ArticleProceedings of the National Academy of Sciences of the United States of America2009
Low-barrier hydrogen bond in photoactive yellow protein.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed.
- PAS-Domain Protein Orientation at a Polyelectrolyte Surface Revealed by Infrared Nanospectroscopy, Chiral Vibrational Spectroscopy, and Molecular Dynamics Simulations.Biomacromolecules · 2026Article
- Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds.Biochemistry · 2026Article
- QM/MM Free Energy Calculations of IRE1 Reveal a Unique Protonation State of the Catalytic Lys599.Journal of computational chemistry · 2025Article
- Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds.bioRxiv : the preprint server for biology · 2025Article
- Arginine: I. Interactions of Its Guanidinium Moiety with Branched Aliphatic Side Chains.The journal of physical chemistry. B · 2025Article
- Neutron and time-resolved X-ray crystallography reveal the substrate recognition and catalytic mechanism of human Nudix hydrolase MTH1.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.Science advances · 2025Article
- Direct evidence for a deprotonated lysine serving as a H-bond "acceptor" in a photoreceptor protein.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Very Strong Hydrogen Bond in Nitrophthalic Cocrystals.Molecules (Basel, Switzerland) · 2024Article
- gmXtal: Cooking Crystals with GROMACS.The protein journal · 2024Article
- Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein.Structural dynamics (Melville, N.Y.) · 2024Review
- Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds.Scientific reports · 2023Article
- Measurement of charges and chemical bonding in a cryo-EM structure.Communications chemistry · 2023Article
- Chemical Features and Machine Learning Assisted Predictions of Protein-Ligand Short Hydrogen Bonds.Research square · 2023Article
- Ensemble-function relationships to dissect mechanisms of enzyme catalysis.Science advances · 2022Article
- Article
- Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement.IUCrJ · 2022Article
- Effective prediction of short hydrogen bonds in proteins via machine learning method.Scientific reports · 2022Article
- Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of FeJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2021Review
- On-off transition and ultrafast decay of amino acid luminescence driven by modulation of supramolecular packing.iScience · 2021Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Low-barrier hydrogen bonds (LBHBs) have been proposed to play roles in protein functions, including enzymatic catalysis and proton transfer. Transient formation of LBHBs is expected to stabilize specific reaction intermediates. However, based on experimental results and theoretical considerations, arguments against the importance of LBHB in proteins have been raised. The discrepancy is caused by the absence of direct identification of the hydrogen atom position. Here, we show by high-resolution neutron crystallography of photoactive yellow protein (PYP) that a LBHB exists in a protein, even in the ground state. We identified approximately 87% (819/942) of the hydrogen positions in PYP and demonstrated that the hydrogen bond between the chromophore and E46 is a LBHB. This LBHB stabilizes an isolated electric charge buried in the hydrophobic environment of the protein interior. We propose that in the excited state the fast relaxation of the LBHB into a normal hydrogen bond is the trigger for photo-signal propagation to the protein moiety. These results give insights into the novel roles of LBHBs and the mechanism of the formation of LBHBs.
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