Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations

Diazanaphthalenes: A 13C NMR investigation on the site of protonation and pKa values

The pH dependence of the 13C chemical shifts (δ) of the diazanaphthalenes has been recorded. From this dependence the pKa values have been determined using the Henderson-Hasselbach equation. The change in 13C chemical shifts under the influence of nitrogen protonation (Δδ) has been predicted using the Δδ values of quinoline and isoquinoline. The correlation between observed and expected Δδ values of the symmetric diazanaphthalenes is very good. Assuming these changes in chemical shifts to be of general validity, the site of protonation in the asymmetric diazanaphthalenes has been determined by comparison of the expected Δδ values for α- and ß-nitrogen protonation with the observed ones. The site of protonation for 1,6- and 1,7-naphthyridine is the ß-nitrogen atom, whereas for cinnoline both monoprotonated species are present in a significant amount

Protonation and ring closure of stereoisomeric alpha-substituted cinnamic acids in superacidic media studied by 13C NMR spectroscopy and computations

Five alpha-substituted cinnamic acids [(E)- and (Z)-2,3-diphenyl-, (E)- and (Z)-3-(2-methoxyphenyl)-2-phenyl- and (E)-2-(2-methoxyphenyl)-3-phenyl-propenoic acids] have been protonated in fluorosulfonic acid at -78 degrees C, Protonation of the carboxylic group and a second protonation on the methoxy group at -78 degrees C or the ring bearing the methoxy group at 0 degrees C have been observed by C-13 NMR spectroscopy Upon protonation (Z)-alpha-phenylcinnamic acid is transformed to a protonated indenol derivative, Dehydrative ring closure begins at -78 degrees C and goes to completion at 0 degrees C, Similar transformations of the other studied Z-acid are suppressed by the deactivating effect of the protonated methoxy group. Only protonation has been observed for the E-acids at -78 degrees C as well as 0 degrees C, Calculations at the HF/3-21G level provide the equilibrium structures of the corresponding cations, Results of IGLO/C-13 NMR shift calculations are in good agreement with the experimental findings

Carbon-13 n.m.r. investigation on the nitrogen methylation of the mono- and diazanaphthalenes

The 13C n.m.r. spectra of the N-methylated mono- and diazanaphthalenes have been recorded and analysed. It has been shown that N-methylation as well as N-protonation in cinnoline occur predominantly at the -nitrogen atom. N-methylation and N-protonation show a similar effect on the 13C chemical shift

Electron transport through dipyrimidinyl-diphenyl diblock molecular wire: protonation effect

Recently, rectifying direction inversion has been observed in dipyrimidinyl-diphenyl (PMPH) diblock molecular wire [J. Am. Chem. Soc. (2005) 127, 10456], and a protonation mechanism was suggested to explain this interesting phenomena. In this paper, we study the protonation effect on transport properties of PMPH molecule by first principles calculations. No significant rectification is found for the pristine diblock molecular wire. Protonation leads to conductance enhancement and rectification. However, for all considered junctions with rectifying effect, the preferential current directions are samely from dipyrimidinyl side to diphenyl side. Effect of molecule-electrode anchoring geometry is studied, and it is not responsible for the discrepancy between experiment and theory.Comment: 17 pages, 8 figure

Hydrogen Generation Catalyzed by Fluorinated Diglyoxime−Iron Complexes at Low Overpotentials

Fe^(II) complexes containing the fluorinated ligand 1,2-bis(perfluorophenyl)ethane-1,2-dionedioxime (dAr^FgH_2; H = dissociable proton) exhibit relatively positive Fe^(II/I) reduction potentials. The air-stable difluoroborated species [(dAr^FgBF_2)_2Fe(py)_2] (2) electrocatalyzes H_2 generation at −0.9 V vs SCE with i_(cat)/i_p ≈ 4, corresponding to a turnover frequency (TOF) of ~ 20 s^(–1) [Faradaic yield (FY) = 82 ± 13%]. The corresponding monofluoroborated, proton-bridged complex [(dArFg2H-BF2)Fe(py)2] (3) exhibits an improved TOF of ~ 200 s^(–1) (i_(cat)/i_p ≈ 8; FY = 68 ± 14%) at −0.8 V with an overpotential of 300 mV. Simulations of the electrocatalytic cyclic voltammograms of 2 suggest rate-limiting protonation of an Fe“0” intermediate (k_(RLS) ≈ 200 M^(–1) s^(–1)) that undergoes hydride protonation to form H_2. Complex 3 likely reacts via protonation of an Fe^I intermediate that subsequently forms H_2 via a bimetallic mechanism (k_(RLS) ≈ 2000 M^(–1) s^(–1)). 3 catalyzes production at relatively positive potentials compared with other iron complexes

DFT Study of Nitroxide Radicals. 1. Effects of solvent on structural and electronic characteristics of 4-amino-2,2,5,5-tetramethyl-3-imidazoline-N-oxyl

Imidazoline-based nitroxide radicals are often used as spin probes for medium acidity and polarity in different systems. In this work, using the density functional theory (DFT) approach, we have studied how physico-chemical characteristics (geometry, atomic charges and electron spin density distribution) of pH-sensitive spin label 4-amino-2,2,5,5-tetramethyl-3-imidazoline-N-oxyl (ATI) depend on protonation and aqueous surroundings. Our calculations demonstrate that ATI protonation should occur at the nitrogen atom of the imidazoline ring rather than at the amino group. Protonation of ATI leads to a decrease in a spin density on the nitrogen atom of the nitroxide fragment >N-O. For simulation of ATI hydration effects, we have constructed a water shell around a spin label molecule by means of gradual (step-by-step) surrounding of ATI with water molecules (n = 2-41). Calculated spin density on the nitrogen atom of the nitroxide fragment increased with an extension of a water shell around ATI. Both protonation and hydration of ATI caused certain changes in calculated geometric parameters (bond lengths and valence angles). Investigating how structural and energy parameters of a system ATI-(H2O)n depend on a number of surrounding water molecules, we came to the conclusion that a hydrogen-bonded cluster of n ≥ 41 water molecules could be considered as an appropriate model for simulation of ATI hydration effects.Comment: 30 pages, 11 figures, 6 table

Electrochemistry of potential bioreductive alkylating quinones : Part 2. Electrochemical properties of 2,5-bis(1-aziridinyl)-3,6-bis(ethoxycarbonylamino)-1,4-benzoquinone and some model compounds

The reduction mechanism of 2,5-bis(1-aziridinyl)-3,6-bis(ethoxycarbonylamino)-1,4-benzoquinone (Diaziquone, AZQ) and several model compounds of the mono- and bis(1-aziridinyl)quinone type at the dropping mercury electrode in aqueous solutions was studied. In addition, the influence of methyl substitution of the aziridinyl moiety at the 2-position on the protonation of the aziridine nitrogen was investigated. Substituent effects on quinone reduction and aziridine protonation prior to and following quinone reduction were studied qualitatively

Proton Availability at the Air/Water Interface

The acidity of the water surface sensed by a colliding gas is determined in experiments in which the protonation of gaseous trimethylamine (TMA) on aqueous microjets is monitored by online electrospray mass spectrometry as a function of the pH of the bulk liquid (pH_(BLK)). TMAH^+ signal intensities describe a titration curve whose equivalence point at pH_(BLK) 3.8 is dramatically smaller than the acidity constant of trimethylammonium in bulk solution, pK_A(TMAH^+) = 9.8. Notably, the degree of TMA protonation above pH_(BLK) 4 is enhanced hundred-fold by submillimolar LiCl or NaCl and weakly inhibited at larger concentrations. Protonation enhancements are associated with the onset of significant direct kinetic solvent hydrogen isotope effects. Since TMA(g) can be protonated by H_2O itself only upon extensive solvent participation, we infer that H3O^+ emerges at the surface of neat water below pH_(BLK) 4

Ocean acidification affects marine chemical communication by changing structure and function of peptide signalling molecules

Ocean acidification is a global challenge that faces marine organisms in the near future with a predicted rapid drop in pH of up to 0.4 units by the end of this century. Effects of the change in ocean carbon chemistry and pH on the development, growth and fitness of marine animals are well documented. Recent evidence also suggests that a range of chemically mediated behaviours and interactions in marine fish and invertebrates will be affected. Marine animals use chemical cues, for example, to detect predators, for settlement, homing and reproduction. But while effects of high CO₂ conditions on these behaviours are described across many species, little is known about the underlying mechanisms, particularly in invertebrates. Here we investigate the direct influence of future oceanic pH conditions on the structure and function of three peptide signalling molecules with an interdisciplinary combination of methods. NMR spectroscopy and quantum chemical calculations were used to assess the direct molecular influence of pH on the peptide cues and we tested the functionality of the cues in different pH conditions using behavioural bioassays with shore crabs (Carcinus maenas) as a model system. We found that peptide signalling cues are susceptible to protonation in future pH conditions, which will alter their overall charge. We also show that structure and electrostatic properties important for receptor-binding differ significantly between the peptide forms present today and the protonated signalling peptides likely to be dominating in future oceans. The bioassays suggest an impaired functionality of the signalling peptides at low pH. Physiological changes due to high CO₂ conditions were found to play a less significant role in influencing the investigated behaviour. From our results we conclude that the change of charge, structure and consequently function of signalling molecules presents one possible mechanism to explain altered behaviour under future oceanic pH conditions