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07:57
Accurate Determination of the Equilibrium Surface Tension Values with Area Perturbation Tests
Published on: August 30, 2019
On the precision of calculated solvent-accessible surface areas.
Marian Novotny1, Marvin Seibert, Gerard J Kleywegt
1Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden.
Acta Crystallographica. Section D, Biological Crystallography
|January 24, 2007
Summary
Protein structure models have limited accuracy, affecting calculated solvent-accessible surface areas (ASA). This study reveals ASA precision is often within 50-100 A², suggesting reporting higher precision is unrealistic.
Area of Science:
- Structural biology
- Biophysics
- Computational chemistry
Background:
- Protein structures are inherently dynamic.
- Experimental methods like X-ray crystallography, electron microscopy (EM), and nuclear magnetic resonance (NMR) yield models with inherent inaccuracies.
- These structural limitations impact the precision of calculated molecular properties, such as solvent-accessible surface areas (ASA).
Purpose of the Study:
- To investigate the precision of calculated solvent-accessible surface areas (ASA).
- To quantify the impact of atomic coordinate variations on ASA values.
- To establish realistic precision limits for reporting ASA in structural biology.
Main Methods:
- Analysis of selected protein structures of varying sizes.
- Introduction of random shifts to atomic coordinates to assess ASA variability.
- Calculation of ASA for multiple structures within the Protein Data Bank (PDB) ensembles.
- Examination of a molecular dynamics (MD) trajectory for lysozyme.
- Comparison of ASA values computed using different software packages.
Main Results:
- Standard deviations in ASA calculations ranged from approximately 10 to 80 A² due to coordinate variations.
- A set of 69 hen egg-white lysozyme structures showed a standard deviation of 81 A² for ASA.
- ASA values exhibited a range of over 800 A² during molecular dynamics simulations.
- Different programs yielded ASA values with a spread of nearly 600 A² for a small protein.
- No correlation was found between ASA precision and resolution or temperature factors.
Conclusions:
- Reporting ASA values with precision better than 10 A² is generally unrealistic.
- A prudent precision for reporting ASA values is between 50-100 A².
- The precision of buried surface area calculations for protein complexes also warrants consideration.
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