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 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:

$E = 0.084 \left\{ \frac{1}{r_{ON}} + \frac{1}{r_{CH}} - \frac{1}{r_{OH}} - \frac{1}{r_{CN}} \right\} \cdot 332 \, \mathrm{kcal/mol}$

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 $\overrightarrow{C_i^\alpha C_{i+2}^\alpha}$ and $\overrightarrow{C_{i-2}^\alpha C_i^\alpha}$ is less than 70°), and a blank (or space) is used if no other rule applies, referring to loops.^[2] 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).

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.^[3]

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. "DSSP manual"
3. 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.

See also

• STRIDE (protein) an alternative algorithm
• Chris Sander (Scientist)

External links

• DSSP Analysis tool
• Continuous DSSP tool