I want to understand how a motif is present or not, can be deduced from a PDB file. Are there any rule of thumb for forming 3D motifs? Like a series of helices and sheets in some direction will lead to a particular 3D motif? Are there any such rules? If so, any resources that you can provide me with?
For example, beta-hairpin. What should be the sequence of amino acids or helix/sheet that would result in the formation of beta-hairpin motif?
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A motif is a pattern that you discover in a structure by analysis. For example, common sequence motifs are short sequence fragments with parts similar to a regular expression. So, if you have a motif like "A*C" this matches to the sequences "AAC" and "ACC" but not to "ACA". You can reverse the process to discover the motif from the sequences.
Similarly with structural motifs in proteins. A beta-hairpin is :
The motif consists of two strands that are adjacent in primary structure, oriented in an antiparallel direction ... and linked by a short loop of two to five amino acids.
So first you have to determine where the strands and loops are, then how the strands are connected into sheets, and finally recognise the hairpins. It is the definition of the motif itself that determines how you discover it.
Some resources that might be helpful are:
- Motivated proteins (Small h-bonded motifs)
- The protein topology graph library (Larger motifs)
- The protein geometry database (Not really motifs, but interesting)
- PDBeMotif (define and search for motifs in the PDB)
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$\begingroup$ How do I derive from PDB where the strands and loops are and how the strands are connected into sheets? $\endgroup$– girl101Jul 22, 2016 at 6:30
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$\begingroup$ @Rishika That's a big topic. There are tools out there to do this, DSSP for example. In addition, the PDB file often has secondary structure information provided by the authors. Or you could even just view it in a structure viewer, which will generally show you the strands and loops. Jmol has a DSSP implemention. It depends what you want to do, exactly. $\endgroup$– gilleainJul 22, 2016 at 8:08