ArticleProceedings of the National Academy of Sciences of the United States of America2012
Energetics of short hydrogen bonds in photoactive yellow protein.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- 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
- Stretching vibrational frequencies and pKBiophysical journal · 2023Article
- Article
- Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Class A β-lactamase.FEBS letters · 2021Article
- A quantum crystallographic approach to short hydrogen bonds.CrystEngComm · 2021Article
- Protonation Equilibrium in the Active Site of the Photoactive Yellow Protein.Molecules (Basel, Switzerland) · 2021Article
- On the Case of the Misplaced Hydrogens.Chembiochem : a European journal of chemical biology · 2021Review
- Low barrier hydrogen bonds in protein structure and function.Biochimica et biophysica acta. Proteins and proteomics · 2021Review
- Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems.The journal of physical chemistry. B · 2020Article
- Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Visualization of H atoms in the X-ray crystal structure of photoactive yellow protein: Does it contain low-barrier hydrogen bonds?Protein science : a publication of the Protein Society · 2019Article
- Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation.The journal of physical chemistry. B · 2019Article
- Nuclear quantum effect and H/D isotope effect on Cl· + (HRSC advances · 2018Article
- Neutron crystallography of photoactive yellow protein reveals unusual protonation state of Arg52 in the crystal.Scientific reports · 2017Article
- Active-Site pKa Determination for Photoactive Yellow Protein Rationalizes Slow Ground-State Recovery.Biophysical journal · 2017Article
- Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter.Biophysical journal · 2016Article
- Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein.Computational and structural biotechnology journal · 2016Article
- Sequence-Dependent Conformational Heterogeneity and Proton-Transfer Reactivity of the Fluorescent Guanine Analogue 6-Methyl Isoxanthopterin (6-MI) in DNA.The journal of physical chemistry. B · 2015Article
- Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography.Journal of the American Chemical Society · 2015Article
- Biochemistry and theory of proton-coupled electron transfer.Chemical reviews · 2014Review
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2 authors.
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Abstract
Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energetics of the short H bond by two independent methods: electrostatic pK(a) calculations and a quantum mechanical/molecular mechanical (QM/MM) approach. (i) In the QM/MM optimized geometry, we reproduced the two short H-bond distances of the crystal structure: Tyr42-pCA (2.50 Å) and Glu46-pCA (2.57 Å). However, the H atoms obviously belonged to the Tyr or Glu moieties, and were not near the midpoint of the donor and acceptor atoms. (ii) The potential-energy curves of the two H bonds resembled those of standard asymmetric double-well potentials, which differ from those of LBHB. (iii) The calculated pK(a) values for Glu46 and pCA were 8.6 and 5.4, respectively. The pK(a) difference was unlikely to satisfy the prerequisite for LBHB. (iv) The LBHB in PYP was originally proposed to stabilize the ionized pCA because deprotonated Arg52 cannot stabilize it. However, the calculated pK(a) of Arg52 and QM/MM optimized geometry suggested that Arg52 was protonated on the protein surface. The short H bond between Glu46 and ionized pCA in the PYP ground state could be simply explained by electrostatic stabilization without invoking LBHB.
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