The DSSP algorithm is the standard method for assigning
secondary structure to the
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...
s of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm,
where it is the name of the
Pascal program that implements the algorithm ''Define Secondary Structure of Proteins''.
Algorithm
DSSP begins by identifying the intra-backbone
hydrogen bonds of the protein using a purely electrostatic definition, assuming partial charges of -0.42 ''e'' and +0.20 ''e'' to the carbonyl oxygen and amide hydrogen respectively, their opposites assigned to the carbonyl carbon and amide nitrogen. A hydrogen bond is identified if ''E'' in the following equation is less than -0.5 kcal/mol:
:
where the
terms indicate the distance between atoms A and B, taken from the carbon (C) and oxygen (O) atoms of the C=O group and the nitrogen (N) and hydrogen (H) atoms of the N-H group.
Based on this, eight types of secondary structure are assigned. The
310 helix,
α helix and
π helix have symbols G, H and I and are recognized by having a repetitive sequence of hydrogen bonds in which the residues are three, four, or five residues apart respectively. Two types of
beta sheet structures exist; a
beta bridge
Beta (, ; uppercase , lowercase , or cursive Greek, cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents th ...
has symbol B while longer sets of hydrogen bonds and
beta bulge A beta bulge can be described as a localized disruption of the regular hydrogen bonding of beta sheet by inserting extra residues into one or both hydrogen bonded β-strands.
Types
β-bulges can be grouped according to their length of the disruptio ...
s have symbol E. T is used for turns, featuring hydrogen bonds typical of helices, S is used for regions of high curvature (where the angle between
and
is at least 70°), and a blank (or space) is used if no other rule applies, referring to loops.
[DSSP manual]
These eight types are usually grouped into three larger classes: helix (G, H and I), strand (E and B) and loop (S, T, and C, where C sometimes is represented also as blank space).
π helices
In the original DSSP algorithm, residues were preferentially assigned to α helices, rather than
π helices. In 2011, it was shown that DSSP failed to annotate many "cryptic" π helices, which are commonly flanked by α helices.
In 2012, DSSP was rewritten so that the assignment of π helices was given preference over α helices, resulting in better detection of π helices.
[DSSP manual]
Versions of DSSP from 2.1.0 onwards therefore produce slightly different output from older versions.
Variants
In 2002, a continuous DSSP assignment was developed by introducing multiple hydrogen bond thresholds, where the new assignment was found to correlate with protein motion.
See also
*
STRIDE (algorithm) an alternative algorithm
*
Chris Sander (scientist)
Chris Sander is a computational biologist based at the Dana-Farber Cancer Center and Harvard Medical School. Previously he was chair of the Computational Biology Programme at the Memorial Sloan–Kettering Cancer Center in New York City. In 2015, ...
References
External links
DSSP Analysis toolContinuous DSSP tool
{{Protein secondary structure
Protein structure