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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 ...
The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm, [2] where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.
The secondary structure of a β-sheet can be described roughly by giving the number of strands, their topology, and whether their hydrogen bonds are parallel or antiparallel. β-sheets can be open , meaning that they have two edge strands (as in the flavodoxin fold or the immunoglobulin fold ) or they can be closed β-barrels (such as the TIM ...
The alpha helix is also commonly called a: Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure); 3.6 13-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen)
Carbon atoms grey, oxygen atoms red and nitrogen atoms blue. The defining hydrogen bond is shown as a magenta line. The hydrogen bond criterion for beta turns, applied to polypeptides whose amino acids are linked by trans peptide bonds, gives rise to just four categories, as shown by Venkatachalam in 1968. They are called types I, II, I’ and ...
A hairpin is a special case of a turn, in which the direction of the protein backbone reverses and the flanking secondary structure elements interact. For example, a beta hairpin connects two hydrogen-bonded , antiparallel β-strands (a rather confusing name, since a β-hairpin may contain many types of turns – α, β, γ, etc.).
A protein is a polyamide. Secondary structure: regularly repeating local structures stabilized by hydrogen bonds. The most common examples are the α-helix, β-sheet and turns. Because secondary structures are local, many regions of distinct secondary structure can be present in the same protein molecule.
[1] [2] [3] The hydrogen bonding pattern in an alpha sheet is similar to that of a beta sheet, but the orientation of the carbonyl and amino groups in the peptide bond units is distinctive; in a single strand, all the carbonyl groups are oriented in the same direction on one side of the pleat, and all the amino groups are oriented in the same ...