Extended structures 3, helix

We have so far described the structure of DNA as an extended double helix The crys tallographic evidence that gave rise to this picture was obtained on a sample of DNA removed from the cell that contained it Within a cell—its native state—DNA almost always adopts some shape other than an extended chain We can understand why by doing a little arithmetic Each helix of B DNA makes a complete turn every 3 4 X 10 m and there are about 10 base parrs per turn A typical human DNA contains 10 base parrs Therefore... 

Neuropeptide Y (NPY) is a 36 amino acid polypqrtide with tyrosine residues at both ends of the molecule. It is characterised structurally by a PP-fold consisting of an extended polyproline helix and an a-helix connected by a (3-tum [1]. Based on structural and evolutionary criteria, NPY is closely related to peptide YY (PYY) and pancreatic polypeptide (PP). 

Fig. 1. Schematic diagram of nuclease A131A in the folded conformation. The alpha helices and beta strands are labeled. NMR analysis suggests the two turns and one helix in black are modestly populated in the denatured state, whereas the shaded helix is slightly populated. Strands / l-/ 2-/ 3 form an extended structure about which littie is known. Reproduced from Barron, L. D., Hecht, L., Blanch, E. W., and Bell, A. F. (2000). Prog. Biophys. Mol Chem. 73, 1-49. 2000, with permission from Elsevier Science.

Figures 9 and 10 represent a selected comparison of amide V and I+II FTIR and VCD for four proteins in D2O solution. Of these, myoglobin (MYO) has a very high fraction of a-helix, immunoglobulin (IMU) has substantial /1-sheet component, lactoferrin (LAF) has both a and j3 contributions, and a-casein (CAS) supposedly has no extended structure. The FTIR spectra of these proteins change little, the primary difference...

The LBP-20 proteins were predicted to be rich in a-helix, and with very little, if any, (i/extended structure, and this has been confirmed by circular... 

A few other helical conformations occur occasionally in globular protein structures. The polyproline helix, of the same sort as one strand out of a collagen structure, has been found in pancreatic trypsin inhibitor (Huber et al., 1971) and in cytochrome c551 (Almassy and Dickerson, 1978). An extended e helix has been described as occurring in chymotrypsin (Srinivasan et al., 1976). In view of the usual variability and irregularity seen in local protein conformation it is unclear that either of these last two helix types is reliably distinguishable from simply an isolated extended strand however, the presence of prolines can justify the designation of polyproline helix. 

Altenbach, C., Cai, K., Khorana, H. G., and Hubbell, W. L. (1999a). Structural features and light-dependent changes in the sequence 306-322 extending from helix VII to the palmitoylation sites in rhodopsin A site-directed spin-labeling study. Biochemistry 38, 7931-7937. 

The size and shape of a macromolecule can be determined by measuring the physical properties of isolated macromolecules in solution. Large rigid macromolecules that are derived from extended structures including the collagen triple helix result in rodlike rigid or semirigid structures. The size, shape, and physical parameters for macromolecules discussed in this book... 

Figure 16 (a) The structure of calcmeurin with suhunit A in cyan. The catalytic site containing a Zn-Fe hinding site is in dark red. Subunit B in orange contains four calciimi (green) ions hound to the EF-hand motifs. Both N- and C-terminal domains of calcineurin B interact to the same extended a-helix of calcineurin A. (h) The inhibitor complex cyclosporin A (red) and cyclophilin (violet) interacts with both calcineurin subunits and blocks the catal)dic site of calcineurin ... 

To keep the optimization of PLS parameters as simple as possible, only three types of structure, helix, extended, and turn, were used in constructing the basis sets. By the eventual addition of ordered and disordered helix, 3 o helix, and other components (20), it is likely that the standard error and the level of structural detail available from the method can be improved. 

The standard errors for the optimal analysis parameters here are similar to those obtained using PLS analysis of transmission FTIR spectra, for example, Dousseau and Pezolet (20) found average standard deviations of 11.7% for a-helix, 6.6% for extended structure ((3), and 6.7% for turn + other structures using a 3 component analysis. 

Pauling and Corey discovered another periodic structural motif, which they named the p pleated sheet (P because it was the second structure that they elucidated, the a helix having been the first). The P pleated sheet (or, more simply, the P sheet) differs markedly from the rodlike a helix. A polypeptide chain, called a P strand, in a P sheet is almost fully extended rather than being tightly coiled as in the a helix. A range of extended structures are sterically allowed (Figure 3.35). 

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