title: pKa measurements from nuclear magnetic resonance for the B1 and B2 immunoglobulin G-binding domains of protein G: comparison with calculated values for nuclear magnetic resonance and X-ray structures.
abstract: Two-dimensional homo- and heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine pKa values for all of the acidic residues in the B1 and B2 immunoglobulin G- (IgG-) binding domains of protein G. Due to the stability of protein G over a wide pH range, estimates of ionization constants were also obtained for some basic residues. These experimentally determined ionization constants were compared with values calculated from both X-ray and NMR-derived structures of B1 and B2 using the UHBD algorithm [Antosiewicz, J., et al. (1994) J. Mol. Biol. 238, 415-436]. This algorithm has been found to be predictive for pKa measurements in proteins and, in combination with experimental measurements, allowed some evaluation of the NMR and X-ray structures. Three regions where significant differences exist between the X-ray and NMR structures are (1) the position of the E56 side chain relative to the backbone amides of K10 and D40, (2) residues 33-37 in the helix, and (3) the Y45 side-chain conformation. For all three cases, the experimental pH titration curves are notably more consistent with the X-ray structures than the NMR structures. In contrast, a number of solvent-accessible side chains have experimental pKas more in agreement with mean pKas calculated from families of NMR structures. The conformations of these side chains may be susceptible to crystal packing effects. From titration experiments under basic conditions, it is noteworthy that the chemical shift of the Y45 C epsilonH resonance is invariant up to pDcorr 12. The Y45 side-chain hydroxyl group appears to maintain a nativelike hydrogen bond with D47 at pDcorr 12, even though the protein is approximately 90% unfolded. These results suggest that this short-range (i, i + 2) interaction, located in the beta3-beta4 hairpin, is present in the high-pH denatured state and may therefore form early in the folding of protein G.
authors.affiliation: Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA.
authors.forename: D
authors.initials: D
authors.lastname: Khare
authors.forename: P
authors.initials: P
authors.lastname: Alexander
authors.forename: J
authors.initials: J
authors.lastname: Antosiewicz
authors.forename: P
authors.initials: P
authors.lastname: Bryan
authors.forename: M
authors.initials: M
authors.lastname: Gilson
authors.forename: J
authors.initials: J
authors.lastname: Orban
mesh_terms: D001224:Aspartic Acid; D001665:Binding Sites; D018360:Crystallography, X-Ray; D018698:Glutamic Acid; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D007074:Immunoglobulin G / Q000378:metabolism*; D008239:Lysine; D009682:Magnetic Resonance Spectroscopy; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity; D014443:Tyrosine
chemical_list: C029152:G-substrate; D007074:Immunoglobulin G; D009419:Nerve Tissue Proteins; D001224:Aspartic Acid; D018698:Glutamic Acid; D014443:Tyrosine; D011494:Protein Kinases; D008239:Lysine