title: Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
abstract: Site-specific pK(a) values measured by NMR spectroscopy provide essential information on protein electrostatics, the pH-dependence of protein structure, dynamics and function, and constitute an important benchmark for protein pK(a) calculation algorithms. Titration curves can be measured by tracking the NMR chemical shifts of several reporter nuclei versus sample pH. However, careful analysis of these curves is needed to extract residue-specific pK(a) values since pH-dependent chemical shift changes can arise from many sources, including through-bond inductive effects, through-space electric field effects, and conformational changes. We have re-measured titration curves for all carboxylates and His 15 in Hen Egg White Lysozyme (HEWL) by recording the pH-dependent chemical shifts of all backbone amide nitrogens and protons, Asp/Glu side chain protons and carboxyl carbons, and imidazole protonated carbons and protons in this protein. We extracted pK(a) values from the resulting titration curves using standard fitting methods, and compared these values to each other, and with those measured previously by ¹H NMR (Bartik et al., Biophys J 1994;66:1180–1184). This analysis gives insights into the true accuracy associated with experimentally measured pK(a) values. We find that apparent pK(a) values frequently differ by 0.5–1.0 units depending upon the nuclei monitored, and that larger differences occasionally can be observed. The variation in measured pK(a) values, which reflects the difficulty in fitting and assigning pH-dependent chemical shifts to specific ionization equilibria, has significant implications for the experimental procedures used for measuring protein pK(a) values, for the benchmarking of protein pK(a) calculation algorithms, and for the understanding of protein electrostatics in general.
authors.affiliation: School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Helen
authors.initials: H
authors.lastname: Webb
authors.forename: Barbara Mary
authors.initials: BM
authors.lastname: Tynan-Connolly
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Lee
authors.forename: Damien
authors.initials: D
authors.lastname: Farrell
authors.forename: Fergal
authors.initials: F
authors.lastname: O'Meara
authors.forename: Chresten R
authors.initials: CR
authors.lastname: Søndergaard
authors.forename: Kaare
authors.initials: K
authors.lastname: Teilum
authors.forename: Chandralal
authors.initials: C
authors.lastname: Hewage
authors.forename: Lawrence P
authors.initials: LP
authors.lastname: McIntosh
authors.forename: Jens Erik
authors.initials: JE
authors.lastname: Nielsen
mesh_terms: D000465:Algorithms; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D015203:Reproducibility of Results