NACCESS Computer Program, Department of Biochemistry and Molecular Biology.
[http://www.bioinf.manchester.ac.uk/naccess/]
Accessible surface area (ASA) analysis Link
The ASA is the area of the protein surface which can be in contact with the solvent.
The total apolar (and the complementary polar) component of the entire accessible
surface area of each protein in its quaternary form was calculated with the server
GETAREA http://curie.utmb.edu/getarea.html webcite with default settings [44]. The contribution of different atomic types to the polar area, namely oxygens, side-chain
oxygens, nitrogens and side-chain nitrogens was also investigated. To compare the
different surface areas of halophilic and non-halophilic proteins, they were normalized
by division by the total accessible surface area of the corresponding protein.
The differences between the fraction of apolar accessible surface area in the unfolded
and folded form of each protein considered (ΔApAU-F) were calculated through the web server http://roselab.jhu.edu/utils/unfolded.html webcite[28]. The differences between the ΔApAU-F in each halophilic protein and in its corresponding homolog (ΔΔApAU-F) were calculated and statistically tested.
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