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A beta hairpin is a common supersecondary motif composed of two anti-parallel beta strands connected by a loop. The structure resembles a hairpin and is often found in globular proteins. The loop between the beta strands can range anywhere from 2 to 16 residues. However, most loops contain less than seven residues. [2]
The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. Cruciform DNA
An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined ...
For example, the β-hairpin motif consists of two adjacent antiparallel β-strands joined by a small loop. It is present in most antiparallel β structures both as an isolated ribbon and as part of more complex β-sheets. Another common super-secondary structure is the β-α-β motif, which is frequently used to connect two parallel β-strands.
Over very long evolutionary timescales, very few residues show detectable amino acid sequence conservation, however secondary structural elements and tertiary structural motifs are highly conserved. Some protein dynamics [8] and conformational changes of the protein structure may also be conserved, as is seen in the serpin superfamily. [9]
To do this it marks a local motif alignment with flags to indicate which residues simultaneously satisfy more stringent criteria: 1) Local structure overlap 2) regular secondary structure 3) 3D-superposition 4) same ordering in primary sequence.
Secondary and tertiary structure of the coiled-coil motif. The heptad repeat often consists of specific amino acids, seen in the figure. Knobs into packing is also shown. [27] The general problem of deciding on the folded structure of a protein when given the amino acid sequence (the so-called protein folding problem) has only been solved ...