DSSP (algorithm) explained

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.

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, nine 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 has symbol B while longer sets of hydrogen bonds and beta bulges 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°). As of DSSP version 4, PPII helices are also detected based on a combination of backbone torsion angles and the absence of hydrogen bonds compatible with other types. PPII helices have symbol P. A blank (or space) is used if no other rule applies, referring to loops.^[3] 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.^[4] 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.^[3] 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.^[5]

See also

• STRIDE (algorithm) an alternative algorithm
• Chris Sander (scientist)

External links

• DSSP Analysis tool
• Continuous DSSP tool

Notes and References

1. Web site: DSSP.
2. Kabsch W, Sander C . Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features . Biopolymers . 22 . 12 . 2577–637 . 1983 . 6667333 . 10.1002/bip.360221211. 29185760 .
3. "DSSP manual "
4. 10.1016/j.jmb.2010.09.034 . Cooley RB, Arp DJ, Karplus PA . 2010 . Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices enhancing protein functionality. J Mol Biol . 404 . 2 . 232–246 . 20888342 . 2981643.
5. Andersen CA, Palmer AG, Brunak S, Rost B . Continuum secondary structure captures protein flexibility . Structure . 10 . 2 . 175–184 . 2002 . 11839303 . 10.1016/S0969-2126(02)00700-1. free .