I have been reading the following (open access) journal, In this paper, they have collected data samples from the loop region and categorically classified into TURN, COIL and BRIDGE, 3-10 helix etc. They say that classification is based on the STRIDE program. I couldn't understand how the secondary structure are classified based on the STRIDE program. In particular, what is bridge? How turn and coil are different from each other. Suggest me a reference or anything to understand more about loop structure
Article Neighbor-Dependent Ramachandran Probability Distributions of...
Dear Vigneshwaran Kannan ,
The distinction is rather detailed. The important resource for (known) protein structures “Uniprot” uses basically three secondary structure elements: Turns, Beta strand and Helical.
These three elements are then subdivided according to the so-called DSSP secondary structure code as described originally in:
Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen‐bonded and geometrical features. Biopolymers: Original Research on Biomolecules, 22(12), 2577-2637.
https://rostlab.org/sites/default/files/fileadmin/teaching/SoSe18/pbl/Kabsch%2C%20Sander%20-%201983%20-%20Dictionary%20of%20protein%20secondary%20structure%20Pattern%20recognition%20of%20hydrogen%20bonded%20and%20geometrical%20features.pdf
In short you have hydrogen-bonded beta strands (often called beta-sheets) and residues in isolated ‘couples’ are called (beta) bridges.
Turns are well-described in the above paper as well. Random coil is another chapter where some think it is basically non-existing while others (active in for example circular dichroism) consider it as a ‘true’ unordered structure.
Hope this helps a bit in this pretty complicated and highly specialized issue.
Best regards.
Dear Vigneshwaran Kannan ,
The distinction is rather detailed. The important resource for (known) protein structures “Uniprot” uses basically three secondary structure elements: Turns, Beta strand and Helical.
These three elements are then subdivided according to the so-called DSSP secondary structure code as described originally in:
Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen‐bonded and geometrical features. Biopolymers: Original Research on Biomolecules, 22(12), 2577-2637.
https://rostlab.org/sites/default/files/fileadmin/teaching/SoSe18/pbl/Kabsch%2C%20Sander%20-%201983%20-%20Dictionary%20of%20protein%20secondary%20structure%20Pattern%20recognition%20of%20hydrogen%20bonded%20and%20geometrical%20features.pdf
In short you have hydrogen-bonded beta strands (often called beta-sheets) and residues in isolated ‘couples’ are called (beta) bridges.
Turns are well-described in the above paper as well. Random coil is another chapter where some think it is basically non-existing while others (active in for example circular dichroism) consider it as a ‘true’ unordered structure.
Hope this helps a bit in this pretty complicated and highly specialized issue.
Best regards.
You can access stride over the web: http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py if you want to tra it, or download it for local use.
The method used by stride is described in this paper: http://webclu.bio.wzw.tum.de/stride/stride.pdf and Article STRIDE: a Web server for secondary structure assignment from...
Read these two papers for the exact classifications used by stride
Loops: Connect alpha helices and beta sheets
Turns: Loops made up of 4-5 amino acid residues and internal hydrogen bonds are called turns. Turns are further classified into alpha turns, beta turns, hairpins, beta hairpins. (Mainly based on orientation)
Coil or random coil: As the name suggests, coils are random, unordered, and randomly oriented.
Bridges or Salt Bridges: A salt bridge is a combination of two non-covalent interactions: hydrogen bonding and ionic bonding . (Wikipedia)
3-10 helix: The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier; this repeated i + 3 → i hydrogen bonding defines a 310-helix. (Wikipedia)
For a better understanding of these secondary and supersecondary structures, I would suggest you to go through (apart from the sources suggested by the experts in previous answers) Introduction to Protein Structure by Branden and Tooz or Biochemistry by Lubert Stryer if you have access to these books in your library.
- Badges
- Science topic
- Similar topics
- Computer Science
- Program