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The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone N−H group hydrogen ...
A relatively polar amphiphilic α-helix can adopt a transmembrane orientation in the translocon (although it would be at the membrane surface or unfolded in vitro), because its polar residues can face the central water-filled channel of the translocon. Such mechanism is necessary for incorporation of polar α-helices into structures of ...
Proline and glycine are sometimes known as "helix breakers" because they disrupt the regularity of the α helical backbone conformation; however, both have unusual conformational abilities and are commonly found in turns. Amino acids that prefer to adopt helical conformations in proteins include methionine, alanine, leucine, glutamate and ...
The 21 proteinogenic α-amino acids found in eukaryotes, grouped according to their side chains' pK a values and charges carried at physiological pH (7.4) 2-, alpha-, or α-amino acids [21] have the generic formula H 2 NCHRCOOH in most cases, [b] where R is an organic substituent known as a "side chain". [22]
A transmembrane domain (TMD) is a membrane-spanning protein domain.TMDs may consist of one or several alpha-helices or a transmembrane beta barrel.Because the interior of the lipid bilayer is hydrophobic, the amino acid residues in TMDs are often hydrophobic, although proteins such as membrane pumps and ion channels can contain polar residues.
The plot reveals whether hydrophobic amino acids are concentrated on one side of the helix, usually with polar or hydrophilic amino acids on the other. This arrangement is common in alpha helices within globular proteins, where one face of the helix is oriented toward the hydrophobic core and one face is oriented toward the solvent-exposed surface.
A coiled coil is a structural motif in proteins in which 2–7 [1] alpha-helices are coiled together like the strands of a rope. (Dimers and trimers are the most common types.) They have been found in roughly 5-10% of proteins and have a variety of functions. [2] They are one of the most widespread motifs found in protein-protein interactions.
These amino acids are spaced out in each region's polypeptide sequence in such a way that when the sequence is coiled in a 3D alpha-helix, the leucine residues line up on the same side of the helix. This region of the alpha-helix - containing the leucines which line up - is called a ZIP domain, and leucines from each ZIP domain can weakly ...