Hi Rob, Hyunchul Kim and Miguel,
I was just about to write a comment on this, but Rob was quicker..
Rob is right, our dataset of hen egg-white lysozymes does not contain
any structures with resolution lower than 2.3 A....one may say that
these are all relatively high-resolution structures, therefore we can
not claim there is no correlation between ASA and resolution in general.
Nevertheless, we cannot see any correlation in our (limited) dataset.
On the other hand, we also saw that two structures of the same protein
differed by hundreds of sq A in their ASA just because a few residues
could not be seen in one of these two structures.
The conclusion of our paper was identical with Rob's last paragraph
(although we forget to use the word "biodegradable"), and it is even
more true when one look at individual residues.
I think that The EDS server can provide some hints concerning the
reliability of ASA values for individual residues...it allows to check
how well are individual residues supported by experimental data, so if a
deposited residue conformation is well supported by its electron density
map, then its ASA can be quite reliable regardless resolution of a whole
structure. However, proteins are dynamic and therefore ASA for
individual residues will fluctuate substantially during time (regardless
of resolution).
best regards,
--marian
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Marian Novotny
Department of Animal Physiology and Developmental Biology
Faculty of Natural Sciences
Charles University in Prague
Vinicna 7
Praha 2
128 43
Czech Republic
GPS: 50¡4'20.07"N,14¡25'27.02"E
mail: [log in to unmask]
tel: +420221951766
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