Amino Acid Tautomerization Reactions in Aqueous Solution via Concerted and Assisted Mechanisms Using Free Energy Curves from MD Simulation

Temperature driven transformations of glycine molecules embedded in interstellar ice

The formation of glycine amino acid on ice grains in space raises fundamental questions about glycine chemistry in interstellar media. In this work, we studied glycine conformational space and the related tautomerization mechanisms in water media by means of QM/MM molecular dynamics simulations of four glycine conformational isomers (cc, ct, tc, and tt). Interstellar low density amorphous (LDA) ice and T = 20 K were considered as representative for a cold interstellar ice environment, while temperatures of 250 and 450 K were included to model rapid local heating in the ice. In addition to the LDA environment, water clusters with 4, 17, and 27 H2O molecules were subjected to QM/MM dynamics simulations that allowed glycine tautomerization behaviour to be evaluated in water surface-like environments. The tautomerization processes were found to be strongly dependent on the number of water molecules and specific isomer structure. All the glycine isomers mostly preserve their canonical "neutral" conformations under interstellar conditions.

Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface

We undertake steps to overcome four challenges that have hindered the understanding of ZnO/biomolecule interfaces at the atomic scale: parametrization of a classical force field, ZnO surface termination and amino acid protonation state in methanol, and convergence of enhanced sampling molecular dynamics simulations. We predict adsorption free energies for histidine, serine, cysteine, and tryptophan in remarkable agreement with experimental measurements obtained via a novel indicator-displacement assay. Adsorption is driven by direct surface/amino-acid interactions mediated by terminal hydroxyl groups and stabilized by strongly structured methanol solvation shells.

Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins

Amide-imide tautomerization presents a pervasive class of chemical transformations in organic chemistry of natural compounds. In this Perspective, we describe two distinctively different protein systems, in which the amide-imide tautomerization in the glutamine side chain takes place in enzymatic or photochemical reactions. First, hydrolysis of guanosine triphosphate (GTP) catalyzed by the Ras-GAP protein complex suggests the occurrence of the imide tautomer of glutamine in reaction intermediates. Second, photoexcitation of flavin-binding protein domains (BLUFs) initiates a chain of reactions in the chromophore-binding pocket, including amide-imide tautomerization of glutamine. Mechanisms of these reactions at the atomic level have been revealed in quantum mechanics/molecular mechanics (QM/MM) simulations. To reinforce conclusions on the critical role of amide-imide tautomerization of glutamine in these reactions we describe results of new quantum chemistry and QM/MM calculations for relevant molecular model systems. We reexamine results of the recent IR spectroscopy studies of BLUF domains, which provide experimental evidences of Gln tautomerization in proteins. We also propose to validate the glutamine-assisted mechanism of enzymatic GTP hydrolysis by using IR spectroscopy in a proper range of wavenumbers.

A computational model of the glycine tautomerization reaction in aqueous solution

A theoretical study of the internal proton transfer reaction of glycine (Gly) in aqueous solution was performed by means of steered molecular dynamics (SMD) simulation with solute-solvent interaction potentials derived from AMBER van der Waals parameters and QM/MM electrostatic charges in solution. Thermodynamic calculations and the analysis of the solvation structure, dynamic properties, and vibrational spectra associated with the species involved in the tautomerization process were performed. The results obtained for the Gibbs free energy activation and reaction (ΔG(≠) =5.28 kcal mol⁻¹ and ΔG(R)=-6.65 kcal mol⁻¹), the solute-solvent interaction energy of the different glycine structures, and the hydrogen-bond lifetimes are in agreement with previous studies. These hydrations drive an increase in the diffusion coefficient and a decrease in the time of reorientation when the process takes place in the direction Z-Gly → TS-Gly → N-Gly. The vibrational spectrum associated with the normal modes of the bridge hydrogen atoms shows the N-H stretching at ν(s)=3,470 cm⁻¹ and ν(as)=3,470 cm⁻¹, the O-H stretching at 3,205 cm⁻¹, and the NHO bending at about 1,400 cm⁻¹, in agreement with previously reported data.

Amide-imide tautomerism of acetohydroxamic acid in aqueous solution: quantum calculation and SMD simulations

The kinetics and the thermodynamics of the amide-imide tautomerizations of acetohydroxamic acid in aqueous solution are studied from a theoretical point of view.