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I'm reading the papers linked below and all three of them mention a 20% cut-off for buried/exposed residues, by calculating a relative solvent accessibility (RSA) value.

I understand how the RSA is calculated, by dividing the calculated solvent accessibility against its total solvent accessibility values from paper 4 table 2.

RSA = calculated/total

e.g. if arginine is calculated to have a solvent accessibility of 55.43 and its total solvent accessibility is 241 then the RSA = 55.43/241 = 23%, so this arginine is considered exposed (see statement 1 below).

What leaves me confused is the definition or lack of the 20% method for defining an exposed or buried residue.

I am assuming it means one of the following:

  1. If an amino acids RSA is below 20% it is buried and above 20% it is exposed. So for an amino acid with an RSA of 21% is considered exposed, this value seems a little low for me. I think statement 2 would make for sense.

  2. If an amino acids RSA is below 20% it is buried and above 80% it is exposed.

Which statement if any is correct?

Paper 1 - see methods section first paragraph

Paper 2 - see figure 5 and table 3

Paper 3 - see abstract and dataset

Paper 4 - see table 2 for total values

harpalss
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2 Answers2

5

Its 1. Below cutoff, buried, above cutoff accessible.

Paper 1: "A cutoff of 20% was used to define the two states, buried or exposed. With this definition, the dataset was, roughly, evenly split between the two states."

Only two states are possible: solvent accessible and buried.

Paper 2: "A given residue is defined as exposed (e) if its RSA is larger than the cutoff value, and otherwise it is defined as buried (b)."

Abstract for Paper 3: a cutoff of 20% for two-state definition of solvent accessibility.

If it were def #2 it would be a three state definition.

Paper 4: "On average, 15% of residues in small proteins and 32% in larger ones may be classed as “buried residues”, having less than 5% of their surface accessible to the solvent..."

This paper, by the dean of structural analysis Cyrus Chothia, uses a 5% cutoff, not 20%...

The abstract goes on to say... "The accessibilities of most other residues are evenly distributed in the range 5 to 50%."

This passage hints that SA doesn't even go up to 80%. Just considering that you often won't get more than say 60% with this calculation. I'm just guessing; but the thought being that unless you are at a terminus of the protein, which is often disordered and doesn't show up in a crystal structure, you will have two adjoining amino acids for each residue - just the solvent accesible area taken up by the contact with neighbors could easily be 20% of total.

shigeta
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  • y welcome! papers are like a wall of words. This belies the fact that the methods are often the simplest method you can think of. – shigeta Feb 20 '13 at 17:46
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Are you sure that the RSA formula is right? I have found a different description：Relative solvent accessibility classes are usually derived from the DSSP program by normalizing it at the maximum value of exposed surface area obtainable for each residue.Different arbitrary threshold values of solvent accessibility are chosen to define binary categories (buried and exposed) or ternary categories (buried, partially exposed, or exposed).

Pollastri, G., Baldi, P., Fariselli, P., & Casadio, R. (2002). Prediction of coordination number and relative solvent accessibility in proteins. Proteins: Structure, Function, and Bioinformatics, 47(2), 142-153.

Anders Jing
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