Secondary Structure Dependence and Hydration Effect of the Infrared Intensity of the Amide II Mode of Peptide Chains

Ultrasound protein-copolymer microbubble library engineering through poly(vinylpyrrolidone-co-acrylic acid) structure

HYPOTHESIS

While albumin-coated microbubbles are routine contrast agents for ultrasound imaging, their short duration of contrast enhancement limits their use, yet can be improved by incorporating protein-copolymer hybrids into microbubble shells. The incorporation of N-vinyl-2-pyrrolidone and acrylic acid copolymer (P(VP-AA)) has been shown to enhance the performance of bovine serum albumin (BSA)-coated microbubbles. However, the impact of the copolymer structural properties on key microbubble characteristics (i.e., concentration, mean diameter and acoustic response) remains poorly understood. Therefore, we hypothesize that the copolymer structure affects its capacity to form micelle-like nanoaggregates, protein-copolymer hybrids, and microbubble shells, ultimately influencing the physicochemical and acoustic properties of the microbubbles.

EXPERIMENTS

Here we evaluate the production and performance of BSA@P(VP-AA) microbubbles synthesized using a series of P(VP-AA) copolymers with -C8H17 and -C18H37 end groups and molecular weight cutoffs between 3.5 and 15 kDa. Both simulation and experimental data demonstrate that interactions between BSA and the copolymers significantly influence the performance of the resulting microbubbles across the library of 60 formulations.

FINDINGS

The introduction of -C8H17 terminated copolymers into microbubble shells resulted in up to 200-fold higher concentration, 7-fold greater acoustic response, and 5-fold longer ultrasound contrast enhancement compared to plain BSA microbubbles. The enhanced acoustic performance was sustained during in vivo cardiac ultrasound imaging, without altering liver accumulation after copolymer introduction. These findings underscore how optimizing copolymer structure (specifically the terminal end group and molecular weight) can tailor the formation and performance of protein-copolymer-coated microbubbles, offering valuable insights for designing ultrasound contrast agents.

Modeling of the Hydrogen Bond-Induced Frequency Shifts of the HOH and HOD Bending Modes of Water

The intramolecular bending mode of water is a possible useful probe of the hydrogen-bond situations in aqueous systems, but the behavior of its frequency and intensity should be further elucidated for better understanding on its nature and, hence, for its better utilization as a probe. Here, an analysis toward this goal is conducted by doing theoretical calculations on molecular clusters of normal isotopic and deuterated species of water and examining the correlations among the vibrational, structural, and electrostatic properties. It is shown that electrostatic interactions, particularly both of the in-plane components of the electric field along the OH bond and perpendicular to it, play a major role in controlling the hydrogen bond-induced shifts of the force constant, but additional factors, including the intermolecular structural and/or charge-transfer properties, are also important. Models of the hydrogen bond-induced shifts of the force constant are presented in a form that may be combined with classical molecular dynamics. With regard to the infrared intensity changes, it is shown on the basis of the electron density analysis that the intermolecular charge flux and polarization effect play an important role, depending on the angular characteristics of the hydrogen bond.

Singular value decomposition analysis of the electron density changes occurring upon electrostatic polarization of water

In-depth elucidation of how molecules are electrically polarized would be one key factor for understanding the properties of those molecules under various thermodynamic and/or spatial conditions. Here this problem is tackled for the case of hydrogen-bonded water by conducting singular value decomposition of the electron density changes that occur upon electrostatic polarization. It is shown that all those electron density changes are approximately described as linear combinations of ten orthonormal basis “vectors”. One main component is the interatomic charge transfer through each OH bond, while some others are characterized as the atomic dipolar polarizations, meaning that both of these components are important for the electrostatic polarization of water. The interaction parameters that reasonably well reproduce the induced dipole moments are derived, which indicate the extent of mixing of the two components in electrostatic polarization.

The main features of the electron density changes that occur upon electrostatic polarization of water are elucidated by conducting singular value decomposition analysis of those changes.

Hidden Halogen-Bonding Ability of Fluorine Manifesting in the Hydrogen-Bond Configurations of Hydrogen Fluoride

Elucidating how the intermolecular interactions of a covalently bonded fluorine atom are similar to and different from those of the other halogen atoms will be helpful for a better unified understanding of them. In the present study, the case of hydrogen fluoride is theoretically studied from this viewpoint by using the techniques of electron density analysis, molecular dynamics of liquid, and others. It is shown that the extra-point model, which locates an additional charge site on the line extended from (not within) the covalent bond and has been adopted for halogen-bonding systems as a key to the generation of proper stability and directionality, works well also in this case. A significantly bent hydrogen-bond configuration, which is characteristic of the intermolecular interactions of hydrogen fluoride, is reasonably well reproduced, meaning that it is a manifestation of the latent halogen-bonding ability, which is hidden by the strongly electronegative nature.

Role of Intermolecular Charge Fluxes in the Hydrogen-Bond-Induced Frequency Shifts of the OH Stretching Mode of Water

The relation between the vibrational properties and the electrostatic situations of the vibrating functional group is useful to predict vibrational spectroscopic features based on, for example, classical molecular dynamics of liquids or biomolecular systems, but to pursue its generality or the extent of applicability, it is required to understand the mechanisms giving rise to it. Here such an analysis is carried out for the OH stretching mode of water. By examining the correlations among various (structural, vibrational, and electrostatic) properties and by analyzing the spatial characteristics of the behavior of electrons occurring upon the vibration, it is shown that the dependence of the vibrational frequency and the dipole derivative of the OH stretching mode on the electric field is not of purely electrostatic origin, and the delocalized electronic motions occurring with this mode, called intermolecular charge fluxes, related to both the dipole first and second derivatives play important roles.

Dissecting the electric quadrupolar and polarization effects operating in halogen bonding through electron density analysis with a focus on bromine

The form of the electron density change (or difference) is usable as a kind of fingerprint of the electronic structural origin or mechanism that gives rise to intermolecular interactions. Here, this method is applied to halogen-bonding brominated systems to dissect the electric quadrupolar effect (arising from the anisotropic distribution of the valence electrons and intrinsic to the s²p_x ²p_y ²p_z electronic configuration) and the polarization effect (induced by a partial negative charge of the halogen-bond accepting atom). It is shown that a suitable location of the "extra point" for placing a partial positive charge to represent the former is crucial and is clearly found from the electron density difference from the spherically isotropic Br^- ion, while the latter consists of the dipolar polarization of the Br atom and the delocalized polarization of the whole molecule. A practical way for application to molecular dynamics simulations, etc., to represent these two factors is discussed.

Specific Ion Effects on Protein Thermal Aggregation from Dilute Solutions to Crowded Environments

We have investigated specific ion effects on protein thermal aggregation from dilute solutions to crowded environments. Ovalbumin and poly(ethylene glycol) have been employed as the model protein and crowding agent, respectively. Our studies demonstrate that the rate-limiting step of ovalbumin thermal aggregation is changed from the aggregation of unfolded protein molecules to the unfolding of the protein molecules, when the solution conditions are varied from a dilute solution to a crowded environment. The specific ion effects acting on the thermal aggregation of ovalbumin generated by kosmotropic and chaotropic ions are different. The thermal aggregation of ovalbumin molecules is promoted by kosmotropic anions in dilute solutions via an increase in protein hydrophobic interactions. In contrast, ovalbumin thermal aggregation is facilitated by chaotropic ions in crowded environments through accelerated unfolding of protein molecules. Therefore, there are distinct mechanisms causing the ion specificities of protein thermal aggregation between dilute solutions and crowded environments. The ion specificities are dominated by ion-specific hydrophobic interactions between protein molecules and ion-specific unfolding of protein molecules in dilute solutions and crowded environments, respectively.

Direct Anionic Effect on Water Structure and Indirect Anionic Effect on Peptide Backbone Hydration State Revealed by Thin-Layer Infrared Spectroscopy

In this work, the anionic effect on water structure and on the peptide backbone and water interaction was investigated directly in aqueous solution using thin-layer transmission infrared spectroscopy. The chaotropic anions were found to weaken the water hydrogen-bonding strength and red shift the HOH bending frequency, while the kosmotropic anions were found to strengthen the water hydrogen-bonding network and blue shift the HOH bending frequency. The kosmotropes, especially F^-, blue shift the vibrational frequencies of both amide II and amide III bands of N-methylacetamide (NMA), indicating NMA is in the "salting-in" state; while the chaotropes (Cl^-, NO₃^-, Br^-, I^-, and SCN^-) red shift the frequencies of the two normal modes, indicating NMA is in the "salting-out" state. Furthermore, the changes of the vibrational frequencies of the HOH bending, amide II and III bands were found to generally follow the Hofmeister anionic series. Our results suggest that hydrated anion influences the peptide backbone mainly through the N-H group, but a weak and indirect effect through the amide C═O group also contributes. Thus, these amide modes can be used as vibrational measures of anionic influences on peptide backbone's hydration state. Our work also suggests that deuteration of the amide unit decreases the sensitivity of the amide II and III vibrational modes in this regard.

Intermolecular charge fluxes and far-infrared spectral intensities of liquid formamide

Intermolecular charge fluxes induced by hydrogen-bond length modulations occurring upon molecular librations lead to intensity enhancement of the far-infrared spectrum.

Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins

For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe²⁺ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities. It is shown that, for the stretching frequencies and NMR chemical shifts, it is possible to construct reasonable electrostatic interaction models that encompass the situations of hydration and uniform electric field environment and thus are applicable also to the cases of nonuniform electrostatic situations, which are highly expected for inside of proteins.

Roles of the scalar and vector components of the solvation effects on the vibrational properties of hydrogen- or halogen-bond accepting stretching modes

Solvation-induced vibrational frequency shifts and infrared (IR) intensity changes of the hydrogen- or halogen-bond accepting stretching modes, especially their dependence on the angular position of the hydrogen- or halogen-bond donating molecule, are examined theoretically. Calculations are carried out for some modes of hydrogen- or halogen-bonding molecular complexes, including the S[double bond, length as m-dash]O stretch of dimethyl sulfoxide-(13)C2H2O, the C[triple bond, length as m-dash]N stretch of acetonitrileH2O, and the amide I' mode of the N-methylacetamide-d1BrNC 1 : 1 complex. It is shown that, in all the example cases dealt with in this study, the frequency shift depends rather strongly on the hydrogen- or halogen-bond angle (e.g., S[double bond, length as m-dash]OH angle), with a larger low-frequency shift as the hydrogen or halogen bond becomes more bent, indicating the generality of the results obtained for the amide I' mode of the N-methylacetamide-d1(2)H2O 1 : 1 complex in a previous study. Contrary to our vague expectation, the frequency shift is not well correlated to the hydrogen- or halogen-bond distance or strength, but nevertheless, it is well reproduced by an electrostatic interaction model if it is carefully constructed by considering the scalar and vector components separately in a reasonable way. On the basis of this electrostatic interaction model, the reason why our vague expectation is not realized is clarified, and a unified understanding is achieved on the hydration-induced high-frequency shift of the C[triple bond, length as m-dash]N stretch and the low-frequency shifts of the S[double bond, length as m-dash]O stretch and amide I'. With regard to the IR intensity, it is shown that, in some of the example cases, it also has rather strong angular position dependence. The mechanism of the IR intensity changes is estimated by analyzing the dipole derivative vector, especially its angular relation with the hydrogen or halogen bond.