how it folds up in a three-dimensional conformation and how it performs its precise biochemical task. 

Strichartz An alternative explanation is that these mutations affect the conformation of the channel and indirectly affect the binding site. So when we change them, the channel will still inactivate, but it folds up into a tighter or a looser situation, so this binding site, which has a weak stereoselectivity to begin with, is altered. 

The second reaction amounts to an aza-ene reaction with the most remote alkene providing the ene partner and the imine. The molecule folds up 179 to give a chair conformation in the developing six-membered ring and the product 176 is easily transformed into ( )-methyl homo-secodaphniphyllate 180. 

Because of rotational flexibility in the polypeptide backbone, primarily around the N— (p) and C —C (f/r) angles, there is a very large number of possible conformations that any one polypeptide molecule may adopt. Unlike most synthetic polymers, however, proteins have the ability to fold up (under the right conditions) into specific conformations, and it is these conformations (structures) that give rise to their individual properties. 

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