Sheet structures antiparallel’ mode

When allylic alcohols were used as a guest molecule instead of the ethers (THF and diethyl ether), the arrangement of the dipeptide molecules was changed to an antiparallel / -sheet-like structure. By crystallization from methanol-methallyl alcohol, we obtained the single crystal of an inclusion compound, which consisted of 2, methanol, and methallyl alcohol. The X-ray structure shows an antiparallel mode... 

Raman spectroscopy of proteins runs parallel to IR spectroscopy. The same vibrational transitions associated with the same normal vibrational modes centred on atom motions within peptide links are observed (Table 4.3 Figure 4.10). The same is true for the Raman spectroscopy of nucleic acids as well. Arguably, Raman spectroscopy of a globular protein of interest gives an even more precise characterisation of vibrational transitions than IR spectroscopy, allowing for the clear discrimination and identification of random coil structure as well as a-helix, parallel jd-sheet and antiparallel jd-sheet secondary structures. 

Fig. 16 Tapping mode AFM image (3 x 3 ixm) for PMLG-g-PAA after incubation for 48 h in water/TFE (8 2 v/v) (pH 4.0) at room temperature. The PMLG-g-PAA formed nanofiber structures with conformational transition from a-helix to antiparallel )3-sheet structure. z-Scale 0-40 nm. [MLG] = 1.1 x lO" M...

Fig. 5. Comparison of ab initio, DFT/BPW91/6-31G -computed IR and VCD spectra over the amide I, II, and III regions for model peptides (of the generic sequence Ac-Alaw-NHCH3). These are designed to reproduce the major structural features of an o -helix (top left, n— 6, in which the center residue is fully H-bonded), a 3i helix (PLP Il-like, top right, n— 4), and an antiparallel /1-sheet (n= 2, 3 strands, central residue fully H-bonded) in planar (bottom left) and twisted (bottom right) conformations. The computations also encompass all the other vibrations in these molecules, but those from the CH3 side chains were shifted by H/D exchange (CH3) to reduce interference with the amide modes.

The main spectroscopic observation that required explanation was the 60-cm splitting in the infrared-active amide 1 (mainly CO s) modes of antiparallel-chain pleated sheet (APPS) polypeptides. Miyazawa (1960a) proposed that such splittings must be a consequence of the interactions between similar oscillators within the repeat unit of the structure, namely, the four peptide groups in the present case. He showed by a perturbation treatment that the frequencies for the four possible coupled modes would depend on the relative phases of the vibrations and the magnitudes of the interactions between peptide groups according to the relation... 

Two structures have been proposed for (Gly) I an antiparallel-chain pleated sheet (APPS) and a similar rippled sheet (APRS) (see Section III,B,1). These structures have different symmetries the APPS, with D2 symmetry, has twofold screw axes parallel to the a axis [C (a)] and the b axis [C (b)], and a twofold rotation axis parallel to the c axis [62(0)] the APRS, with C2h symmetry, has a twofold screw axis parallel to the b axis ( 2(6)], an inversion center, i, and a glide plane parallel to the ac plane, o-Sj. Once these symmetry elements are known, together with the number of atoms in the repeat, it is possible to determine a number of characteristics of the normal modes the symmetry classes, or species, to which they belong, depending on their behavior (character) with respect to the symmetry operations the numbers of normal modes in each symmetry species, both internal and lattice vibrations their IR and Raman activity and their dichroism in the IR. These are given in Table VII for both structures. 

The sheet thus plays an important role in the structure of proteins. In some it is the main secondary structural component (e.g., con-canavalin A and Bence-Jones proteins) in others it is found in conjunction with a-helical segments and in many proteins it occurs as a mixed sheet of parallel and antiparallel strands. To date, normal-mode analy-... 

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