DSSP (algorithm)
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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,cite-ref-kabsch1983-2-0[2] where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.
Contents
• Variants
• See also
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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:
E = 0.084 { 1 r O N + 1 r C H − − 1 r O H − − 1 r C N } ⋅ ⋅ 332 k c a l / m o l {\displaystyle E=0.084\left\{{\frac {1}{r_{ON}}}+{\frac {1}{r_{CH}}}-{\frac {1}{r_{OH}}}-{\frac {1}{r_{CN}}}\right\}\cdot 332\,\mathrm {kcal/mol} }
where the r A B {\displaystyle r_{AB}} 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 C i α α C i + 2 α α → → {\displaystyle {\overrightarrow {C_{i}^{\alpha }C_{i+2}^{\alpha }}}} and C i − − 2 α α C i α α → → {\displaystyle {\overrightarrow {C_{i-2}^{\alpha }C_{i}^{\alpha }}}} 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.cite-ref-dsspmanual-3-0[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.cite-ref-pmid20888342-4-0[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.cite-ref-dsspmanual-3-1[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.cite-ref-andersen2002-5-0[5]
See also
References
cite-note-11. "DSSP". Archived from the original on 2022-09-20. Retrieved 2018-04-30.
cite-note-dsspmanual-33. ↑ "DSSP manual Archived 2015-05-22 at the Wayback Machine"
cite-note-pmid20888342-44. ↑ citerefcooleyarpkarplus2010Cooley 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.
External links