Polar sheet structures

This is an extracellular deposition of an insoluble protein, which has adopted a (3-sheet structure due to an unknown event that induced misfolding of unstable proteins. The name amyloid has been given according to the amyloid staining properties, which are similar to carbohydrate deposits, e.g., amyloid can be identified with Congo red and seen under polarized light (birefringence test). 

The availability of the purified transporter in large quantity has enabled investigation of its secondary structure by biophysical techniques. Comparison of the circular dichroism (CD) spectrum of the transporter in lipid vesicles with the CD spectra of water-soluble proteins of known structure indicated the presence of approximately 82% a-helix, 10% ) -turns and 8% other random coil structure [97]. No / -sheet structure was detected either in this study or in a study of the protein by the same group using polarized Fourier transform infrared (FTIR) spectroscopy [98]. In our laboratory FTIR spectroscopy of the transporter has similarly revealed that... 

Porphyrin and nonporphyrin metals associated with asphaltenes have not been easy to identify in terms of molecular structure. This is partly due to the fact that the characteristics (i.e., spectra) of all possible model nonporphyrin compounds have not been studied. Nonporphyrin metals are probably small polar molecules that precipitate as asphaltenes (Filby, 1975) or complex at defect sites in large aromatic sheet structures of the type shown in Fig. 10. Porphyrins with increased aromaticity and systems with low aromaticity due to discontinued ring conjugation are both characterized as nonporphyrin species. These compounds do not have the characteristic visible absorption spectra and hence are not readily identified. It is also possible that some of the porphyrin in the residuum may not be extracted and identified due to intermolecular association with the asphaltene-generating molecules. 

Fig. 3.17. Amphiphilic secondary structures. By specifying the locations of polar (light gray) and nonpolar (dark gray) residues through simple binary patterns, amphiphilic helical or pi-sheet structures can be designed [154].

Two methods have been used to determine the secondary structure and orientation of membrane proteins in supported bilayers polarized ATR-FTIR spectroscopy and oriented CD spectroscopy. SFVS may also be applied to study peptide and protein structures in supported bilayers. Polarized ATR-FTIR spectroscopy is sensitive enough that high-quality spectra can be obtained from a single bilayer. Beta-sheet structures are readily distinguished from a-helical and random stmctures, and the orientations of a-helices are determined from the linear dichroism of the peptide amide 1 bands (20). Multiple stacks of supported bilayers have to be used to gain enough sensitivity to determine the stmcture and orientation of a-helices in lipid bilayers by oriented CD spectroscopy (60, 93). 

The dominance of sheet structures among the actinyl orthophosphates and orthoarsenates is a consequence of the polarized distribution of bond strengths in actinyl polyhedra, and their resulting polymerization through only their equatorial ligands. However, fiamework structures can form by linkages through non-actinyl polyhedra in the third dimension, as in the structure of [(U02)3(P04)0(0H)(H20)2](H20) (Fig. 41). 

Figure 20.10. Amphiphilic ionic self-complementary peptides. This class of peptides has 16 amino acids, c. 5 nm in size, with an alternating polar and non-polar pattern. They form stable (3-strand and 3-sheet structures thus, the side chains partition into two sides, one polar and the other non-polar. They undergo self-assembly to form nanofibers with the non-polar residues inside positively and negatively charged residues form complementary ionic interactions, like a checkerboard. These nanofibers form interwoven matrices that further form a scaffold hydrogel with a very high water content ( 99.5%). The simplest peptide scaffold may form compartments to separate molecules into localized places where they can not only have high concentration, but also form a molecular gradient, one of the key prerequisites for prebiotic molecular evolution.

All O atoms involved in H bonding. H bonding to form zig-zag spirals parallel to b-axis. Further H bonding across ends of molecules to give sandwich sheet structure with non-polar exteriors. Na and HjO inside hydrophilic bilayers. Van der Waals contact of hydro-phobic bilayers. Counterion steroid-OH bonding... 

Physicochemical studies of the synthetic peptide spanning residues 106-126 of human PrP led to similar conclusions. PrP106-126 consists of an N-terminal polar head (KTNMKHM-) followed by a long hydrophobic tail (-AGAAAAGAWGGLG) and its structural features are markedly influenced by solvent composition, ionic strength, and pH. CD spectroscopy showed that the peptide adopts a random coil conformation in deionized water, a combination of random coil and p sheet in phosphate buffer pH 7.0, a predominantly P-sheet structure in phosphate buffer pH 5.0, and an a-helical structure in trifluoroethanol or in the presence of micelles formed by a 5% SDS solution. Notably, the P-sheet conformation is extremely stable, because it is not affected by trifluoroethanol if the peptide was previously suspended in phosphate buffer pH 5.0 (De Gioia et al., 1994). 

Hg and Zn have similar fractional patterns. Antimony is strongly concentrated in the asphaltene,s and As shows the lowest enrichment of the elements studied. The asphaltenes and resins exist in the oil in colloidal form, and the crude oil system may be regarded as a transition from the polar aromatic micelle of the asphaltenes to the less polar resins to the nonpolar hydrocarbons of the bulk crude oil. The trace elements concentrated in the asphaltenes may be present in small highly polar molecules, which would precipitate with the asphaltenes or might complex in the asphaltene sheet structure at sites bounded by hetero atoms such as 0, N, or S. Gel permeation chromatography was used to investigate this. 

In both a-helical and P sheet structures, the polar peptide bonds of the main chain are involved in internal hydrogen bonding, thereby eliminating potential hydrogen bond formation with water. Overall the secondary structures are less polar than the corresponding linear amino acid sequences. 

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