Specific Ion Effects on an Oligopeptide: Bidentate Binding Matters for the Guanidinium Cation

Deciphering Spectroscopic Signatures of Competing Ca2+ - Peptide Interactions

Calcium-protein interactions are of paramount importance in biochemistry. They are a key element in a number of biological processes, such as neuronal signaling. Therefore, an understanding of the interaction at the molecular level is highly desirable. Here, we study the zwitterionic model peptide l-alanyl-l-alanine (2Ala), which has two distinct and competing binding sites for Ca2+: The carbonyl of the peptide bond and the C-terminus, the carboxylate group. We perform linear and two-dimensional IR spectroscopy experiments and find that the spectroscopic signatures of both moieties in the IR spectra change in amplitude and peak position upon the addition of CaCl2: A blueshift of the asymmetric carboxylate band and a redshift for the amide I mode. Ab initio molecular dynamics simulations confirm the direct interaction of the Ca2+ ion at both the carboxylate and the amide CO site leading to different spectral responses. The blueshift of the asymmetric carboxylate band is caused by a localization of the charge, leading to a decoupling of the CO stretching modes of the carboxylate group. The slight redshift of the amide I mode of 2Ala upon the addition of CaCl2 contrasts the blueshift that has been observed for isolated amide motifs, such as N-methylacetamide (NMA). This difference is caused by the smaller number of water molecules being replaced by the Ca2+ ion for 2Ala's amide compared to less sterically hindered, isolated amide carbonyls, in conjunction with vibrational Stark effects. Our results highlight the importance of considering potential competing binding sites, such as the amide CO backbone, the termini and residues, as well as the nature of the hydration of both peptide and ion, when exploring ions' interacting with small peptides and larger proteins.

Modeling separation of lanthanides via heterogeneous ligand binding

Individual lanthanide elements have physical/electronic/magnetic properties that make each useful for specific applications. Several of the lanthanides cations (Ln3+) naturally occur together in the same ores. They are notoriously difficult to separate from each other due to their chemical similarity. Predicting the Ln3+ differential binding energies (ΔΔE) or free energies (ΔΔG) at different binding sites, which are key figures of merit for separation applications, will help design of materials with lanthanide selectivity. We apply ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) to calculate ΔΔG for Ln3+ coordinated to ligands in water and embedded in metal-organic frameworks (MOFs), and ΔΔE for Ln3+ bonded to functionalized silica surfaces, thus circumventing the need for the computational costly absolute binding (free) energies ΔG and ΔE. Perturbative AIMD simulations of water-inundated simulation cells are applied to examine the selectivity of ligands towards adjacent Ln3+ in the periodic table. Static DFT calculations with a full Ln3+ first coordination shell, while less rigorous, show that all ligands examined with net negative charges are more selective towards the heavier lanthanides than a charge-neutral coordination shell made up of water molecules. Amine groups are predicted to be poor ligands for lanthanide-binding. We also address cooperative ion binding, i.e., using different ligands in concert to enhance lanthanide selectivity.

Optical rectification and electro-optic sampling in quartz

We report the electro-optic sampling (EOS) response and the terahertz (THz) optical rectification (OR) of the z-cut α-quartz. Due to its small effective second-order nonlinearity, large transparency window and hardness, freestanding thin quartz plates can faithfully measure the waveform of intense THz pulses with MV/cm electric-field strength. We show that both its OR and EOS responses are broad with extension up to ∼8 THz. Strikingly, the latter responses are independent of the crystal thickness, a plausible indication of dominant surface contribution to the total second-order nonlinear susceptibility of quartz at THz frequencies. Our study introduces the crystalline quartz as a reliable THz electro-optic medium for high field THz detection, and characterize its emission as a common substrate.

Guanidinium–amino acid hydrogen-bonding interactions in protein crystal structures: implications for guanidinium-induced protein denaturation

Structural analysis of guanidinium–amino acid interaction pairs in protein crystal structures is coupled with an effective scheme for classifying the optimized pairs, to gain understanding of the guanidinium:protein hydrogen bonding modes.

Ion-specific binding of cations to the carboxylate and of anions to the amide of alanylalanine

Studies of ion-specific effects on oligopeptides have aided our understanding of Hofmeister effects on proteins, yet the use of different model peptides and different experimental sensitivities have led to conflicting conclusions. To resolve these controversies, we study a small model peptide, L-Alanyl-L-alanine (2Ala), carrying all fundamental chemical protein motifs: C-terminus, amide bond, and N-terminus. We elucidate the effect of GdmCl, LiCl, KCl, KI, and KSCN by combining dielectric relaxation, nuclear magnetic resonance (¹H-NMR), and (two-dimensional) infrared spectroscopy. Our dielectric results show that all ions reduce the rotational mobility of 2Ala, yet the magnitude of the reduction is larger for denaturing cations than for anions. The NMR chemical shifts of the amide group are particularly sensitive to denaturing anions, indicative of anion-amide interactions. Infrared experiments reveal that LiCl alters the spectral homogeneity and dynamics of the carboxylate, but not the amide group. Interaction of LiCl with the negatively charged pole of 2Ala, the COO^- group, can explain the marked cationic effect on dipolar rotation, while interaction of anions between the poles, at the amide, only weakly perturbs dipolar dynamics. As such, our results provide a unifying view on ions' preferential interaction sites at 2Ala and help rationalize Hofmeister effects on proteins.

Time-resolved terahertz-Raman spectroscopy reveals that cations and anions distinctly modify intermolecular interactions of water

The solvation of ions changes the physical, chemical and thermodynamic properties of water, and the microscopic origin of this behaviour is believed to be ion-induced perturbation of water's hydrogen-bonding network. Here we provide microscopic insights into this process by monitoring the dissipation of energy in salt solutions using time-resolved terahertz-Raman spectroscopy. We resonantly drive the low-frequency rotational dynamics of water molecules using intense terahertz pulses and probe the Raman response of their intermolecular translational motions. We find that the intermolecular rotational-to-translational energy transfer is enhanced by highly charged cations and is drastically reduced by highly charged anions, scaling with the ion surface charge density and ion concentration. Our molecular dynamics simulations reveal that the water-water hydrogen-bond strength between the first and second solvation shells of cations increases, while it decreases around anions. The opposite effects of cations and anions on the intermolecular interactions of water resemble the effects of ions on the stabilization and denaturation of proteins.

Ion-Specific Effects on Vesicle-to-Micelle Transitions of an Amino Acid Surfactant Probed by Chemical Trapping

Ion-specific effects widely exist in biological and chemical systems and cannot be explained by classical theories. The complexity of ion-specific effects in protein systems at the molecular level necessitates the use of mimetic models involving smaller molecules, such as amino acids, oligopeptides, and other organic molecules bearing amide bonds. Therefore, it is of theoretical value to determine the effect of additional salts on the aggregation transitions of acyl amino acid surfactants. Herein, the effects of specific tetraalkylammonium ions (TAA⁺) on sodium lauroyl glycinate (SLG) aggregation were studied by dynamic light scattering (DLS) and transmission electron microscopy. Although previous studies have shown that the kosmotropic TAA⁺ ions tend to induce micellar growth or micelle-to-vesicle transitions of some anionic surfactants, TAA⁺ addition in the present study induced partial vesicle-to-micelle transitions in SLG solutions. The chemical trapping (CT) method was employed to estimate changes in the interfacial molarities of water, amide bonds, and carboxylate groups during such transitions. The vesicle-to-micelle transitions were accompanied by a marked rise in interfacial water molarity and a decline in interfacial amide bonds molarity, suggesting that the hydrated TAA⁺ entered the interfacial region and disrupted hydrogen bonding, thus preventing the SLG monomers from packing tightly. Molecular dynamic simulation was also performed to demonstrate the salt-induced cleavage of amide-amide bonds between SLG headgroups. Furthermore, both CT and DLS results show that the ability of tetraalkylammonium cations to induce such transitions increased with increasing size and hydrophobicity of the cation, which follows the Hofmeister series. The current study offers critical molecular-level evidence for understanding the specific effects of tetraalkylammonium ions on the aggregation transitions of an acyl amino acid surfactant.

The electrostatic origins of specific ion effects: quantifying the Hofmeister series for anions

Life as we know it is dependent upon water, or more specifically salty water. Without dissolved ions, the interactions between biological molecules are insufficiently complex to support life. This complexity is intimately tied to the variation in properties induced by the presence of different ions. These specific ion effects, widely known as Hofmeister effects, have been known for more than 100 years. They are ubiquitous throughout the chemical, biological and physical sciences. The origin of these effects and their relative strengths is still hotly debated. Here we reconsider the origins of specific ion effects through the lens of Coulomb interactions and establish a foundation for anion effects in aqueous and non-aqueous environments. We show that, for anions, the Hofmeister series can be explained and quantified by consideration of site-specific electrostatic interactions. This can simply be approximated by the radial charge density of the anion, which we have calculated for commonly reported ions. This broadly quantifies previously unpredictable specific ion effects, including those known to influence solution properties, virus activities and reaction rates. Furthermore, in non-aqueous solvents, the relative magnitude of the anion series is dependent on the Lewis acidity of the solvent, as measured by the Gutmann Acceptor Number. Analogous SIEs for cations bear limited correlation with their radial charge density, highlighting a fundamental asymmetry in the origins of specific ion effects for anions and cations, due to competing non-Coulombic phenomena.

Counteranions in the Stimulation Solution Alter the Dynamics of Exocytosis Consistent with the Hofmeister Series

We show that the Hofmeister series of ions can be used to explain the cellular changes in exocytosis observed by single-cell amperometry for different counteranions. The formation, expansion, and closing of the membrane fusion pore during exocytosis was found to be strongly dependent on the counteranion species in solution. With stimulation of chaotropic anions (e.g., ClO₄^–), the expansion and closing time of the fusion pore are longer, suggesting chaotropes can extend the duration of exocytosis compared with kosmotropic anions (e.g., Cl^–). At a concentration of 30 mM, the two parameters (e.g., t_1/2 and t_fall) that define the duration of exocytosis vary with the Hofmeister series (Cl^– < Br^– < NO₃^– ≤ ClO₄^– < SCN^–). More interestingly, fewer (e.g., N_foot/N_events) and smaller (e.g., I_foot) prespike events are observed when chaotropes are counterions in the stimulation solution, and the values can be sorted by the reverse Hofmeister series (Cl^– ≥ Br^– > NO₃^– > ClO₄^– > SCN^–). Based on ion specificity, an adsorption-repulsion mechanism, we suggest that the exocytotic Hofmeister series effect originates from a looser swelling lipid bilayer structure due to the adsorption and electrostatic repulsion of chaotropes on the hydrophobic portion of the membrane. Our results provide a chemical link between the Hofmeister series and the cellular process of neurotransmitter release via exocytosis and provide a better physical framework to understand this important phenomenon.

Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application

The configuration of most current academic high-performance computing (HPC) resources tends to enforce ways of working with, and thinking about, molecular dynamics (MD) simulations that are not always optimal. For example, when the aim of the simulation(s) is to produce a representative sample of a Boltzmann weighted ensemble, the ideal scenario would be to be able to do just that-i.e. to tap into a running simulation of indefinite length, collect data from it in real time, and only terminate the simulation once the quality of a sample was assured. Current approaches, based on batch jobs of proscribed maximum length, and a postprocessing style of data analysis, inhibit this. In the spirit of the Internet of Things, we have developed Tios, a Python application that turns MD simulations into remotely discoverable and accessible streaming web applications to which researchers can connect and download data as they please. Tios is freely available, works with standard MD codes, and requires no modifications to them. In this paper we outline how Tios works and present a number of test cases that demonstrate its capabilities.