On the precision of calculated solvent-accessible surface areas.
The fact that protein structures are dynamic by nature and that structure models determined by X-ray crystallography, electron microscopy (EM) and nuclear magnetic resonance (NMR) spectroscopy have limited accuracy limits the precision with which derived properties can be reported. Here, the issue of the precision of calculated solvent-accessible surface areas (ASAs) is addressed. A number of protein structures of different sizes were selected and the effect of random shifts applied to the atomic coordinates on ASA values was investigated. Standard deviations of the ASA calculations were found to range from approximately 10 to approximately 80 A2. Similar values are obtained for a handful of cases in the Protein Data Bank (PDB) where ;ensembles' of crystal structures were refined against the same data set. The ASA values for 69 hen egg-white lysozyme structures were calculated and a standard deviation of the ASA of 81 A2 was obtained (the average ASA value was 6571 A2). The calculated ASA values do not show any correlation with factors such as resolution or overall temperature factors. A molecular-dynamics (MD) trajectory of lysozyme was also analysed. The ASA values during the simulation covered a range of more than 800 A2. If different programs are used, the ASA values obtained for one small protein show a spread of almost 600 A2. These results suggest that in most cases reporting ASA values with a precision better than 10 A2 is probably not realistic and a precision of 50-100 A2 would seem prudent. The precision of buried surface-area calculations for complexes is also discussed.
Novotny
Marian
M
Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden.
Seibert
Marvin
M
Kleywegt
Gerard J
GJ
D003198:Computer Simulation; D004527:Egg Proteins / Q000737:chemistry; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry*; D015203:Reproducibility of Results; D012997:Solvents / Q000737:chemistry*
D004527:Egg Proteins; D012997:Solvents; D009113:Muramidase