Protein structure patterns 3 strands

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

Ribbon diagrams. These diagrams are highly schematic and most commonly used to accent a few dramatic aspects of protein structure, such as the a helix (a coiled ribbon), the P strand (a broad arrow), and loops (simple lines), so as to provide simple and clear views of the folding patterns of proteins. 

Three popnlar early methods are dne to Chon and Fasman, Ganuer et al., and Lim." ° The Chon-Fasman method is based on statistical propensities of residues to form an a-helix or a P-strand, combined with a series of rules. Many methods, like Chon-Fasman, are based on statistical analyses of structural databases. The GOR method adopts an information theory approach. Although the theory is a little daunting, this is transparent to the user and the method has a firm statistical foundation that permitted extension to more subtle analyses of a larger structural database." Methods may also be based on the physico-chemical principles underlying protein structure. For example, a-helices often have a distinct pattern of hydrophobic residues, leading to a hydrophobic face that can facilitate the packing of the helix in the protein. A series of such rules forms the basis of the Lim method. ... 

In structural studies, a low concentration of iodine is advisable in order to obtain a structure-dependent modification pattern. In footprinting of proteins on RNA the optimal conditions should permit reaction with all the free phophorothioates (i.e. those not interacting with the protein). Since iodine also reacts strongly with proteins the quantitative strand scission may be limited by the dissociation of the protein-RNA complex. 

Comparisons of protein structures uncovered common patterns of protein architecture, which have been applied in protein structure predictions. Secondary structure elements, such as P turns and a helices, are formed by sequentially contiguous amino acid residues p sheets are formed by extended strands, which are often distant in sequence. Although these secondary structure elements are stabilized primarily by hydrogen-bond interactions between amide units of the peptide backbone, they cor-... 

The folding patterns of hexapeptide fragments have been determined from the atomic coordinates of the protein structures using the standard procedure of Kabsch and Sander [66]. Every residue is given a secondary structure descriptor. To reduce complexity, residues were classified as helical h (G, H or I in Kabsch-Sander nomenclature), extended strand s (E), P turn t (T) or remained unassigned n. With these four structural classes there are still 4096 possible folding patterns for hexapep-... 

Fig. 7.8. Ribbon drawing showing the arrangement of secondary structures into a three-dimensional pattern in domain 1 of lactate dehydrogenase. The individual polyjjeptide strands in the six-stranded P-sheet are shown with arrows. Different strands are connected by helices and by nonrepetitive structures (mrns, coils and loops), shown in blue. This domain is the nucleotide binding fold. NAD is bound to a site created by the helices (upper left of figure.) (Modified from Richardson JS. Adv Protein Chem. The anatomy and taxonomy of protein structure 1981 34 167).

Fig. 24. Biomesogenic backbone geometries providing structural prerequisites for dynamic order-disorder patterns (left to right and top to bottom) phospholipid and helical protein, nucleic acid strand and protein helix, protein-nucleic acid backbone interplays, presumably engaged in the induction of in terferon. ...

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