English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
 
 
DownloadE-Mail
  The low barrier hydrogen bond in the photoactive yellow protein: A vacuum artifact absent in the crystal and solution.

Graen, T., Inhester, L., Clemens, M., Grubmüller, H., & Groenhof, G. (2016). The low barrier hydrogen bond in the photoactive yellow protein: A vacuum artifact absent in the crystal and solution. Journal of the American Chemical Society, 138(51), 16620-16631. doi:10.1021/jacs.6b05609.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-11C8-A Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-AE6C-A
Genre: Journal Article

Files

show Files
hide Files
:
2367825.pdf (Publisher version), 6MB
Name:
2367825.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
:
2367825_Suppl.pdf (Supplementary material), 11MB
Name:
2367825_Suppl.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Locators

show

Creators

show
hide
 Creators:
Graen, T.1, Author              
Inhester, L.1, Author              
Clemens, M., Author
Grubmüller, H.1, Author              
Groenhof, G., Author
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

Content

show
hide
Free keywords: -
 Abstract: There has been a 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.,USA, 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 large 1H-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 pKa upshift with respect to PYP in solution. The crystal and solution environments resulted in almost identical 1H 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.

Details

show
hide
Language(s): eng - English
 Dates: 2016-11-302016-12-28
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1021/jacs.6b05609
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Journal of the American Chemical Society
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 138 (51) Sequence Number: - Start / End Page: 16620 - 16631 Identifier: -