Esam A. Orabi

Ammonium transporters achieve charge transfer by fragmenting their substrate.

Proteins of the Amt/MEP family facilitate ammonium transport across the membranes of plants, fungi, and bacteria and are essential for growth in nitrogen-poor environments. Some are known to facilitate the diffusion of the neutral NH(3), while others, notably in plants, transport the positively charged NH(4)(+). On the basis of the structural data for AmtB from Escherichia coli , we illustrate the mechanism by which proteins from the Amt family can sustain electrogenic transport. Free energy calculations show that NH(4)(+) is stable in the AmtB pore, reaching a binding site from which it can spontaneously transfer a proton to a pore-lining histidine residue (His168). The substrate diffuses down the pore in the form of NH(3), while the excess proton is cotransported through a highly conserved hydrogen-bonded His168-His318 pair. This constitutes a novel permeation mechanism that confers to the histidine dyad an essential mechanistic role that was so far unknown.

Molecular modelling of cation–π interactions

Cation–π interactions have long been considered a challenge for molecular modelling and a shortcoming of most of the commonly used biomolecular force fields. In this article, we provide an overview of current research on molecular modelling of cation–π interactions, with an emphasis on applications to proteins and on our recent polarisable models based on the classical Drude oscillator. We describe the main approaches used to model cation–π interactions in solution and illustrate their relevance to a few case studies: the stability of the villin headpiece subdomain, the blockade of potassium channels by quaternary ammonium ions, and the permeation of ammonium across transporters of the Amt/MEP family.

Mechanism of NH4+ Recruitment and NH3 Transport in Rh Proteins

In human cells, membrane proteins of the rhesus (Rh) family excrete ammonium and play a role in pH regulation. Based on high-resolution structures, Rh proteins are generally understood to act as NH3 channels. Given that cell membranes are permeable to gases like NH3, the role of such proteins remains a paradox. Using molecular and quantum mechanical calculations, we show that a crystallographically identified site in the RhCG pore actually recruits NH4(+), which is found in higher concentration and binds with higher affinity than NH3, increasing the efficiency of the transport mechanism. A proton is transferred from NH4(+) to a signature histidine (the only moiety thermodynamically likely to accept a proton) followed by the diffusion of NH3 down the pore. The excess proton is circulated back to the extracellular vestibule through a hydrogen bond network, which involves a highly conserved and functionally important aspartic acid, resulting in the net transport of NH3.

Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia.

A polarizable potential model for M(+)-NH3 interactions (M(+) = Li(+), Na(+), K(+), Rb(+), Cs(+)) is optimized based on the ab initio properties of the ion-ammonia dimers calculated at the MP2 level of theory. The optimized model reproduces the ab initio binding energies of M(+)(NH3)n (n = 2-4) and M(+)(NH3)n(H2O)m (n, m = 1-3 and n + m ≤ 4) clusters and gives relative solvation free energies in liquid ammonia in good agreement with experimental data, without further adjustments. It also reproduces binding cooperativity in ion-ammonia and ion-ammonia-water clusters. The model is used in molecular dynamics simulations of isolated ions in liquid ammonia and in aqueous ammonia solutions with various ammonia molar fractions (0.0 ≤ xNH3 ≤ 1.0). Simulations in liquid ammonia show coordination numbers of 4.0 for Li(+), 5.3 for Na(+), 6.1 for K(+), 6.7 for Rb(+), and 7.7 for Cs(+), in very good agreement with available experimental results. Simulations of ions in aqueous ammonia show preferential solvation by water in their first solvation shells and preferential solvation by ammonia in their second shells. Potentials of mean force are calculated between each ion and NH3 in liquid water, and between each ion and H2O in liquid ammonia. The results suggest that, in liquid water, Li(+) and Na(+) bind NH3 in their second solvation shells only, while Cs(+) binds NH3 in its first solvation shell only (K(+) and Rb(+) ions show only weak affinity for NH3 in water). In liquid ammonia, the ions bind H2O in their first solvation shells with an affinity following the trend Li(+) > Na(+) > K(+) ≈ Rb(+) > Cs(+).

Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia.

A polarizable model for ammonia is optimized based on the ab initio properties of the NH3 molecule and the NH3-NH3 and NH3-H2O dimers calculated at the MP2 level. For larger (NH3)m, NH3(H2O)n, and H2O(NH3)n clusters (m = 2-7 and n = 1-4), the model yields structural and binding energies in good agreement with ab initio calculations without further adjustments. It also reproduces the structure, density, heat of vaporization, self-diffusion coefficient, heat capacity, and isothermal compressibility of liquid ammonia at the boiling point. The model is further validated by calculating some of these properties at various temperatures and pressures spanning the liquid and supercritical phases of the fluid (up to 700 K and 200 MPa). The excellent transferability of the model suggests that it can be used to investigate properties of fluid ammonia under conditions for which experiments are not easy to perform. For aqueous ammonia solutions, the model yields liquid structures and densities in good agreement with experimental data and allows the nonlinearity in the density-composition plot to be interpreted in terms of structural changes with composition. Finally, the model is used to investigate the solvation structure of ammonia in liquid water and of water in liquid ammonia and to calculate the solvation free energy of NH3 and H2O in aqueous ammonia as a function of solution composition and temperature. The simulation results suggest the presence of a transition around 50% molar NH3/H2O compositions, above which water molecules are preferably solvated by ammonia.

Simulation of Liquid and Supercritical Hydrogen Sulfide and of Alkali Ions in the Pure and Aqueous Liquid.

A polarizable model for hydrogen sulfide (H2S) is optimized based on the experimental properties of the monomer and of the bulk liquid. The model is characterized by rigid SH bonds but flexible HSH angle and the polarizability is based on the Drude oscillator model. Bonded parameters and atomic charges are based on the experimental properties of the gaseous monomer. Atomic Lennard-Jones (LJ) parameters are adjusted based on the density of H2S around the critical point (in the temperature range 363-393 K and pressure range 8.023-10.013 MPa). The model gives binding energies for H2S dimers, trimers, and tetramers in good agreement with ab initio MP2(full)/6-311++G(d,p) results. It shows a liquid structure in very good agreement with neutron diffraction data. The model also gives density, self-diffusion coefficient, heat of vaporization, and dielectric constant of liquid hydrogen sulfide at the normal boiling point in good agreement with experimental data. In addition, the model is transferable to high temperature and pressure conditions, as evidenced from simulations up to 542.2 K and 40 MPa. The model is used in combination with the SWM4-NDP water model, with LJ parameters between the S and O atoms adjusted to reproduce the experimental hydration free energy of H2S. Simulations suggest that, in its first solvation shell, a single H2O molecule is solvated by 10 H2S molecules while a single H2S molecule is solvated by 20.5 H2O molecules. Pair-specific LJ parameters between alkali ions (Li(+), Na(+), K(+), Rb(+), Cs(+)) and the S atom are adjusted to reproduce ab initio binding energies of the ion-H2S pairs at the CCSD(T) level. Simulations based on these parameters show that alkali ions have higher coordination numbers and lower solvation free energies in liquid H2S than in liquid water or liquid ammonia. The model is also used to investigate the preferential solvation of the ions in aqueous solutions with a 10% H2S mole fraction. Results show that the ions are preferentially solvated by water in their first solvation shell but have no significant selectivity to either ligands in their second shells.

Modeling Protein S–Aromatic Motifs Reveals Their Structural and Redox Flexibility

S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H2S, MeSH) and Met (Me2S) models with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), and His (imidazole, 4-methylimidazole). The most stable gas-phase conformers exhibit binding energies of -2 to -6 kcal/mol, and the S atom lies perpendicular to the ring plane. This reveals preferential interaction with the ring π-system, except in the imidazoles where S binds edge-on to an N atom. Complexation tunes the gas-phase vertical ionization potentials of the ligands over as much as 1 eV, and strong σ- or π-type H-bonding supports charge transfer to the H-bond donor, rendering it more oxidizable. When the S atom acts as an H-bond acceptor (N/O-Har···S), calibration of the CHARMM36 force field (by optimizing pair-specific Lennard-Jones parameters) is required. Implementing the optimized parameters in molecular dynamics simulations in bulk water, we find stable S-aromatic complexes with binding free energies of -0.6 to -1.1 kcal/mol at ligand separations up to 8 Å. The aqueous S-aromatics exhibit flexible binding conformations, but edge-on conformers are less stable in water. Reflecting this, only 0.3 to 10% of the S-indole, S-phenol, and S-imidazole structures are stabilized by N/O-Har···S or S-H···Oar/Nar σ-type H-bonding. The wide range of energies and geometries found for S-aromatic interactions and their tunable redox properties expose the versatility and variability of the S-aromatic motif in proteins and allow us to predict a number of their reported properties.

Cation−π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution

Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH3+ and RN(CH3)3+) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA+) and tetraethylammonium (TEA+). Polarizable molecular models are calibrated for NH4+, TMA+, and TEA+ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH4+ > TMA+ > TEA+, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA+ (the largest ion), the most stable solvent-separated complexes involve TMA+ (the intermediate-size ion).

A Simple Additive Potential Model for Simulating Hydrogen Peroxide in Chemical and Biological Systems

Hydrogen peroxide (H2O2) has numerous industrial, environmental, medical, cosmetic, and biological applications. Given its importance, we provide a simple model as an alternative to experiment for studying the properties of pure liquid H2O2 and its concentrated aqueous solutions, which are hazardous, and for understanding the biological roles of H2O2 at the molecular level. A four-site additive model is calibrated for H2O2 based on the ab initio and experimental properties of the gaseous monomer and the density and heat of vaporization of liquid H2O2 at 0 °C. Our model together with the TIP3P water model reproduce the ab initio binding energies of (H2O2) m, H2O2· nH2O, and nH2O2·H2O clusters ( m = 2, 3 and n = 1, 2) calculated at the MP2 level using the 6-311++G(d,p) or the 6-311++G(3df,3pd) basis set. It yields structure, the self-diffusion coefficient, heat capacity, and densities at temperatures up to 200 °C of the pure liquid in good agreement with experiment. The model correctly predicts the hydration free energy of H2O2 and reproduces the experimental density of aqueous H2O2 solutions at 0-96 °C. Investigation of the solvation of H2O2 and H2O in aqueous H2O2 solutions reveals that, as in the gas phase, H2O2 is a better H-bond donor but poorer acceptor than H2O and the bonding stability follows the order Op-Hp···Ow > Ow-Hw···Ow ≥ Op-Hp···Op > Ow-Hw···Op. Stronger H-bonding in H2O/H2O2 mixtures than in the pure liquids is consistent with exothermic heats of mixing and explains why the observed density and vapor pressure of the aqueous solutions are higher and lower, respectively, than expected from ideal mixing. Results also show that H2O2 adopts a skewed equilibrium geometry in gas and liquid phases but more polar cis and nonpolar trans conformations also are accessible and will stabilize H2O2 in environments of different polarity. In sum, our simple model presents a reliable tool for simulating H2O2 in chemistry and biology.