Folded Backbones

The parameters of the 4 - 1 hydrogen bond appear to be independent of cyclization or chain length, although a minimum of three peptide groups is required. Removal of the cysteine residue from the oxytocin fragment yields the tripeptide LPro-LLeu-Gly-NH2, which does fold into a p bend (Reed and Johnson, 1973), but the 4 1 hydrogen bond is now shifted to encompass 

Finally, there is the case of the tetrapeptide LPro-LTyr-Llle-LLeu-OH, a fragment of neurotensin, which has a folded backbone but in which internal NH 0=C bonding does not occur (Cotrait et ai, 1979). The molecule has an approximate H shape in which the four side chains are extended in the legs of the H and the center bar consists of the peptide unit between L-tyrosine and L-isoleucine. 

A review of the known structures of linear peptides in the crystalline state indicates that their conformations are quite unpredictable. Di- and tripeptides are probably greatly affected by packing forces and by the large number of hydrogen bonds usually present between different peptide molecules and to the cocrystallized solvent, usually water. Their backbones are never fully extended but take on a variety of twists and bends. The longer peptides usually contain intramolecular hydrogen bonds, and their conformations appear to be much less influenced by packing forces. The proline residue is often associated with a jS bend however, it is also often associated with a cis conformation for the amide bond. 

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In general, the slow oligomer growth process hampers the discovery phase (i.e., identification of new folding backbones) in foldamer research, and impedes the development of a facile molecular weight-secondary structure relationship. 

Fig. 5 Gallery of NH-)t interactions between an aromatic residne (Phe, Tyr or Tip) and a backbone amide NH bond, from gas phase IR/UV laser spectroscopy of a series of model capped peptides a folded backbone (y-tum), without and with a NH-ic interaction within the Phe residue [70], an extended backbone on Phe, with the interaction of Phe with NH of the next residue [84, 94]) and various aryl-rich dipeptides, leading to sandwich-Uke conformations of the NH embedded in the aryl environment and to significantly red shifted IR NH stretch signatures [112]. In the latter cases, the simultaneous presence of two it H-txaids raiginating from the same NH moiety (made possible through a direct interactiim between aromatic side chains) is indicated by the 3D-NCI plot of these interactions [193, 194]...

En me Mechanism. Staphylococcal nuclease (SNase) accelerates the hydrolysis of phosphodiester bonds in nucleic acids (qv) some 10 -fold over the uncatalyzed rate (r93 and references therein). Mutagenesis studies in which Glu43 has been replaced by Asp or Gin have shown Glu to be important for high catalytic activity. The enzyme mechanism is thought to involve base catalysis in which Glu43 acts as a general base and activates a water molecule that attacks the phosphodiester backbone of DNA. To study this mechanistic possibiUty further, Glu was replaced by two unnatural amino acids. 

Investigation has shown that chain transfer to polymer occurs predominantly on the acetate methyl group in preference to the chain backbone one estimate of the magnitude of the predominance is 40-fold (92,93). The number of branches per molecule of poly(vinyl acetate) polymerised at 60°C is ca 3, at 80% conversion. It rises rapidly thereafter and is ca 15 at 95% conversion and 1-2 x lO" number-average degrees of polymerisation. 

Unit cells of pure cellulose fall into five different classes, I—IV and x. This organization, with recent subclasses, is used here, but Cellulose x is not discussed because there has been no recent work on it. Crystalline complexes with alkaU (50), water (51), or amines (ethylenediamine, diaminopropane, and hydrazine) (52), and crystalline cellulose derivatives also exist. Those stmctures provide models for the interactions of various agents with cellulose, as well as additional information on the cellulose backbone itself. Usually, as shown in Eigure la, there are two residues in the repeated distance. However, in one of the alkah complexes (53), the backbone takes a three-fold hehcal shape. Nitrocellulose [9004-70-0] heUces have 2.5 residues per turn, with the repeat observed after two turns (54). 

ES Huang, P Koehl, M Levitt, RV Pappu, JW Ponder. Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods. Proteins 33 204-217, 1998. 

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