DSSP gives the letter B for a "residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)", according to Wikipedias page for secondary structure (and various other proper sources). Can somebody please explain what this is in some more detail please? If I google it all that comes up is pretty much the same as what wikipedia gives.
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$\begingroup$ kinemage.biochem.duke.edu/teaching/anatax/html/anatax.2b.html $\endgroup$– rg255Commented Feb 24, 2016 at 22:46
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$\begingroup$ @rg255 Thanks for the link. This seems to describe beta sheets (which I am familiar with). A quick cntrl+f of "bridge" doesn't return any results? I will have a proper read in the morning if you think it will help. $\endgroup$– HBeelCommented Feb 24, 2016 at 23:08
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In Kabash and Sander's paper related to DSSP (Biopolymers 1983 vol. 22 (12) pp. 2577-637) the following appears in the abstract:
We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.”
It seems from this that they are using the term bridge to mean one hydrogen bond of the type found in a beta-sheet, ladder as two protein strands joined by many hydrogen bonds, and sheets as beta-sheets — more than two protein strands joined by many hydrogen bonds. The term beta-bridge in the DSSP documentation (http://www.cmbi.ru.nl/dssp.html) is presumably equivalent to a bridge in the paper
In the DSSP files residues that are in ladders or beta-sheets are designated E, and B is used for instances where there is a single hydrogen bond. The former are very common, wheres the latter are quite rare — some proteins have none. I have prepared an image of an example for residues 74 and 79 (side-chains omitted for clarity) in a loop in the protein 1PPR.pdb (a light-harvesting protein). The other loop residues 75-78 are designated as T (turn) in the DSSP file, whereas residues 73 and 78 have no structure designation. Hence the hydrogen bond between Ser-74 and Val-79 is an isolated singleton and designated B.
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$\begingroup$ Thanks for this answer David. I agree with you're reasons and I think you're correct. I appreciate you tackling the literature better than I had and the example! $\endgroup$– HBeelCommented Mar 2, 2016 at 14:27
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1$\begingroup$ You're welcome. The DSSP nomenclature is not straight-forward and some protein chemists are not too enthusiastic about some of the designations of rarer structures. $\endgroup$– DavidCommented Mar 2, 2016 at 14:30