DSSP (hydrogen bond estimation algorithm)

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,[1] where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.


DSSP
Original author(s) Wolfgang Kabsch, Chris Sander
Developer(s) Maarten Hekkelman[2]
Initial release 1983
Stable release
3.01 / 6 April 2018 (2018-04-06)
Repository github.com/cmbi/xssp
Written in C++
License Boost License
Website swift.cmbi.umcn.nl/gv/dssp/

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 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°), and 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

References

  1. ↑ Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers. 22 (12): 2577–637. doi:10.1002/bip.360221211. PMID 6667333.
  2. ↑ https://swift.cmbi.umcn.nl/gv/dssp/
  3. 1 2 "DSSP manual"
  4. ↑ 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. doi:10.1016/j.jmb.2010.09.034. PMC 2981643. PMID 20888342.
  5. ↑ Andersen CA, Palmer AG, Brunak S, Rost B (2002). "Continuum secondary structure captures protein flexibility". Structure. 10 (2): 175–184. doi:10.1016/S0969-2126(02)00700-1. PMID 11839303.
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