Antiparallel-chain structure

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. 

P, Parallel-chain structure A, antiparallel-chain structure. 

Figure 5-8. Antiparallel-chain structure of polyglycine II. (From [123])...

The antiparallel-chain structure (Figure 5-8) has only a screw axis of symmetry, and its modes are distributed as follows A-62 modes, Raman, IR B-61 modes, Raman, IR. As for PGI, extensive IR spectra on isotopic derivatives (NH, CD2 ND, CH2 and ND, CD2) were available [97] as well as Raman spectra on the N-deuterated molecule [98]. The PGI force field [96] was used as a starting point, and refinement required small adjustments in 10 of 70 intramolecular force constants [123]. Amide mode frequencies are given in Table 5-12 the overall rms frequency error is 5.4 cm" b... 

A -ray diffraction studies have confirmed the antiparallel chain structure for a-chitin. The structure contains two types of amide groups which differ in... 

The p sheets have the usual twist, and when two such twisted p sheets are packed together, they form a barrel-like structure (Figure 5.1). Antiparallel P structures, therefore, in general have a core of hydrophobic side chains inside the barrel provided by residues in the P strands. The surface is formed by residues from the loop regions and from the strands. The aim of this chapter is to examine a number of antiparallel p structures and demonstrate how these rather complex structures can be separated into smaller comprehensible motifs. 

In addition to the antiparallel p-structures, there is a novel fold called the P helix. In the p-helix structures the polypeptide chain is folded into a wide helix with two or three p strands for each turn. The p strands align to form either two or three parallel p sheets with a core between the sheets completely filled with side chains. 

Figure 26.6 (a) The /3-pleated sheet secondary structure of proteins is stabilized by hydrogen bonds between parallel or antiparallel chains, (b) The structure of concanavalin A, a protein with extensive regions of antiparallel / sheets, shown as flat ribbons. 

Extrapolation of the molecular structure of an a-maltohexaose duplex com-plexed with triiodide in single crystals leads to a left-handed, 8-fold, antiparallel double-helix for amylose.90 The pitch of this idealized helix is 18.6 A, so h is only 2.33 A. Although this model is no contender to the fiber data, in terms of biosynthesis, it is doubtful that the native amylose helix favors antiparallel chains. 

Fig. 2.30 Comparison of antiparallel hairpin structures in / -peptides 120-122. (A) / -Pep-tides 120, 121 with a 12-membered R/S dini-pecotic (Nip or/ -HPro) turn segment (gray color). Summary of backbone-backbone and side-chain-side-chain NOEs collected in CD2CI2 and X-ray crystal structure of 121 (stereo-view) [154, 193], The intramolecular H-bond N" 0 distances are shown. The angles (N-H -O) are 170.8° (inner H-bond) and 1 72.3 ° (outer H-bond). (B) jS-Peptide 122 with...

Finally, a highly complex structure is created when /ra s-Cd(4-ampy)2 (4-ampy = 4-aminopyri-dine) and Cd(4-ampy)(ame) Ag(CN)2 units (ame = 2-aminoethanol) are linked by bridging //- Ag(CN)2 groups to form a 2-D network with rhombus meshes and almost linear chains. These antiparallel chains in pairs embrace the nets.221... 

Fig. 2. The differences that might be observed in the fiber diffraction patterns from oriented samples of antiparallel /1-structures depending on whether the chains are aligned along (A, B) or perpendicular to (C, D) the fiber axis. Color coding on (A, B) as in Fig. 1.

Fig. 22. An example of a long two-stranded ribbon of antiparallel jS structure, from lactate dehydrogenase (residues 263-294). Side chains are not shown hydrogen bonds are dotted. As is typical of isolated two-stranded ribbons, the chains show a very strong twist (180° in about five residues).

The remaining three antiparallel /3 structures form a miscellaneous category (see Fig. 84). Lactate dehydrogenase d2 and gene 5 protein each has several two-stranded antiparallel j8 ribbons, but they do not coalesce into any readily described overall pattern. The N-terminal domain of tomato bushy stunt virus protein has a unique /3 structure in which equivalent pieces of chain from three different subunits wrap around a 3-fold axis to form what has been called a /3 annulus (Harrison et ah, 1978). Each of the three chains contributes a short strand segment to each of three three-stranded, interlocking /3 sheets. This domain provides one of the subunit contacts that hold the virus... 

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... 

A molecular structural property wherein a rotation of 180° leads to the same superimposable structure. Because proteins are made up of L-amino acid residues, neither a single subunit nor a multisubunit protein can possess a plane or point of symmetry. However, proteins do exhibit dyad symmetry. This structural property allows many DNA-binding proteins to make equivalent contacts to the two antiparallel chains of the nucleic acid. 

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