Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1.

SUCROSE-NON-FERMENTING1-RELATED PROTEIN KINASE1 (SnRK1), a central plant metabolic sensor kinase, phosphorylates its target proteins, triggering a global shift from anabolism to catabolism. Molecular modeling revealed that upon binding of KIN10 to GEMINIVIRUS REP-INTERACTING KINASE1 (GRIK1), KIN10's activation T-loop reorients into GRIK1's active site, enabling its phosphorylation and activation. Trehalose 6-phosphate (T6P) is a proxy for cellular sugar status and a potent inhibitor of SnRK1. T6P binds to KIN10, a SnRK1 catalytic subunit, weakening its affinity for GRIK1. Here, we investigate the molecular details of T6P inhibition of KIN10. Molecular dynamics simulations and in vitro phosphorylation assays identified and validated the T6P binding site on KIN10. Under high-sugar conditions, T6P binds to KIN10, blocking the reorientation of its activation loop and preventing its phosphorylation and activation by GRIK1. Under these conditions, SnRK1 maintains only basal activity levels, minimizing phosphorylation of its target proteins, thereby facilitating a general shift from catabolism to anabolism.

Influence of Peptoid Sequence on the Mechanisms and Kinetics of 2D Assembly.

Two-dimensional (2D) materials have attracted intense interest due to their potential for applications in fields ranging from chemical sensing to catalysis, energy storage, and biomedicine. Recently, peptoids, a class of biomimetic sequence-defined polymers, have been found to self-assemble into 2D crystalline sheets that exhibit unusual properties, such as high chemical stability and the ability to self-repair. The structure of a peptoid is close to that of a peptide except that the side chains are appended to the amide nitrogen rather than the α carbon. In this study, we investigated the effect of peptoid sequence on the mechanism and kinetics of 2D assembly on mica surfaces using in situ AFM and time-resolved X-ray scattering. We explored three distinct peptoid sequences that are amphiphilic in nature with hydrophobic and hydrophilic blocks and are known to self-assemble into 2D sheets. The results show that their assembly on mica starts with deposition of aggregates that spread to establish 2D islands, which then grow by attachment of peptoids, either monomers or unresolvable small oligomers, following well-known laws of crystal step advancement. Extraction of the solubility and kinetic coefficient from the dependence of the growth rate on peptoid concentration reveals striking differences between the sequences. The sequence with the slowest growth rate in bulk and with the highest solubility shows almost no detachment; i.e., once a growth unit attaches to the island edge, there is almost no probability of detaching. Furthermore, a peptoid sequence with a hydrophobic tail conjugated to the final carboxyl residue in the hydrophilic block has enhanced hydrophobic interactions and exhibits rapid assembly both in the bulk and on mica. These assembly outcomes suggest that, while the π-π interactions between adjacent hydrophobic blocks play a major role in peptoid assembly, sequence details, particularly the location of charged groups, as well as interaction with the underlying substrate can significantly alter the thermodynamic stability and assembly kinetics.

Development of a Systematic and Extensible Force Field for Peptoids (STEPs).

Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. Equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.

Regioselectivity mechanism of the Thunbergia alata Δ6-16:0-acyl carrier protein desaturase.

Plant plastidial acyl-acyl carrier protein (ACP) desaturases are a soluble class of diiron-containing enzymes that are distinct from the diiron-containing integral membrane desaturases found in plants and other organisms. The archetype of this class is the stearoyl-ACP desaturase which converts stearoyl-ACP into oleoyl (18:1Δ9cis)-ACP. Several variants expressing distinct regioselectivity have been described including a Δ6-16:0-ACP desaturase from black-eyed Susan vine (Thunbergia alata). We solved a crystal structure of the T. alata desaturase at 2.05 Å resolution. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position C6 and C7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Δ6 desaturase to Δ9 regioselectivity. Additional modeling between ACP and the mutant variants confirmed the predicted regioselectivity. To validate the in-silico predictions, we synthesized two variants of the T. alata desaturase and analyzed their reaction products using gas chromatography-coupled mass spectrometry. Assay results confirmed that mutants designed to convert T. alata Δ6 to Δ9 selectivity exhibited the predicted changes. In complementary experiments, variants of the castor desaturase designed to convert Δ9 to Δ6 selectivity lost some of their Δ9 desaturation ability and gained the ability to desaturate at the Δ6 position. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.

Protonation of Serine in Gas and Condensed and Microsolvated States in Aqueous Solution.

Identification of molecules and elucidation of their chemical structure are ubiquitous problems in chemistry. Mass spectrometry (MS) can be used due to its sensitivity and versatility. For detection to occur, analytes must be ionized and transferred to the gas phase. Soft ionization processes such as electrospray ionization are popular; however, resulting microsolvated phases can alter the chemistry of analytes and therefore detection and identification. To understand these processes, we use computational methods to probe the ionization propensity of serine in the gas phase, aqueous microsolvated clusters, and aqueous solution. We show that the tautomeric form of serine is altered by the presence of water, as five water molecules can stabilize the zwitterionic tautomer. Inclusion of cosolutes such as ions can stabilize the zwitterion with as few as one or two water molecules present. We demonstrate that ionization propensity, as measured by gas phase bacisity, can increase by over 100 kJ/mol when placed in a small water-serine cluster, showing the sensitivity of the chemistry of microsolvated analytes. Finally, detailed analysis reveals that small droplets (less than seven water molecules) are extremely sensitive to addition of further water molecules. Beyond this limit, structural and electronic properties change little with droplet size.

Role of Hydration in Magnesium versus Calcium Ion Pairing with Carboxylate: Solution and the Aqueous Interface.

The binding of group II metal cations such as Ca2+ and Mg2+ has been largely categorized as electrostatic or ionic using carboxylate symmetric and asymmetric stretching frequency assignments that have been historically used with little regard for the solvation environment of aqueous solutions. However, given the importance of these cations and their binding mechanisms related to biological function and in revealing surface enrichment factors for ocean to marine aerosol transfer, it is imperative that a deeper understanding be sought to include hydration effects. Here, infrared reflection-absorption and Raman spectra for surface and solution phase carboxylate binding information, respectively, are compared against bare (unbound) carboxylate and bidentate Zn2+:carboxylate spectral signatures. Spectral non-coincidence effect analysis, temperature studies, and spectral and potential of mean force calculations result in a concise interpretation of binding motifs that include the role of mediating water molecules, that is, contact and solvent-shared ion pairs. Calcium directly binds to the carboxylate group in contact ion pairs where magnesium rarely does. Moreover, we reveal the dominance of the solvent-shared ion pair of magnesium with carboxylate at the air-water interface and in solution.

Early-Stage Aggregation and Crystalline Interactions of Peptoid Nanomembranes.

Fully synthetic peptoid membranes are known to mimic important features of biological membranes, with several advantages over other biomimetic membranes. A fundamental understanding of how the individual peptoid amphiphiles assemble in solution to form the bilayer membrane is key to unlocking their versatility for application in a broad range of processes. In this study, in situ X-ray scattering and molecular dynamics simulations are used to understand the early stages of assembly of three different peptoids that exhibit distinctly different crystallization kinetics. The in situ measurements reveal that the peptoids aggregate first into a nascent phase that is less crystalline than the assembled peptoid membrane. Anisotropic aromatic interactions are determined to be the dominant driving force in the early stages of membrane formation. These results provide key insights into how the peptoid assembly may be manipulated during the early stages of assembly and nucleation and growth.

Atomistic insight on structure and dynamics of spinach acyl carrier protein with substrate length.

The plant acyl-acyl carrier protein (ACP) desaturases are a family of soluble enzymes that convert saturated fatty acyl-ACPs into their cis-monounsaturated equivalents in an oxygen-dependent reaction. These enzymes play a key role in biosynthesis of monounsaturated fatty acids in plants. ACPs are central proteins in fatty acid biosynthesis that deliver acyl chains to desaturases. They have been reported to show a varying degree of local dynamics and structural variability depending on the acyl chain size. It has been suggested that substrate-specific changes in ACP structure and dynamics have a crucial impact on the desaturase enzymatic activity. Using molecular dynamics simulations, we investigated the intrinsic solution structure and dynamics of ACP from spinach with four different acyl chains: capric (C10), myristic (C14), palmitic (C16), and stearic (C18) acids. We found that the fatty acids can adopt two distinct structural binding motifs, which feature different binding free energies and influence the ACP dynamics in a different manner. Docking simulations of ACP to castor Δ9-desaturase and ivy Δ4-desaturase suggest that ACP desaturase interactions could lead to a preferential selection between the motifs.

Solvent reaction coordinate for an SN2 reaction.

We study the prototypical SN2 reaction Cl- + CH3Cl → CH3Cl + Cl- in water using quantum mechanics/molecular mechanics (QM/MM) computer simulations with transition path sampling and inertial likelihood maximization. We have identified a new solvent coordinate to complement the original atom-exchange coordinate used in the classic analysis by Chandrasekhar, Smith, and Jorgensen [J. Am. Chem. Soc. 107, 154 (1985)]. The new solvent coordinate quantifies instantaneous solvent-induced polarization relative to the equilibrium average charge density at each point along the reaction pathway. On the basis of likelihood scores and committor distributions, the new solvent coordinate improves upon the description of solvent dynamical effects relative to previously proposed solvent coordinates. However, it does not increase the transmission coefficient or the accuracy of a transition state theory rate calculation.

Resolving Heterogeneous Dynamics of Excess Protons in Aqueous Solution with Rate Theory.

Rate theories have found great utility across the chemical sciences by providing a physically transparent way to analyze dynamical processes. Here we demonstrate the benefits of using transition state theory and Marcus theory to study the rate of proton transfer in HCl solutions. By using long ab initio molecular dynamics simulations, we show that good agreement is obtained between these two different formulations of rate theory and how they can be used to study the pathways and lifetime of proton transfer in aqueous solution. Since both rate theory formulations utilize identical sets of molecular data, this provides a self-consistent theoretical picture of the rates of aqueous phase proton transfer. Specifically, we isolate and quantify the rates of proton transfer, ion-pair dissociation, and solvent exchange in concentrated HCl solutions. Our analysis predicts a concentration dependence to both proton transfer and ion-pairing. Moreover, our estimate of the lifetime for the Zundel species is 0.8 and 1.3 ps for 2 M and 8 M HCl, respectively. We demonstrate that concentration effects can indeed be quantified through the combination of state-of-the-art simulation and theory and provides a picture of the important correlations between the cation (hydronium) and the counterion in acid solutions.

Visualization of Aluminum Ions at the Mica Water Interface Links Hydrolysis State-to-Surface Potential and Particle Adhesion.

When hydrolyzable cations such as aluminum interact with solid-water interfaces, macroscopic interfacial properties (e.g., surface charge and potential) and interfacial phenomena (e.g., particle adhesion) become tightly linked with the microscopic details of ion adsorption and speciation. We use in situ atomic force microscopy to directly image individual aluminum ions at a mica-water interface and show how adsorbate populations change with pH and aluminum activity. Complementary streaming potential measurements then allow us to build a triple layer model (TLM) that links surface potentials to adsorbate populations, via equilibrium binding constants. Our model predicts that hydrolyzed species dominate the mica-water interface, even when unhydrolyzed species dominate the solution. Ab initio molecular dynamics (AIMD) simulations confirm that aluminum hydrolysis is strongly promoted at the interface. The TLM indicates that hydrolyzed adsorbates are responsible for surface-potential inversions, and we find strong correlations between hydrolyzed adsorbates and particle-adhesion forces, suggesting that these species mediate adhesion by chemical bridging.

Quantifying the hydration structure of sodium and potassium ions: taking additional steps on Jacob's Ladder.

The ability to reproduce the experimental structure of water around the sodium and potassium ions is a key test of the quality of interaction potentials due to the central importance of these ions in a wide range of important phenomena. Here, we simulate the Na+ and K+ ions in bulk water using three density functional theory functionals: (1) the generalized gradient approximation (GGA) based dispersion corrected revised Perdew, Burke, and Ernzerhof functional (revPBE-D3) (2) the recently developed strongly constrained and appropriately normed (SCAN) functional (3) the random phase approximation (RPA) functional for potassium. We compare with experimental X-ray diffraction (XRD) and X-ray absorption fine structure (EXAFS) measurements to demonstrate that SCAN accurately reproduces key structural details of the hydration structure around the sodium and potassium cations, whereas revPBE-D3 fails to do so. However, we show that SCAN provides a worse description of pure water in comparison with revPBE-D3. RPA also shows an improvement for K+, but slow convergence prevents rigorous comparison. Finally, we analyse cluster energetics to show SCAN and RPA have smaller fluctuations of the mean error of ion-water cluster binding energies compared with revPBE-D3.

Molecular-level origin of the carboxylate head group response to divalent metal ion complexation at the air-water interface.

We exploit gas-phase cluster ion techniques to provide insight into the local interactions underlying divalent metal ion-driven changes in the spectra of carboxylic acids at the air-water interface. This information clarifies the experimental findings that the CO stretching bands of long-chain acids appear at very similar energies when the head group is deprotonated by high subphase pH or exposed to relatively high concentrations of Ca2+ metal ions. To this end, we report the evolution of the vibrational spectra of size-selected [Ca2+·RCO2-]+·(H2O) n=0to12 and RCO2-·(H2O) n=0to14 cluster ions toward the features observed at the air-water interface. Surprisingly, not only does stepwise hydration of the RCO2- anion and the [Ca2+·RCO2-]+ contact ion pair yield solvatochromic responses in opposite directions, but in both cases, the responses of the 2 (symmetric and asymmetric stretching) CO bands to hydration are opposite to each other. The result is that both CO bands evolve toward their interfacial asymptotes from opposite directions. Simulations of the [Ca2+·RCO2-]+·(H2O) n clusters indicate that the metal ion remains directly bound to the head group in a contact ion pair motif as the asymmetric CO stretch converges at the interfacial value by n = 12. This establishes that direct metal complexation or deprotonation can account for the interfacial behavior. We discuss these effects in the context of a model that invokes the water network-dependent local electric field along the C-C bond that connects the head group to the hydrocarbon tail as the key microscopic parameter that is correlated with the observed trends.

The Diverse Nature of Ion Speciation at the Nanoscale Hydrophobic/Water Interface.

Many biological systems are composed of nanoscale structures having hydrophobic and hydrophilic groups adjacent to one another and in contact with aqueous electrolyte solution. The interaction of ions with such structures is of fundamental importance. Although many studies have focused on characterizing planar extended (often air/water) interfaces, little is known about ion speciation at complex nanoscale biological systems. To start understanding the complex mechanisms involved, we use a hexadecane nanodroplet system, stabilized with a dilute monolayer of positively charged dodecyltrimethylammonium cations (DTA+) groups in contact with an electrolyte solution (NaSCN). Using vibrational sum frequency scattering, second harmonic scattering, ζ-potential measurements, and quantum density functional theory, we find DTA+-SCN- ion pairing at concentrations as low as 5 mM. A variety of ion species emerge at different ionic strengths, with differently oriented SCN- groups adsorbed on hydrophilic or hydrophobic parts of the surface. This diverse and heterogeneous chemical environment is surprisingly different from the behavior at extended liquid planar interfaces, where ion pairing is typically detected at molar concentrations and nanoscale system stability is no requirement.

Direct Observation of the Orientational Anisotropy of Buried Hydroxyl Groups inside Muscovite Mica.

Muscovite mica (001) is a widely used model surface for controlling molecular assembly and a common substrate for environmental adsorption processes. The mica (001) surface displays near-trigonal symmetry, but many molecular adsorbates-including water-exhibit unequal probabilities of alignment along its three nominally equivalent lattice directions. Buried hydroxyl groups within the muscovite structure are speculated to be responsible, but direct evidence is lacking. Here, we utilize vibrational sum frequency generation spectroscopy (vSFG) to characterize the orientation and hydrogen-bonding environment of near-surface hydroxyls inside mica. Multiple distinct peaks are detected in the O-H stretch region, which we attribute to Si/Al substitution in the SiO4 tetrahedron and K+ ion adsorption above the hydroxyls based on density functional theory simulations. Our findings demonstrate that vSFG can identify the absolute orientation of -OH groups and, hence, the surface termination at a mica surface, providing a means to investigate how -OH groups influence molecular adsorption and better understand mica stacking-sequences and physical behavior.

Detecting the undetectable: The role of trace surfactant in the Jones-Ray effect.

The surface tension of dilute salt water is a fundamental property that is crucial to understanding the complexity of many aqueous phase processes. Small ions are known to be repelled from the air-water surface leading to an increase in the surface tension in accordance with the Gibbs adsorption isotherm. The Jones-Ray effect refers to the observation that at extremely low salt concentration, the surface tension decreases. Determining the mechanism that is responsible for this Jones-Ray effect is important for theoretically predicting the distribution of ions near surfaces. Here we use both experimental surface tension measurements and numerical solution of the Poisson-Boltzmann equation to demonstrate that very low concentrations of surfactant in water create a Jones-Ray effect. We also demonstrate that the low concentrations of the surfactant necessary to create the Jones-Ray effect are too small to be detectable by surface sensitive spectroscopic measurements. The effect of surface curvature on this behavior is also examined, and the implications for unexplained bubble phenomena are discussed. This work suggests that the purity standards for water may be inadequate and that the interactions between ions with background impurities are important to incorporate into our understanding of the driving forces that give rise to the speciation of ions at interfaces.

Understanding the scale of the single ion free energy: A critical test of the tetra-phenyl arsonium and tetra-phenyl borate assumption.

The tetra-phenyl arsonium and tetra-phenyl borate (TATB) assumption is a commonly used extra-thermodynamic assumption that allows single ion free energies to be split into cationic and anionic contributions. The assumption is that the values for the TATB salt can be divided equally. This is justified by arguing that these large hydrophobic ions will cause a symmetric response in water. Experimental and classical simulation work has raised potential flaws with this assumption, indicating that hydrogen bonding with the phenyl ring may favor the solvation of the TB- anion. Here, we perform ab initio molecular dynamics simulations of these ions in bulk water demonstrating that there are significant structural differences. We quantify our findings by reproducing the experimentally observed vibrational shift for the TB- anion and confirm that this is associated with hydrogen bonding with the phenyl rings. Finally, we demonstrate that this results in a substantial energetic preference of the water to solvate the anion. Our results suggest that the validity of the TATB assumption, which is still widely used today, should be reconsidered experimentally in order to properly reference single ion solvation free energy, enthalpy, and entropy.

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation.

Peptoids are peptide-mimetic biopolymers that are easy to synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semiempirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with a hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids toward these conformations.

Supersaturated calcium carbonate solutions are classical.

Mechanisms of CaCO3 nucleation from solutions that depend on multistage pathways and the existence of species far more complex than simple ions or ion pairs have recently been proposed. Herein, we provide a tightly coupled theoretical and experimental study on the pathways that precede the initial stages of CaCO3 nucleation. Starting from molecular simulations, we succeed in correctly predicting bulk thermodynamic quantities and experimental data, including equilibrium constants, titration curves, and detailed x-ray absorption spectra taken from the supersaturated CaCO3 solutions. The picture that emerges is in complete agreement with classical views of cluster populations in which ions and ion pairs dominate, with the concomitant free energy landscapes following classical nucleation theory.

Water Lone Pair Delocalization in Classical and Quantum Descriptions of the Hydration of Model Ions.

Understanding the nature of ionic hydration at a fundamental level has eluded scientists despite intense interest for nearly a century. In particular, the microscopic origins of the asymmetry of ion solvation thermodynamics with respect to the sign of the ionic charge remains a mystery. Here, we determine the response of accurate quantum mechanical water models to strong nanoscale solvation forces arising from excluded volumes and ionic electrostatic fields. This is compared to the predictions of two important limiting classes of classical models of water with fixed point changes, differing in their treatment of "lone pair" electrons. Using the quantum water model as our standard of accuracy, we find that a single fixed classical treatment of lone pair electrons cannot accurately describe solvation of both apolar and cationic solutes, emphasizing the need for a more flexible description of local electronic effects in solvation processes. However, we explicitly show that all water models studied respond to weak long-ranged electrostatic perturbations in a manner that follows macroscopic dielectric continuum models, as would be expected. We emphasize the importance of these findings in the context of realistic ion models, using density functional theory and empirical models, and discuss the implications of our results for quantitatively accurate reduced descriptions of solvation in dielectric media.