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The most common secondary structures are alpha helices and beta sheets. Other helices, such as the 3 10 helix and π helix , are calculated to have energetically favorable hydrogen-bonding patterns but are rarely observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix.
The pitch of the alpha-helix (the vertical distance between consecutive turns of the helix) is 5.4 Å (0.54 nm), which is the product of 1.5 and 3.6. The most important thing is that the N-H group of one amino acid forms a hydrogen bond with the C=O group of the amino acid four residues earlier; this repeated i + 4 → i hydrogen bonding is the ...
All-β proteins are a class of structural domains in which the secondary structure is composed entirely of β-sheets, with the possible exception of a few isolated α-helices on the periphery. Common examples include the SH3 domain , the beta-propeller domain , the immunoglobulin fold and B3 DNA binding domain .
All beta-barrel transmembrane proteins have simplest up-and-down topology, which may reflect their common evolutionary origin and similar folding mechanism. [7] In addition to the protein domains, there are unusual transmembrane elements formed by peptides. A typical example is gramicidin A, a peptide that forms a dimeric transmembrane β-helix ...
A beta-alpha-beta motif is composed of two beta strands joined by an alpha helix through connecting loops. The beta strands are parallel, and the helix is also almost parallel to the strands. This structure can be seen in almost all proteins with parallel strands. The loops connecting the beta strands and alpha helix can vary in length and ...
Two main types of secondary structure, the α-helix and the β-strand or β-sheets, were suggested in 1951 by Linus Pauling. [5] These secondary structures are defined by patterns of hydrogen bonds between the main-chain peptide groups.
Unlike the alpha helix and beta sheet, the alpha sheet configuration does not require all component amino acid residues to lie within a single region of dihedral angles; instead, the alpha sheet contains residues of alternating dihedrals in the traditional right-handed (α R) and left-handed (α L) helical regions of Ramachandran space.
Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation .