Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy

The influence of KCl concentration on the gelation of myofibrillar protein giant squid (Dosidicus gigas) due to molecular conformation change

Introduction

Protein gelation process is of importance in food industry. The objective of this study is to investigate the influence of salt concentration variation, which induced protein conformation change, on protein's intermolecular interactions and its gelation process.

Methods

Paramyosin has been separated and purified from myofibrillar protein extracted from giant squid. Then Giant squid's paramyosin molecular mass and intermolecular interactions were quantified by means of light scattering techniques. Finally, the micro-rheology study via diffusing wave spectroscopy (DWS) technique revealed that this conformation change dramatically affected myofibrillar protein gelation process.

Results

The obtained apparent molecular weight (ca 2 × 10⁵ g/mol) suggested that protein molecules existed as dimers, while the second virial coefficient A2 significantly reduced from -3.98456 × 10^-5 to -5.07575 × 10^-4 ml mol/g² when KCl concentrated from 0.15 to 1 mol/L. Light scattering data also suggest that paramyosin dimers are stiff, with a persistence length of 120 nm, almost the length of a molecule and independent of salt concentration. Mean-square displacement (MSD) of tracer particles at 5 temperatures with 4 salt concentrations displayed that this conformation change had dramatic effect. Therefore, G' and G" were remarkably altered with at least one order of magnitude difference owing to this event occurrence.

Conclusions

Paramyosin conformation change due to KCl concentrated enhances attractive interactions with apparent molecular mass increase, which resulted in majority paramyosin molecules (> 99%) in dimeric form and promoted aggregates formation. DWS technique revealed that the conformation change dramatic affected this process characterized by the correlation functions, MSD, and G' and G". This study brings forward data on understanding the effect of a major salt supplement, KCl, on the chemical physics of a major muscle protein.

Nitrogen K-Edge X-ray Absorption Spectra of Ammonium and Ammonia in Water Solution: Assessing the Performance of Polarizable Embedding Coupled Cluster Methods

The recent development of liquid jet and liquid leaf sample delivery systems allows for accurate measurements of soft X-ray absorption spectra in transmission mode of solutes in a liquid environment. As this type of measurement becomes increasingly accessible, there is a strong need for reliable theoretical methods for assisting in the interpretation of the experimental data. Coupled cluster methods have been extensively developed over the past decade to simulate X-ray absorption in the gas phase. Their performance for solvated species, on the contrary, remains largely unexplored. Here, we investigate the current state of the art of coupled cluster modeling of nitrogen K-edge X-ray absorption of aqueous ammonia and ammonium based on quantum mechanics/molecular mechanics, where both the level of coupled cluster calculations and polarizable embedding are scrutinized. The results are compared to existing experimental data as well as simulations based on transition potential density functional theory.

The Interfacial Interactions of Glycine and Short Glycine Peptides in Model Membrane Systems

The interactions of amino acids and peptides at model membrane interfaces have considerable implications for biological functions, with the ability to act as chemical messengers, hormones, neurotransmitters, and even as antibiotics and anticancer agents. In this study, glycine and the short glycine peptides diglycine, triglycine, and tetraglycine are studied with regards to their interactions at the model membrane interface of Aerosol-OT (AOT) reverse micelles via ¹H NMR spectroscopy, dynamic light scattering (DLS), and Langmuir trough measurements. It was found that with the exception of monomeric glycine, the peptides prefer to associate between the interface and bulk water pool of the reverse micelle. Monomeric glycine, however, resides with the N-terminus in the ordered interstitial water (stern layer) and the C-terminus located in the bulk water pool of the reverse micelle.

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

Ion-protein interactions are important for protein function, yet challenging to rationalize owing to the multitude of possible ion-protein interactions. To explore specific ion effects on protein binding sites, we investigate the interaction of different salts with the zwitterionic peptide triglycine in solution. Dielectric spectroscopy shows that salts affect the peptide's reorientational dynamics, with a more pronounced effect for denaturing cations (Li⁺ , guanidinium (Gdm⁺ )) and anions (I^- , SCN^- ) than for weakly denaturing ones (K⁺ , Cl^- ). The effects of Gdm⁺ and Li⁺ were found to be comparable. Molecular dynamics simulations confirm the enhanced binding of Gdm⁺ and Li⁺ to triglycine, yet with a different binding geometry: While Li⁺ predominantly binds to the C-terminal carboxylate group, bidentate binding to the terminus and the nearest amide is particularly important for Gdm⁺ . This bidentate binding markedly affects peptide conformation, and may help to explain the high denaturation activity of Gdm⁺ salts.

Local electronic structure of the peptide bond probed by resonant inelastic soft X-ray scattering

Soft X-ray emission spectroscopy and RIXS are used to determine the local electronic structure of the peptide bond.

Influence of Local Environment on Inner Shell Excitation Spectra, Studied by Electron and X-ray Spectroscopy and Spectromicroscopy

Inner shell excitation spectroscopy is a local probe of the unoccupied electronic structure in the immediate vicinity of the core excited atom. As such, one might expect the inner shell spectrum of a given unit (a molecular fragment or a repeat unit of a solid) to be largely independent of where that unit is located. This is often an implicit assumption in spectral analysis and analytical applications. However, there are situations where inner shell excitation spectra exhibit significant sensitivity to their local environment. Here I categorize the ways in which inner shell spectra are affected by their local environment, and give examples from a career dedicated to developing a better understanding of inner shell excitation spectroscopy, its experimental techniques, and applications.

An insight into hydration structure of sodium glycinate from ab initio quantum chemical study

The hydration structure of sodium glycinate (Na(+)GL(-)) is probed by the Monte-Carlo multiple minimum (MCMM) method combined with quantum mechanical (QM) calculations at the MP2/6-311++G(d,p) level. In the gas phase, the energy of [Na(+)GL(-)]β is more than 30 kJ mol(-1) higher than [Na(+)GL(-)]α. With higher degrees of hydration, our results indicate that the most stable conformers of [Na(+)GL(-)]∙(H2O)8 were derived from [Na(+)GL(-)]β instead of [Na(+)GL(-)]α. The stable conformers determined by the conductor-like polarizable continuum model (CPCM) also show that [Na(+)GL(-)]β is more stable than [Na(+)GL(-)]α in the liquid phase. By analyzing the hydration process, water…water hydrogen bonding interaction will be more preferable than ion…water interaction as the number of water molecules increases. According to the electronic density at the bond critical point on the Na-X bonds (X = O1, O2, N) in the low-energy conformers, Na(+)GL(-) will be dissociated as Na(+) and GL(-) in the bulk water, which is not predicted by the CPCM model. The structure features and the charge redistribution of Na(+)GL(-) will provide a physical explanation for the weakening Na-O1 interaction.

Overview of the effect of salts on biphasic ionic liquid/water solvent extraction systems: anion exchange, mutual solubility, and thermomorphic properties

Hydrophobic (water-immiscible) ionic liquids (ILs) are frequently used as organic phase in solvent extraction studies. These biphasic IL/water extraction systems often also contain metal salts or mineral acids, which can significantly affect the IL trough (un)wanted anion exchange and changes in the solubility of IL in the aqueous phase. In the case of thermomorphic systems, variations in the cloud point temperature are also observed. All these effects have important repercussions on the choice of IL, suitable for a certain extraction system. In this paper, a complete overview of the implications of metal salts on biphasic IL/water systems is given. Using the Hofmeister series as a starting point, a range of intuitive prediction models are introduced, supported by experimental evidence for several hydrophobic ILs, relevant to solvent extraction. Particular emphasis is placed on the IL betainium bis(trifluoromethylsulfonyl)imide [Hbet][Tf2N]. The aim of this work is to provide a comprehensive interpretation of the observed effects of metal salts, so that it can be used to predict the effect on any given biphasic IL/water system instead of relying on case-by-case reports. These prediction tools for the impact of metal salts can be useful to optimize IL synthesis procedures, extraction systems and thermomorphic properties. Some new insights are also provided for the rational design of ILs with UCST or LCST behavior based on the choice of IL anion.

Quantitative characterization of non-classic polarization of cations on clay aggregate stability

Soil particle interactions are strongly influenced by the concentration, valence and ion species and the pH of the bulk solution, which will also affect aggregate stability and particle transport. In this study, we investigated clay aggregate stability in the presence of different alkali ions (Li+, Na+, K+, and Cs+) at concentrations from10-5 to 10-1 mol L-1. Strong specific ion effects on clay aggregate stability were observed, and showed the order Cs+>K+>Na+>Li+. We found that it was not the effects of ion size, hydration, and dispersion forces in the cation-surface interactions but strong non-classic polarization of adsorbed cations that resulted in these specific effects. In this study, the non-classic dipole moments of each cation species resulting from the non-classic polarization were estimated. By comparing non-classic dipole moments with classic values, the observed dipole moments of adsorbed cations were up to 104 times larger than the classic values for the same cation. The observed non-classic dipole moments sharply increased with decreasing electrolyte concentration. We conclude that strong non-classic polarization could significantly suppress the thickness of the diffuse layer, thereby weakening the electric field near the clay surface and resulting in improved clay aggregate stability. Even though we only demonstrated specific ion effects on aggregate stability with several alkali ions, our results indicate that these effects could be universally important in soil aggregate stability.

Probing ion-specific effects on aqueous acetate solutions: Ion pairing versus water structure modifications

The effect of monovalent cations (Li(+), K(+), NH4 (+), Na(+)) on the water structure in aqueous chloride and acetate solutions was characterized by oxygen K-edge X-ray absorption spectroscopy (XAS), X-ray emission spectroscopy, and resonant inelastic X-ray scattering (RIXS) of a liquid microjet. We show ion- and counterion dependent effects on the emission spectra of the oxygen K-edge, which we attribute to modifications of the hydrogen bond network of water. For acetates, ion pairing with carboxylates was also probed selectively by XAS and RIXS. We correlate our experimental results to speciation data and to the salting-out properties of the cations.

L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser

L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.

Reversal of the hofmeister series: specific ion effects on peptides

Ion-specific effects on salting-in and salting-out of proteins, protein denaturation, as well as enzymatic activity are typically rationalized in terms of the Hofmeister series. Here, we demonstrate by means of NMR spectroscopy and molecular dynamics simulations that the traditional explanation of the Hofmeister ordering of ions in terms of their bulk hydration properties is inadequate. Using triglycine as a model system, we show that the Hofmeister series for anions changes from a direct to a reversed series upon uncapping the N-terminus. Weakly hydrated anions, such as iodide and thiocyanate, interact with the peptide bond, while strongly hydrated anions like sulfate are repelled from it. In contrast, reversed order in interactions of anions is observed at the positively charged, uncapped N-terminus, and by analogy, this should also be the case at side chains of positively charged amino acids. These results demonstrate that the specific chemical and physical properties of peptides and proteins play a fundamental role in ion-specific effects. The present study thus provides a molecular rationalization of Hofmeister ordering for the anions. It also provides a route for tuning these interactions by titration or mutation of basic amino acid residues on the protein surface.

Salt effects on the conformational stability of the visual G-protein-coupled receptor rhodopsin

Membrane protein stability is a key parameter with important physiological and practical implications. Inorganic salts affect protein stability, but the mechanisms of their interactions with membrane proteins are not completely understood. We have undertaken the study of a prototypical G-protein-coupled receptor, the α-helical membrane protein rhodopsin from vertebrate retina, and explored the effects of inorganic salts on the thermal decay properties of both its inactive and photoactivated states. Under high salt concentrations, rhodopsin significantly increased its activation enthalpy change for thermal bleaching, whereas acid denaturation affected the formation of a denatured loose-bundle state for both the active and inactive conformations. This behavior seems to correlate with changes in protonated Schiff-base hydrolysis. However, chromophore regeneration with the 11-cis-retinal chromophore and MetarhodopsinII decay kinetics were slower only in the presence of sodium chloride, suggesting that in this case, the underlying phenomenon may be linked to the activation of rhodopsin and the retinal release processes. Furthermore, the melting temperature, determined by means of circular dichroism and differential scanning calorimetry measurements, was increased in the presence of high salt concentrations. The observed effects on rhodopsin could indicate that salts favor electrostatic interactions in the retinal binding pocket and indirectly favor hydrophobic interactions at the membrane protein receptor core. These effects can be exploited in applications where the stability of membrane proteins in solution is highly desirable.

Effects of select anions from the Hofmeister series on the gas-phase conformations of protein ions measured with traveling-wave ion mobility spectrometry/mass spectrometry

The gas-phase conformations of ubiquitin, cytochrome c, lysozyme, and α-lactalbumin ions, formed by electrospray ionization (ESI) from aqueous solutions containing 5 mM ammonium perchlorate, ammonium iodide, ammonium sulfate, ammonium chloride, ammonium thiocyanate, or guanidinium chloride, are examined using traveling-wave ion mobility spectrometry (TWIMS) coupled to time-of-flight (TOF) mass spectrometry (MS). For ubiquitin, cytochrome c, and α-lactalbumin, adduction of multiple acid molecules results in no significant conformational changes to the highest and lowest charge states formed from aqueous solutions, whereas the intermediate charge states become more compact. The transition to more compact conformers for the intermediate charge states occurs with fewer bound H(2)SO(4) molecules than HClO(4) or HI molecules, suggesting ion-ion or salt-bridge interactions are stabilizing more compact forms of the gaseous protein. However, the drift time distributions for protein ions of the same net charge with the highest levels of adduction of each acid are comparable, indicating that these protein ions all adopt similarly compact conformations or families of conformers. No significant change in conformation is observed upon the adduction of multiple acid molecules to charge states of lysozyme. These results show that the attachment of HClO(4), HI, or H(2)SO(4) to multiply protonated proteins can induce compact conformations in the resulting gas-phase protein ions. In contrast, differing Hofmeister effects are observed for the corresponding anions in solution at higher concentrations.