Parallel and antiparallel chains

As the above results show, the gross features of the cellulose I crystal structure predicted by various methods do not differ appreciably, but the accompanying deviations in the R -factors are significant. When these predictions are used to assess, for example, whether the cellulose I crystal structure is based on parallel- or antmarallel-chains, the range in the R"-factors seen for the parallel models (cf. Table II) is comparable to that between the two different polarity models. As shown in Fig. 5, the most probable parallel- and antiparallel-chain structures of cellulose I, refined by minimizing the function O, differ in R -factors by approximately the same extent as the three predictions for the parallel model shown in Fig. 4 and Table II. 

Finally, the question of the ability of the modeling methods to predict the crystal lattice (i.e., the unit cell) from the conformation of the chain should be addressed, despite the expected computational difficulties. Based on previous work, in which the prediction of the unit cells of all four cellulose polymorphs in both parallel and antiparallel chain packing polarities was... 

The defects in the model could not be overcome with the P212 121 space group and it was necessary to consider the lower symmetry, P2i. Refinement was attempted for both parallel and antiparallel chain models. At this point it was found that the data was not sufficiently sensitive to allow simultaneous refinement of more than six variables, and it was necessary first to refine the 1, 2, S, K, and B, and then consider the other variables. The best parallel chain model obtained had R" = 0.25, which could easily be rejected in favor of an antiparallel model at R"=0.16. The 1, 2, and S parameters refined for the antiparallel P2j model were not significantly different from those for the P2 j2 j2 j model. 

This paper is a review of x-ray diffraction work in the authors laboratory to refine the structures of cellulose I and II, and a- and B-chitin, concentrating on the methods used to select between alternate models. Cellulose I is shown to consist of an array of parallel chains, and this conclusion is supported by a separate refinement based on electron diffraction data. In the case of cellulose II, both parallel and antiparallel chain... 

The possibilities of the double helical structures of xanthan were re-examined thoroughly. Among the several possibilities, only parallel and antiparallel 5 double helices could be built and packed into a unit cell. The conformation of single chains in the parallel and antiparallel chains are very similar to each other. These double helical structures are compatible with several properties of xanthan in solution. 

Atalla and Van der Hart (11, 12) concluded, based on their Raman and NMR spectra, that the molecules in cellulose I and II have different conformations. Based on x-ray analyses, Sarko et al. (13i H) and Blackwell et al. (15, 16) both concluded that crystal structures of cellulose I and II were based on parallel and antiparallel packing, respectively, of chains that have similar backbone conformations. Sarko (17) concluded that the allomorphs in the I and II families were based on parallel and antiparallel chains, respectively. The irreversibility may arise from the increase in entropy when parallel packing is converted to antiparallel packing. 

By analogy with the IR spectra, the 1- C NMR spectra showed that there were common differences based on the cellulose families at signals related to the chain conformation. The results were given a more reasonable interpretation through our hypothesis than the proposal of parallel and antiparallel chain systems. 

The vacuum uv CD has been reported for films of protected homooligomers, Boc-(LLeu) -OMe, where n = 2-7. The hexamer and heptamer take up a jS conformation in which both parallel and antiparallel chains are present (Kelly et aL, 1977). 

Cellulose III. Cellulose III results from treatment of cellulose with Hquid ammonia (ammonia mercerization) or amines. Cellulose III can be made from either Cellulose I or II. When treated with water. Cellulose III can revert to its parent stmcture. Some cellulose III preparations are much more stable than other preparations. The intensities on diffraction patterns from Cellulose III differ slightly depending on whether the Cellulose III was made from Cellulose I or II, and thus these allomorphs are called IIIj or IHjj- Workers studying III concluded, based partiy on the results of I and II, that the packings of IIIj and IIIjj are parallel and antiparallel, respectively (67). IIIjj also is thought to have hydrogen bonds between the corner and center chains. 

Two antiparallel helices, related by space group symmetry, are packed in an orthorhombic unit cell (Fig. 39b). There is substantial interdigitation between the helices so that side chains and main chains are linked by hydrogen bonds, such as 0-4E-0-4D (2,73 A) and 0-4D-0-3F (2.84 A) involving parallel and antiparallel strands, respectively. Plausible sites for sodium ions are near the... 

Fig. 2.27 The two types of extended /1-peptide strands with conformation requirements around the C(a)-C(/1) bonds. (A) Parallel and antiparallel polar sheets with antiperiplanar conformations around the C(a)-C fl) bond are promoted by unlike-fi -ami-no acids with alkyl side-chains. Antiperiplanar side-chains at C(a) and C(/3) occupy positions approximately perpendicular to the amide planes. (B) Extended strands formed by alternating +)-sc and (-)-sc conformations...

Fig. 1. Cross-/] structure of amyloid fibrils. (A) Cartoon representation of a cross-/] X-ray diffraction pattern. The defining features are a meridional reflection at 4.7 A and an equatorial reflection on the order of 10 A. The 4.7-A reflection is generally much brighter and sharper than the reflection at 10 A. (B) The cross-/] core structure of amyloid fibrils. Parallel /(-sheets are depicted, but the structure could equivalendy be composed of antiparallel /(-sheets or a mix of parallel and antiparallel. The 4.7-A spacing of /(-strands within each /(-sheet is parallel to the long fibril axis. The depicted 10-A sheet-to-sheet spacing actually ranges from about 5 to 14 A (Fandrich and Dobson, 2002), depending on the size and packing of amino acid side chains. Amyloid fibrils have diameters on the order of 100 A.

The question of parallel vs. antiparallel chain packing in cellulose I has been a controversial one practically since the first cellulose structure was proposed. A consensus appears to be forming, however, based on both diffraction analysis and other experimental evidence, that one of two possible... 

Theoretical calculations indicate that the CD of parallel and antiparallel (3-sheets are quite similar. This conclusion is supported by the CD spectrum of pelC,[1011021 a protein that has a parallel (3-helix motif, 1031 and therefore is more than 30% parallel (3-sheet with no antiparallel (3-sheet. Moreover, the parallel (3-sheet has a rather small degree of twist. The band positions and relative amplitudes in the CD spectrum of this protein resemble those for poly(Lys) in the (3-sheet form, which is an antiparallel sheet that is expected to be only slightly twisted because of the linear side chains. 

Correct answer = C. p-Bends often contain pro line, which provides a kink. The a-helix differs from the p-sheet in that it always involves the coiling of a single polypeptide chain. The P-sheet occurs in both parallel and antiparallel forms. Motifs are elements of tertiary structure. The a-helix is stabilized primarily by hydrogen bonds between the -C=0 and -NH- groups of peptide bonds. 

What we have shown in this brief review is that a combination of denaturation experiments with circular dichroism, air oxidation, and redox equilibrium experiments can lead to an understanding of the specificity of coiled-coil formation (hetero- versus homodimer formation or parallel versus antiparallel chain orientation). 

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