Software: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.
| Original author(s) | Wolfgang Kabsch, Chris Sander |
|---|---|
| Developer(s) | Maarten Hekkelman[2] |
| Initial release | 1983 |
| Stable release | 4.0.5
/ 3 May 2022 |
| Repository | github |
| Written in | C++ |
| License | Boost License |
| Website | swift |
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:
- [math]\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} }[/math]
where the [math]\displaystyle{ r_{AB} }[/math] 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 [math]\displaystyle{ \overrightarrow{C_i^\alpha C_{i+2}^\alpha} }[/math] and [math]\displaystyle{ \overrightarrow{C_{i-2}^\alpha C_i^\alpha} }[/math] 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
- STRIDE (protein) an alternative algorithm
- Chris Sander (scientist)
References
- ↑ "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers 22 (12): 2577–637. 1983. doi:10.1002/bip.360221211. PMID 6667333.
- ↑ "DSSP". https://swift.cmbi.umcn.nl/gv/dssp/.
- ↑ 3.0 3.1 "DSSP manual"
- ↑ "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. 2010. doi:10.1016/j.jmb.2010.09.034. PMID 20888342.
- ↑ "Continuum secondary structure captures protein flexibility". Structure 10 (2): 175–184. 2002. doi:10.1016/S0969-2126(02)00700-1. PMID 11839303.
External links
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