Hydrophobic Core Of Protein, Pdb

Question

[Rishika Sengupta]

How do I know the hydrophobic core of a protein from its PDB structure?

[Pierre Poulain]

Could you be more specific? What do mean by "know"? The residues in the hydrophobic core? The size of the hydrophobic core? What did you read/do so far? Eventually, the PDB is a database and by extension a file format. The end of your question should be "structure" instead of "PDB"...

[Rishika Sengupta]

In the beginning I want to know what residues are lying in the hydrophobic core. Then I want to know which atoms of the above mentioned residues are lying in the core.

[Rishika Sengupta]

I have edited the question

Answer 1

[Chris]

As a starting point: Look for residues with lowest solvent accessibility (use DSSP for that) and high hydrophobicity (-> e.g. Kyte Doolittle scale).

[Keith Callenberg]

I agree DSSP is one good starting point. One could look for a region where the solvent accessibility values are all nearly zero. I imagine this would bring a lot of false positives though -- there are often residues that are not quite in the core but are still somewhat buried.

It's not clear whether OP just needs to evaluate this qualitatively or whether an actual algorithm is needed, but I think if we were to turn this into an unsupervised algorithm, we would need to consider the distance from the other buried residues.

[Rishika Sengupta]

Can you please specify what is the difference between a buried residue and a core residue?

[Keith Callenberg]

Some residues may be buried -- not accessible to solvent -- yet not in the core. Perhaps they could be considered an additional, separate core in this case, but I think the word "core" generally refers to a central continuous region in the protein structure.

I upvoted this question because I think it would be cool to have an app that - given a PDB structure and a solvent accessibility cutoff - could tell you which residues are in the (putative) core. I looked and it doesn't look like this currently exists.

[Rishika Sengupta]

Thanks for the answer. But I think there can be more than one core, as "The definition of a hydrophobic core is a set of residues located within regions of regular secondary structure, whose side chains interact with each other and buried"....Please verify.

[Rishika Sengupta]

Also, it will be really good to know, why do I need to know the solvent accessibility for determining the core?

[Rishika Sengupta]

Also I would really like to thank you for your input :).

Answer 2

[Chris Evelo]

There are a lot of PDB viewers around and many of them allow you to color the hydrophobic aminoacid residues. That would give you a nice impression of where the hydrophobic core is. I am not entirely sure which viewers will allow you to do that again. But I would try [?]Yasara[?] (also see introduction [?] here[?]), [?]Rasmol[?] or [?]Deepview[?],

[boczniak767]

You could try chimera: http://www.cgl.ucsf.edu/chimera/download.html

Answer 3

[Woa]

How about this method which tells that(essentially what Chris mentioned in the previous reply), "The definition of a hydrophobic core is a set of residues located within regions of regular secondary structure, whose side chains interact with each other and buried"

http://www.jsbi.org/pdfs/journal1/GIW92/Oral/GIW92OC04.pdf

For more about buried residues:

http://www.mrc-lmb.cam.ac.uk/tcb/pdf/chc/65_jmb_196_641_87.pdf

[Rishika Sengupta]

I have read the previous paper but could not work out the algorithm.