An evaluation review of the prediction of protonation states in proteins versus crystallographic experiment

• Published in: Crystallography reviews 2009-10, Vol.15 (4), p.231-259
• Main Authors: Fisher, Stuart J., Wilkinson, James, Henchman, Richard H., Helliwell, John R.
• Format: Article
• Language: English
• Subjects: amino acids; Analytical, structural and metabolic biochemistry; Biological and medical sciences; Condensed matter: structure, mechanical and thermal properties; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; Miscellaneous; neutron crystallography; NMR; Organic compounds; Physics; predictions; protein pK; Proteins; protonation states; Structure of solids and liquids; crystallography; Structure of specific crystalline solids; X-ray crystallography
• ISSN: 0889-311X; 1476-3508
• DOI: 10.1080/08893110903213700

The known protonation states of protein crystal structures obtained using X-ray and neutron crystallographic data, and including relevant NMR derived experimental information, have been predicted using three pK a calculation tools, namely PROPKA, H++ and MCCE. Comparisons between the experimental and predicted protonation states have been carried out in order to assess whether the results are of sufficient quality to validate their use in predicting the protonation states of two key histidine residues in the lobster carapace colouration protein β-crustacyanin as an example. Significant interest has been shown in the protonation states of these residues, which have been out of reach of experiment thus far and are likely to remain so. †Dedication: 2009 is the 50th Anniversary of the determination of the first protein crystal structure, myoglobin, by a team led by John Kendrew and which included Richard Dickerson and Bror Strandberg. Myoglobin crystal structures feature in our analyses here and so we wish to make our contribution to this important Anniversary by dedicating our article to that pioneering research.