Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness.
Acta Crystallogr D Biol Crystallogr
; 68(Pt 7): 800-9, 2012 Jul.
Article
em En
| MEDLINE
| ID: mdl-22751665
ABSTRACT
A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2â
Å for trypsin (97% complete, 12% H-atom visibility at 2.5σ), 1.26â
Å for subtilisin (100% complete, 11% H-atom visibility at 2.5σ) and 0.65â
Å for lysozyme (PDB entry 2vb1; 98% complete, 30% H-atom visibility at 3σ). These studies provide a wide diffraction resolution range for assessment. The bond-length e.s.d.s obtained are as small as 0.008â
Å and thus provide an exceptional opportunity for bond-length analyses. The results indicate that useful information can be obtained from diffraction data at around 1.2-1.3â
Å resolution and that minor increases in resolution can have significant effects on reducing the associated bond-length standard deviations. The protonation states in histidine residues were also considered; however, owing to the smaller differences between the protonated and deprotonated forms it is much more difficult to infer the protonation states of these residues. Not even the 0.65â
Å resolution lysozyme structure provided the necessary accuracy to determine the protonation states of histidine.
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Base de dados:
MEDLINE
Assunto principal:
Prótons
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Bacillus
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Proteínas de Bactérias
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Subtilisinas
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Tripsina
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Muramidase
Idioma:
En
Ano de publicação:
2012
Tipo de documento:
Article