The role of short hydrogen bonds in mechanisms of enzymatic action

Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivity

The heart of the H+ conductance mechanism in the homotetrameric M2 H+ channel from influenza A is a set of four histidine side chains. Here, we show that protonation of the third of these imidazoles coincides with acid activation of this transmembrane channel and that, at physiological pH, the channel is closed by two imidazole-imidazolium dimers, each sharing a low-barrier hydrogen bond. This unique construct succeeds in distributing a pair of charges over four rings and many atoms in a low dielectric environment to minimize charge repulsion. These dimers form with identical pKas of 8.2 +/- 0.2, suggesting cooperative H+ binding and clearly illustrating high H+ affinity for this channel. The protonation behavior of the histidine side chains has been characterized by using solid-state NMR spectroscopy on the M2 transmembrane domain in fully hydrated lipid bilayers where the tetrameric backbone structure is known. Furthermore, electrophysiological measurements of multichannel and single-channel experiments confirm that these protein constructs are functional.

Toward Understanding Mobile Proton Behavior from First Principles Calculation: The Short Hydrogen Bond in Crystalline Urea−Phosphoric Acid

The dynamics of the intermolecular short hydrogen bond in the molecular complex of urea and phosphoric acid are investigated using plane-wave density functional theory. Results indicate migration of the proton toward the center of the hydrogen bond as temperature is increased, in line with recent experimental measurements. Computed vibrational frequencies show favorable agreement with experimental measurement. An analysis of existing neutron diffraction data leads us to conclude that the effective potential well experienced by the proton is temperature-dependent. Inspired by our computations and theoretical analysis, we offer a possible explanation for the proton migration phenomenon.

Photophysical properties of methyl beta-carboline-3-carboxylate mediated by hydrogen-bonded complexes--a comparative study in different solvents

The hydrogen bonding interactions of methyl beta-carboline-3-carboxylate (BCCM) in both ground and first singlet excited electronic states have been studied in solvents with different properties in the presence of acetic acid, a hydrogen-bonding donor/acceptor. The methyl ester substituent reduces the pyridinic nitrogen basicity of this beta-carboline derivative. This fact has let us study the hydrogen bonding interactions in a higher range of acetic acid concentrations than for other beta-carboline derivatives previously studied. Steady and non-steady photophysical studies have been carried out in two non-polar solvents, benzene and p-dioxane; and in two polar solvents, acetonitrile and dichloromethane. Six different fluorescence emissions have been isolated corresponding to the uncomplexed BCCM, the protonated species and four different complexes between BCCM and acetic acid whose structures we have tried to elucidate.

Evidence for a strong hydrogen bond in the catalytic dyad of transition-state analogue inhibitor complexes of chymotrypsin from proton-triton NMR isotope shifts

We present here the first accurate measurements of 1H (H) versus 3H (T) isotope shift (DeltadeltaT-H = deltaT - deltaH) in a protein. This approach was used to investigate the strength of the hydrogen bond between His57 and Asp102 in the catalytic dyad of chymotrypsin in three transition-state analogue inhibited complexes: N-acetyl-l-phenylalanyl trifluoromethyl ketone (N-AcF-CF3), N-acetyl-l-valyl-l-phenylalanyl trifluoromethyl ketone (N-AcVF-CF3), and N-acetyl-l-leucyl-l--phenylalanyl trifluoromethyl ketone (N-AcLF-CF3). The measured DeltadeltaT-H values for His57 Hdelta1 in these complexes were between -0.63 and -0.68 ppm. These values are consistent with a strong hydrogen bond in each of these complexes, but not with a very strong hydrogen bond, which would be expected to have a DeltadeltaT-H. value near or greater than zero.

Short, strong hydrogen bonds at the active site of human acetylcholinesterase: proton NMR studies

Cholinesterases use a Glu-His-Ser catalytic triad to enhance the nucleophilicity of the catalytic serine. We have previously shown by proton NMR that horse serum butyryl cholinesterase, like serine proteases, forms a short, strong hydrogen bond (SSHB) between the Glu-His pair upon binding mechanism-based inhibitors, which form tetrahedral adducts, analogous to the tetrahedral intermediates in catalysis [Viragh, C., et al. (2000) Biochemistry 39, 16200-16205]. We now extend these studies to human acetylcholinesterase, a 136 kDa homodimer. The free enzyme at pH 7.5 shows a proton resonance at 14.4 ppm assigned to an imidazole NH of the active-site histidine, but no deshielded proton resonances between 15 and 21 ppm. Addition of a 3-fold excess of the mechanism-based inhibitor m-(N,N,N-trimethylammonio)trifluoroacetophenone (TMTFA) induced the complete loss of the 14.4 ppm signal and the appearance of a broad, deshielded resonance of equal intensity with a chemical shift delta of 17.8 ppm and a D/H fractionation factor phi of 0.76 +/- 0.10, consistent with a SSHB between Glu and His of the catalytic triad. From an empirical correlation of delta with hydrogen bond lengths in small crystalline compounds, the length of this SSHB is 2.62 +/- 0.02 A, in agreement with the length of 2.63 +/- 0.03 A, independently obtained from phi. Upon addition of a 3-fold excess of the mechanism-based inhibitor 4-nitrophenyl diethyl phosphate (paraoxon) to the free enzyme at pH 7.5, and subsequent deethylation, two deshielded resonances of unequal intensity appeared at 16.6 and 15.5 ppm, consistent with SSHBs with lengths of 2.63 +/- 0.02 and 2.65 +/- 0.02 A, respectively, suggesting conformational heterogeneity of the active-site histidine as a hydrogen bond donor to either Glu-327 of the catalytic triad or to Glu-199, also in the active site. Conformational heterogeneity was confirmed with the methylphosphonate ester anion adduct of the active-site serine, which showed two deshielded resonances of equal intensity at 16.5 and 15.8 ppm with phi values of 0.47 +/- 0.10 and 0.49 +/- 0.10 corresponding to average hydrogen bond lengths of 2.59 +/- 0.04 and 2.61 +/- 0.04 A, respectively. Similarly, lowering the pH of the free enzyme to 5.1 to protonate the active-site histidine (pK(a) = 6.0 +/- 0.4) resulted in the appearance of two deshielded resonances, at 17.7 and 16.4 ppm, consistent with SSHBs with lengths of 2.62 +/- 0.02 and 2.63 +/- 0.02 A, respectively. The NMR-derived distances agree with those found in the X-ray structures of the homologous acetylcholinesterase from Torpedo californica complexed with TMTFA (2.66 +/- 0.28 A) and sarin (2.53 +/- 0.26 A) and at low pH (2.52 +/- 0.25 A). However, the order of magnitude greater precision of the NMR-derived distances establishes the presence of SSHBs at the active site of acetylcholinesterase, and detect conformational heterogeneity of the active-site histidine. We suggest that the high catalytic power of cholinesterases results in part from the formation of a SSHB between Glu and His of the catalytic triad.

Fractionation factors and activation energies for exchange of the low barrier hydrogen bonding proton in peptidyl trifluoromethyl ketone complexes of chymotrypsin

NMR investigations have been carried out of complexes between bovine chymotrypsin Aalpha and a series of four peptidyl trifluoromethyl ketones, listed here in order of increasing affinity for chymotrypsin: N-Acetyl-L-Phe-CF3, N-Acetyl-Gly-L-Phe-CF3, N-Acetyl-L-Val-L-Phe-CF3, and N-Acetyl-L-Leu-L-Phe-CF3. The D/H fractionation factors (phi) for the hydrogen in the H-bond between His 57 and Asp 102 (His 57-Hdelta1) in these four complexes at 5 degreesC were in the range phi = 0.32-0.43, expected for a low-barrier hydrogen bond. For this series of complexes, measurements also were made of the chemical shifts of His 57-Hepsilon1 (delta2,2-dimethylsilapentane-5-sulfonic acid 8.97-9. 18), the exchange rate of the His 57-Hdelta1 proton with bulk water protons (284-12.4 s-1), and the activation enthalpies for this hydrogen exchange (14.7-19.4 kcal.mol-1). It was found that the previously noted correlations between the inhibition constants (Ki 170-1.2 microM) and the chemical shifts of His 57-Hdelta1 (delta2, 2-dimethylsilapentane-5-sulfonic acid 18.61-18.95) for this series of peptidyl trifluoromethyl ketones with chymotrypsin [Lin, J., Cassidy, C. S. & Frey, P. A. (1998) Biochemistry 37, 11940-11948] could be extended to include the fractionation factors, hydrogen exchange rates, and hydrogen exchange activation enthalpies. The results support the proposal of low barrier hydrogen bond-facilitated general base catalysis in the addition of Ser 195 to the peptidyl carbonyl group of substrates in the mechanism of chymotrypsin-catalyzed peptide hydrolysis. Trends in the enthalpies for hydrogen exchange and the fractionation factors are consistent with a strong, double-minimum or single-well potential hydrogen bond in the strongest complexes. The lifetimes of His 57-Hdelta1, which is solvent shielded in these complexes, track the strength of the hydrogen bond. Because these lifetimes are orders of magnitude shorter than those of the complexes themselves, the enzyme must have a pathway for hydrogen exchange at this site that is independent of dissociation of the complexes.