Are There Really Low-Barrier Hydrogen Bonds in Proteins? The Case of Photoactive Yellow Protein

Abstract

For a long time, low-barrier hydrogen bonds (LBHBs) have been proposed to exist in many enzymes and to play an important role in their catalytic function, but the proof of their existence has been elusive. The transient formation of an LBHB in a protein system has been detected for the first time using neutron diffraction techniques on a photoactive yellow protein (PYP) crystal in a study published in 2009 (Yamaguchi, S.; et al. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 440-444). However, very recent theoretical studies based on electronic structure calculations and NMR resonance experiments on PYP in solution (Saito, K.; et al. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 167-172) strongly indicate that there is not such an LBHB. By means of electronic structure calculations combined with the solution of the nuclear Schrödinger equation, we analyze here under which conditions an LBHB can exist in PYP, thus leading to a more reasonable and conciliating understanding of the above-mentioned studies.

A comprehensive study of isomerization and protonation reactions in the photocycle of the photoactive yellow protein

“…Such a low barrier hydrogen bond (LBHB) transition between Glu46 and PYP has been discussed in previous experimental 40 and theoretical studies. 81 The proton transfer does not introduce any drastic structural changes in pCA, and it proceeds within a short time. Since the fast protonation reaction pR 2 -pB 0 follows the slow bicycle pedal isomerization I CP -pR 2 (16-21 ns), the dynamics and structural spectroscopy of pB 0 overlaps with that of pR 2 .…”

15N and 1H Solid-State NMR Investigation of a Canonical Low-Barrier Hydrogen-Bond Compound: 1,8-Bis(dimethylamino)naphthalene

“…Finally, as well documented in the literature, if the protein of interest functions in solution, then water further reduces the likelihood of LBHBs compared to the solid state because water oxygen can compete with the heteroatoms while the water hydrogen can compete for the lone pairs in the LBHB 61 . For example, Yamaguchi recently reported crystallographic evidence for a LBHB between para -coumaric acid and Glu46 in the photoactive yellow protein; but in solution a small 1 H chemical shift of 15.2 ppm was found for the OHO − proton, and computational modeling further supported a regular H-bond 5, 8–9 . Thus, transient interactions between water and biomolecules substantially decrease the likelihood of LBHBs in solution.…”

Effect of hydrogen bonding on the infrared absorption intensity of OH stretch vibrations

“…Some possible candidates are carboxylic acid dimers (R 2.45Å), HCrO 2 (R 2.49Å), porphycenes 51 , and proton sponges 52 , for which the fundamental, first overtone, and isotope effect could be measured and analysed. Slightly asymmetric biomolecular systems with strong H-bonds that could be investigated include mutated GFP 53 , photoactive yellow protein 54 and the enzyme KSI 55 .…”