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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 resulting structure is a key building block of many RNA secondary structures. Cruciform DNA Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. [3]
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.
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).
Three-dimensional structure of a protein. Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds ...
Secondary structure [4] [5] α-Helices Cylindrical spiral ribbons, with ribbon plane approximately following plane of peptides. β-Strands Arrows with thickness, about one-quarter as thick as they are wide, showing direction and twist of the strand from amino to carboxy end. β-sheets are seen as unified because neighboring strands twist in unison.
The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblance to the jelly or Swiss roll cake. [2] The fold is an elaboration on the Greek key motif and is sometimes considered a form of beta barrel. It is very common in viral proteins, particularly viral capsid proteins.
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.