title: The Low Barrier Hydrogen Bond in the Photoactive Yellow Protein: A Vacuum Artifact Absent in the Crystal and Solution.
abstract: There has been considerable debate on the existence of a low-barrier hydrogen bond (LBHB) in the photoactive yellow protein (PYP). The debate was initially triggered by the neutron diffraction study of Yamaguchi et al. ( Proc. Natl. Acad. Sci., U. S. A. , 2009 , 106 , 440 - 444 ) who suggested a model in which a neutral Arg52 residue triggers the formation of the LBHB in PYP. Here, we present an alternative model that is consistent within the error margins of the Yamaguchi structure factors. The model explains an increased hydrogen bond length without nuclear quantum effects and for a protonated Arg52. We tested both models by calculations under crystal, solution, and vacuum conditions. Contrary to the common assumption in the field, we found that a single PYP in vacuum does not provide an accurate description of the crystal conditions but instead introduces strong artifacts, which favor a LBHB and a large1H NMR chemical shift. Our model of the crystal environment was found to stabilize the two Arg52 hydrogen bonds and crystal water positions for the protonated Arg52 residue in free MD simulations and predicted an Arg52 pKaupshift with respect to PYP in solution. The crystal and solution environments resulted in almost identical1H chemical shifts that agree with NMR solution data. We also calculated the effect of the Arg52 protonation state on the LBHB in 3D nuclear equilibrium density calculations. Only the charged crystal structure in vacuum supports a LBHB if Arg52 is neutral in PYP at the previously reported level of theory ( J. Am. Chem. Soc. , 2014 , 136 , 3542 - 3552 ). We attribute the anomalies in the interpretation of the neutron data to a shift of the potential minimum, which does not involve nuclear quantum effects and is transferable beyond the Yamaguchi structure.
authors.affiliation: Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany.
authors.forename: Timo
authors.identifier: 0000-0002-6552-8477
authors.initials: T
authors.lastname: Graen
authors.affiliation: Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany.
authors.forename: Ludger
authors.initials: L
authors.lastname: Inhester
authors.affiliation: Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany.
authors.forename: Maike
authors.initials: M
authors.lastname: Clemens
authors.affiliation: Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany.
authors.forename: Helmut
authors.initials: H
authors.lastname: Grubmüller
authors.affiliation: Department of Chemistry and Nanoscience Center, University of Jyväskylä , P. O. Box 35, 40014 Jyväskylän Yliopisto, Finland.
authors.forename: Gerrit
authors.initials: G
authors.lastname: Groenhof
mesh_terms: D016477:Artifacts; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D020283:Photoreceptors, Microbial / Q000737:chemistry*; D011487:Protein Conformation; D012996:Solutions; D014618:Vacuum
chemical_list: D001426:Bacterial Proteins; D020283:Photoreceptors, Microbial; D012996:Solutions; C050162:photoactive yellow protein, Bacteria