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The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA from a solved (and generally static) structure.

Chemical probes like diazirine and hydroxyl radicals show some bias regarding where they tend to bind. I'm realizing while I'm writing this question that NMR is a perfectly valid method to determine a solution based structure and then calculate the SASA. Similar strategies has also been used to examine structured RNAs. I'm curious about the variety of these methods and how accurate they are.

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Determining an NMR structure is a lot of work, it's not something you would do just to get that information. There are ways to identify which residues are solvent accessible by NMR (e.g. SEA-TROSY), but they don't give you the area. –  Mad Scientist Apr 21 '12 at 8:11

2 Answers 2

up vote 4 down vote accepted
+50

I only know of one method, but here it is. You create a sphere the diameter of the VdW radius of water, and then 'roll' it along the surface. I know this as a Richards-Lee surface, wikipedia has another name for it.

enter image description here

This looks complicated, but its not. you move the probe sphere along the surface of the molecule in the XY plane until it just touches the vdW radius of the protein, keeping the center of the sphere as the surface, all the way around the molecule. If you like, you can color the surface by the charge of the position too, which is useful for discussing solvent interactions.

Then you translate along the z axis and do another contour until you run out of protein. Apparently jmol and other packages will do this for you.

Wikipedia references a more mathematical method LCPO, which I am not so familiar with.

Is this accurate? As usual with such calculations its more of a guess than an answer. You can do the calculation on any structure or any ensemble of structures (like NMR gives). It doesn't understand how the molecule might be flexible or dynamic. If you read up on your physical chemistry you see that proteins breathe and can allow diffusion into the core rather readily. If I recall right, you can get rather large molecules quenching heme flouresence in hemoglobin at room temperature.

If you are looking to dock 2 proteins, SAS might be more useful. Its an important piece of information, but not an ultimate answer. I'm afraid with proteins that doesn't happen so easily.

@bobthejoe asked about SAS for which no structure exists.
This is an extremely difficult thing to even guess at. The non helpful answer is that the surface of the protein goes as the cube root of the molecular weight of the protein.

By getting a solution of the protein and shooting it in a syhcrotron, you can get a mean radius of gyration pretty easily which will give you an ellipsoidal volume (and surface area) for a protein. Again most of the particulars would be lost and this could easily be off by 25% for an irregularly shaped protein. For a regular globular protein it might give an answer similar to the power law above.

I have seen physical chemistry experiments that look for changes in osmotic pressure when the salt concentration in a solution of the protein changes substantially (Adrian Parsegian's work at NIH in the late 80s).

I doubt you will find any of these answers useful as their mean error is going to be very large (20-200%) and also assumes the protein is soluable and amenable to the experimental conditions.

Solvent probes can help too. For instance exposing the protein to D20 then doing mass spectroscopy on the protein. This is still only going to give you a general idea of how much of the peptide is surface exposed. Protein structure is still pretty necessary to getting any accurate measurement of SAS I think.

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This is the mathematical calculation of SAS. Unfortunately, it doesn't get to the answer of how does one measure SAS sans X-ray/NMR structure. –  bobthejoe May 9 '12 at 18:24
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sorry i missed this. i have added something about this. this is difficult to do as you might have guessed. –  shigeta May 14 '12 at 1:56

I don't think SAS is a well-defined observable. (I like the work by Bertil Halle on this and related problems.) You can measure correlates to SAS that have been calculated according to known structures, using something like the rolling sphere algorithm that @shigeta describes.

I think the best-parametrized approach would be differential scanning calorimetry. Because a lot of proteins have had their folding studied with this technique, a DSC curve can be directly converted into changes in polar and nonpolar SAS. The total SAS would be a sum of those two quantities.

The only ready reference I could find for this is here: https://www.bio.cmu.edu/courses/03438/LecS00/DSC.html

I think most of the analysis was worked out by Ernesto Freire. Basically, the idea is that surface accessible hydrophobic areas organize more solvent (and have a larger entropic footprint) than the polar areas. Since a DSC trace (for a two-state folder) can be deconvoluted into $\Delta$H and $\Delta$S components, it can be mapped onto $\Delta$ASA$_{folding}$. I wouldn't trust this for anything that was non-two-state or that bound cofactors.

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