title: Probing the nature of the blue-shifted intermediate of photoactive yellow protein in solution by NMR: hydrogen-deuterium exchange data and pH studies.
abstract: The nature of the pB intermediate of photoactive yellow protein (PYP) from Ectothiorhodospira halophila has been probed by NMR. pH-dependent changes in the NMR spectrum of the dark state of PYP are shown to closely mimic exchange broadening effects observed previously in the NMR spectrum of the pB intermediate in solution. Amide H-D exchange data show that while pB retains a solid protected core, two regions become significantly less protected than the dark state. The amide exchange data help to rationalize why the conformational exchange process affects the N-terminal 28-residue segment of the protein, which is not close to the site of chromophore rearrangement. At very low pH (pH 1.7), the dark state NMR spectrum displays approximately 30 very sharp signals, which are characteristic of a portion of the molecule becoming unfolded. Similarities between the dark state spectra at pH approximately 3.2 and the spectra of pB suggest a model for pB in solution where the protein exists in an equilibrium between a well-ordered state and a state in which a region is unfolded. Such a two-state model accounts for the exchange phenomena observed in the NMR spectra of pB, and the hydrophobic exposure and lability inferred from thermodynamic data. It is likely that in the crystalline environment the ordered form of pB is strongly favored.
authors.affiliation: Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: C J
authors.initials: CJ
authors.lastname: Craven
authors.forename: N M
authors.initials: NM
authors.lastname: Derix
authors.forename: J
authors.initials: J
authors.lastname: Hendriks
authors.forename: R
authors.initials: R
authors.lastname: Boelens
authors.forename: K J
authors.initials: KJ
authors.lastname: Hellingwerf
authors.forename: R
authors.initials: R
authors.lastname: Kaptein
mesh_terms: D000577:Amides; D001426:Bacterial Proteins / Q000737:chemistry*; D003903:Deuterium; D020607:Halorhodospira halophila; D006863:Hydrogen-Ion Concentration; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D020283:Photoreceptors, Microbial; D011487:Protein Conformation; D017510:Protein Folding; D011522:Protons; D012996:Solutions; D013816:Thermodynamics; D017186:Titrimetry
chemical_list: D000577:Amides; D001426:Bacterial Proteins; D020283:Photoreceptors, Microbial; D011522:Protons; D012996:Solutions; C050162:photoactive yellow protein, Bacteria; D003903:Deuterium