Modeling Water, the Hydrophobic Effect, and Ion Solvation

De novo design of mini-binder proteins against IL-2 receptor β chain

IL-2 regulates the immune response by interacting with different IL-2 receptor (IL-2R) subunits. High dose of IL-2 binds to IL-2Rβγc heterodimer, which induce various side effects while activating immune function. Disrupting IL-2 and IL-2R interactions can block IL-2 mediated immune response. Here, we used a computational approach to de novo design mini-binder proteins against IL-2R β chain (IL-2Rβ) to block IL-2 signaling. The hydrophobic region where IL-2 binds to IL-2Rβ was selected and the promising binding mode was broadly explored. Three mini-binders with amino acid numbers ranging from 55 to 65 were obtained and binder 1 showed the best effects in inhibiting CTLL-2 cells proliferation and STAT5 phosphorylation. Molecular dynamics simulation showed that the binding of binder 1 to IL-2Rβ was stable; the free energy of binder1/IL-2Rβ complex was lower, indicating that the affinity of binder 1 to IL-2Rβ was higher than that of IL-2. Free energy decomposition suggested that the ARG35 and ARG131 of IL-2Rβ might be the key to improve the affinity of binder. Our efforts provided new insights in developing of IL-2R blocker, offering a potential strategy for ameliorating the side effects of IL-2 treatment.

Real-time structural dynamics of the ultrafast solvation process around photo-excited aqueous halides

This work investigates and describes the structural dynamics taking place following charge-transfer-to-solvent photo-abstraction of electrons from I- and Br- ions in aqueous solution following single- and 2-photon excitation at 202 nm and 400 nm, respectively. A Time-Resolved X-ray Solution Scattering (TR-XSS) approach with direct sensitivity to the structure of the surrounding solvent as the water molecules adopt a new equilibrium configuration following the electron-abstraction process is utilized to investigate the structural dynamics of solvent shell expansion and restructuring in real-time. The structural sensitivity of the scattering data enables a quantitative evaluation of competing models for the interaction between the nascent neutral species and surrounding water molecules. Taking the I0-O distance as the reaction coordinate, we find that the structural reorganization is delayed by 0.1 ps with respect to the photoexcitation and completes on a time scale of 0.5-1 ps. On longer time scales we determine from the evolution of the TR-XSS difference signal that I0: e- recombination takes place on two distinct time scales of ∼20 ps and 100 s of picoseconds. These dynamics are well captured by a simple model of diffusive evolution of the initial photo-abstracted electron population where the charge-transfer-to-solvent process gives rise to a broad distribution of electron ejection distances, a significant fraction of which are in the close vicinity of the nascent halogen atoms and recombine on short time scales.

Investigating the effects of solvent polarity and temperature on the molecular, photophysical, and thermodynamic properties of sinapic acid using DFT and TDDFT

Sinapic acid (SA) is widely used in cosmetics, foods, and pharmaceuticals due to its antioxidant, anti-inflammatory, neuroprotective, antimicrobial, antifungal, anticancer, and cardioprotective properties. However, environmental factors such as solvent polarity and temperature can influence its biological activity. This work determined how solvent polarity and temperature affected the molecular, photophysical, and thermodynamic properties of SA in gas and various solvents using semi-empirical (MP6), Hartree-Fock (HF) with the B3LYP method and a 6-311++G(d,p) basis set, and density functional theory (DFT) with various basis sets, such as 3TO-3G*, 3-21G+, 6-31G++G(d,p), 6-311++G(d,p), aug-CC-PVDZ, LanL2DZ, SDD, and DGD2VP. The results indicated that solvent polarity influences molecular and spectroscopic properties, such as bond angles, dihedral angles, bond lengths, FTIR spectra, solvation energy, dipole moments, HOMO-LUMO band gaps, chemical reactivity, and thermodynamic properties, resulting from interactions between the drug and solvent molecules. The findings suggested that increasing the temperature within the range of 100 to 1000 Kelvin leads to an increase in heat capacity, enthalpy, and entropy due to molecular vibrations, ultimately causing degradation and instability in SA. Furthermore, the results showed that SA underwent a redshift in the absorption peak (from 320.18 to 356.26 nm) and a shift in the fluorescence peak (from 381 to 429 nm) in the solvent phase compared to those in the gas phase. Overall, this study provides background knowledge on how solvent polarity and temperature affect the properties of SA molecules.

Differential capacitance of curved electrodes: role of hydration interactions and charge regulation

The functioning of supercapacitors relies on establishing electrostatic double-layer capacitance across a larger surface area, offering numerous advantages over conventional batteries, such as an extended lifespan and elevated safety standards. The differential capacitance is a fundamental property within the electrical double layer, playing a pivotal role in the advancement of electrical double-layer supercapacitors. In addition to electrostatic interactions, multiple theoretical and experimental studies have indicated that the differential capacitance is influenced by factors such as the physical structure of the electrode, solvent-mediated hydration interactions, and the specific type of electrolyte utilized. In this work, we incorporate hydration interactions into the Poisson-Boltzmann theory to explore curved electrodes whose surfaces can be covered by either acidic or basic groups. We examine how the electrostatic interaction, charge regulation, hydration effects, and the finite size of ions collectively modify the differential capacitance. Furthermore, we explore different scenarios of electrode curvature and how it may be used to achieve larger capacitance depending on the electrolyte type and pH.

Perturbative Expansion in Reciprocal Space: Bridging Microscopic and Mesoscopic Descriptions of Molecular Interactions

Determining the Fourier representation of various molecular interactions is important for constructing density-based field theories from a microscopic point of view, enabling a multiscale bridge between microscopic and mesoscopic descriptions. However, due to the strongly repulsive nature of short-ranged interactions, interparticle interactions cannot be formally defined in Fourier space, which renders coarse-grained (CG) approaches in k-space somewhat ambiguous. In this paper, we address this issue by designing a perturbative expansion of pair interactions in reciprocal space. Our perturbation theory, starting from reciprocal space, elucidates the microscopic origins underlying zeroth-order (long-range attractions) and divergent repulsive interactions from higher order contributions. We propose a systematic framework for constructing a faithful Fourier-space representation of molecular interactions, capturing key structural correlations in various systems, including simple model systems and molecular CG models of liquids. Building upon the Ornstein-Zernike equation, our approach can be combined with appropriate closure relations, and to further improve the closure approximations, we develop a bottom-up parameterization strategy for inferring the bridge function from microscopic statistics. By incorporating the bridge function into the Fourier representation, our findings suggest a systematic, bottom-up approach to performing coarse-graining in reciprocal space, leading to the systematic construction of a bottom-up classical field theory of complex aqueous systems.

De novo design of a protein binder against Staphylococcus enterotoxin B

Staphylococcus enterotoxin B (SEB) interacts with MHC-II molecules to overactivate immune cells and thereby to produce excessive pro-inflammatory cytokines. Disrupting the interactions between SEB and MHC-II helps eliminate the lethal threat posed by SEB. In this study, a de novo computational approach was used to design protein binders targeting SEB. The MHC-II binding domain of SEB was selected as the target, and the possible promising binding mode was broadly explored. The obtained original binder was folded into triple-helix bundles and contained 56 amino acids with molecular weight 5.9 kDa. The interface of SEB and the binder was highly hydrophobic. ProteinMPNN optimization further enlarged the hydrophobic region of the binder and improved the stability of the binder-SEB complex. In vitro study demonstrated that the optimized binder significantly inhibited the inflammatory response induced by SEB. Overall, our research demonstrated the applicability of this approach in de novo designing protein binders against SEB, and thereby providing potential therapeutics for SEB induced diseases.

Anomalous Concentration Dependence of Viscosity: Hidden Role of Cross-Correlations in Aqueous Electrolyte Solutions

The viscosity of aqueous electrolyte solutions exhibits well-known composition-dependent anomalies that show certain definitive trends and universal features. The viscosity of LiCl and NaCl solutions increases with concentration in a monotonic fashion, while solutions of KCl, RbCl, and CsCl exhibit a more complex behavior. Here, the viscosity first decreases and then increases with increasing concentration, with a rather broad minimum at intermediate concentrations (ca. 1-3 m). To unearth the origin of such puzzling behavior, we carried out detailed molecular-level analyses by interrogating the exact Green-Kubo expression of viscosity in terms of the stress-stress time correlation function (SS-TCF). The total SS-TCF can be decomposed into a collection of three self- and three cross-SS-TCFs arising from the three constituent components (water, cations, and anions). Mode coupling theory (MCT) analysis for the friction on ions and the viscosity of the solution suggests the possible importance of two-particle static and time-dependent cross-correlations between water and the ions. We calculate the viscosity and other dynamical properties for all five electrolyte (LiCl, NaCl, KCl, RbCl, and CsCl) solutions over a range of concentrations, using two models of water (SPC/E and TIP4P/2005). The total viscosity derives non-negligible contributions from all of the terms. The cross-correlations are found to be surprisingly large and seen to play a hidden role in the concentration dependence. However, the importance of cross-correlations is often not discussed. Our study leads to a theoretical understanding of the microscopic origin of the observed anomalies in the composition dependence of viscosity across all five electrolytes.

The influence of the hydrogen-bond network on the structure and dynamics of the RAPRKKG heptapeptide and its mutants

The structural behaviour of the RAPRKKG heptapeptide after individual or multiple mutations was inspected through molecular dynamics simulation. The nature of the mutations provided information on the flexibility of the heptapeptide and on how water molecules establish hydrogen bonds with it. The structural behaviour of the wild-type and the mutated structures were measured through the analysis of protein‒protein and protein‒solvent hydrogen bonds. The conformational behaviours of the different structures were analysed through free energy landscape analysis. The flexibility characteristics of the mutants seem to depend on the reorganization of water molecules and their static or dynamic behaviour around amino acid side chains.

Simple Model of Liquid Water Dynamics

We develop an analytical statistical-mechanical model to study the dynamic properties of liquid water. In this two-dimensional model, neighboring waters can interact through a hydrogen bond, a van der Waals contact, or an ice-like cage structure or have no interaction. We calculate the diffusion coefficient, viscosity, and thermal conductivity versus temperature and pressure. The trends follow those seen in the water experiments. The model explains that in warm water, heating drives faster diffusion but less interaction, so the viscosity and conductivity decrease. Cooling cold water causes poorer energy exchange because water's ice-like cages are big and immobile and collide infrequently. The main antagonism in water dynamics is not between vdW and H bonds, but it is an interplay between both those pair interactions, multibody cages, and no interaction. The value of this simple model is that it is analytical, so calculations are immediate, and it gives interpretations based on molecular physics.

Ben Naim's four-arm model with density anomaly: Theory and computer simulations

Molecular dynamics, Wertheim's integral equation theory (IET), and thermodynamics perturbation theory (TPT) were used to study the thermodynamics and structure of particles interacting through angle-dependent potential. The particles are modeled as two-dimensional Lennard-Jones disks with four hydrogen bonding arms arranged symmetrically. The model was introduced by Ben-Naim and we call it the BN4 model. The BN4 model exhibits density anomaly and other anomalous properties similar to those in water and in the Mercedes-Benz (MB) model. The IET is based on the orientationally averaged version of the Ornstein-Zernike equation and correctly predicts the pair correlation function of the model at high temperatures. Both TPT and IET are in semiquantitative agreement with the simulation values of the molar volume, isothermal compressibility, thermal expansion coefficient, and heat capacity.

Isochores and Heat Capacity of Liquid Water in Terms of the Ion–Molecular Model

Thermodynamics of liquid water in terms of a non-standard approach—the ion–molecular model—is considered. Water is represented as a dense gas of neutral H2O molecules and single charged H3O+ and OH− ions. The molecules and ions perform thermal collisional motion and interconvert due to ion exchange. The energy-rich process—vibrations of an ion in a hydration shell of molecular dipoles—well known to spectroscopists with its dielectric response at 180 cm−1 (5 THz), is suggested to be key for water dynamics. Taking into account this ion–molecular oscillator, we compose an equation of state of liquid water to obtain analytical expressions for the isochores and heat capacity.

Improved Assessment of Globularity of Protein Structures and the Ellipsoid Profile of the Biological Assemblies from the PDB

In this paper, we present an update to the ellipsoid profile algorithm (EP), a simple technique for the measurement of the globularity of protein structures without the calculation of molecular surfaces. The globularity property is understood in this context as the ability of the molecule to fill a minimum volume enclosing ellipsoid (MVEE) that approximates its assumed globular shape. The more of the interior of this ellipsoid is occupied by the atoms of the protein, the better are its globularity metrics. These metrics are derived from the comparison of the volume of the voxelized representation of the atoms and the volume of all voxels that can fit inside that ellipsoid (a uniform unit Å cube lattice). The so-called ellipsoid profile shows how the globularity changes with the distance from the center. Two of its values, the so-called ellipsoid indexes, are used to classify the structure as globular, semi-globular or non-globular. Here, we enhance the workflow of the EP algorithm via an improved outlier detection subroutine based on principal component analysis. It is capable of robust distinguishing between the dense parts of the molecules and, for example, disordered chain fragments fully exposed to the solvent. The PCA-based method replaces the current approach based on kernel density estimation. The improved EP algorithm was tested on 2124 representatives of domain superfamilies from SCOP 2.08. The second part of this work is dedicated to the survey of globularity of 3594 representatives of biological assemblies from molecules currently deposited in the PDB and analyzed by the 3DComplex database (monomers and complexes up to 60 chains).

Monte Carlo simulations of simple two dimensional water-alcohol mixtures

Simple alcohols such as methanol and ethanol, are organic chemicals that can be used to store energy, which can be used as an alternative to fossil fuels. Each alcohol has at least one hydroxyl group attached to a carbon atom of an alkyl group. They can be considered as organic derivatives of water in which one of the hydrogen atoms is replaced by an alkyl group. In this work, we determined the thermodynamic and structural properties of two dimensional water-alcohol mixtures using the Monte Carlo method. We used two-dimensional Mercedes-Benz (MB) model for water and MB based models for lower alcohols. The structural and thermodynamic properties of the mixtures were studied by Monte Carlo simulations in the isothermal-isobaric ensemble. We show that 2D models display similar trends in the density maxima as in real water-alcohol mixtures. With increasing content of alcohols, the temperature of maxima increases and upon further increase starts to decrease and at high concentrations, the density maxima disappears.

Modeling protein structure as a stable static equilibrium

We present evidence that the protein structure can be modeled as a stable static equilibrium, determined mainly by compressive supports in the nonpolar interior. That is, protein structures derive their structural strength through the same mechanical principles as do conventional structures like bridges and buildings. This is based on the observation that the experimentally elucidated structural determinants, the interior nonpolar side chains, are engaged in strong compressions in static terms. At the same time, major substructures in proteins, helices and h-bonded strands, because of their geometry, inherently leave gaps in the space they occupy. Under the compressive force, nonpolar side chains from one substructure can protrude into the gaps of another neighboring substructure and block its motion. As a result, interlocking of substructures can form, which builds up the nonpolar core assembly. The native structure then is the one with the structurally most stable core assembly. While intuitively appealing, this is a radical departure from the prevailing thinking that protein native structure is determined by global energy minimum, which is founded on thermodynamic hypothesis. Furthermore, to develop an effective model for analyzing protein structure with conventional tools, a proper mechanical representation must be established. By proving that the stability of the equilibrium in compressive interactions is conditioned on a form of mechanical energy minimum, we show that our notion of native structure can be equally consistent with the thermodynamic hypothesis. By mathematically treating the blocking action, an interaction, as a bar, a physical object, we succeed in representing and analyzing the core assembly as truss, a conventional structure. In this paper we define and expound step-by-step increasingly integrated interlocking patterns. We then analyze the core assemblies of a large set of diverse protein database structures. A native structure can be distinguished from decoys by comparing the composition and strength of their core assemblies. We show the results for two sets of native structures vs decoys.

Hydration, Refinement, and Dissolution of the Crystalline Phase in Polyamide 6 Polymorphs for Ultimate Thermomechanical Properties

Timescales of polyamide 6 melt-shaping technologies, relative to the dynamics of conformational rearrangements upon crystallization, challenge the formation of the most thermodynamically favorable chain packing and thus optimum performance. In this publication, we make use of the mediation of hydrogen bonding by water molecules in the superheated state of water, i.e., above 100 °C in a closed environment, in the structural refinement of polyamide 6 for enhanced thermomechanical performance. The paper addresses dissolution and (re)crystallization of different polyamide 6 polymorphs in the superheated state of water by time-resolved simultaneous small- and wide-angle X-ray scattering and solid-state ¹H NMR spectroscopy and the effect on mechanical properties. The experiments reveal that upon heating in the superheated state of water, the pseudo-hexagonal phase dissolves at relatively low temperature and instantly crystallizes in a defected monoclinic phase that successively refines to a perfected monoclinic structure. The dissolution temperature of the pseudo-hexagonal phase of polyamide 6 is found to be dependent on the degree of crystal perfection originating from conformational disorder and misalignment of hydrogen bonding in the lattice, retrospectively, to the Brill transition temperature. The perfected monoclinic phase below the dissolution temperature can be preserved upon cooling but is plasticized by hydration of the amide moieties in the crystalline phase. The removal of water from the hydrated crystals, in the proximity of Brill transition temperature, strengthening the hydrogen bonding, occurs. Retrospectively, the most thermodynamically stable crystallographic phase is preserved and renders an increase in mechanical properties and dimensional stability of the product. The insight obtained on the influence of superheated water on the structural refinement of imperfected crystallographic states assists in polyamide 6 postprocessing strategies for enhanced performance.

Efficient aqueous remote loading of peptides in poly(lactic-co-glycolic acid)

Poly(lactic-co-glycolic acid) (PLGA) long-acting release depots are effective for extending the duration of action of peptide drugs. We describe efficient organic-solvent-free remote encapsulation based on the capacity of common uncapped PLGA to bind and absorb into the polymer phase net positively charged peptides from aqueous solution after short exposure at modest temperature. Leuprolide encapsulated by this approach in low-molecular-weight PLGA 75/25 microspheres slowly and continuously released peptide for over 56 days in vitro and suppressed testosterone production in rats in an equivalent manner as the 1-month Lupron Depot®. The technique is generalizable to encapsulate a number of net cationic peptides of various size, including octreotide, with competitive loading and encapsulation efficiencies to traditional methods. In certain cases, in vitro and in vivo performance of remote-loaded PLGA microspheres exceeded that relative to marketed products. Remote absorption encapsulation further removes the need for a critical organic solvent removal step after encapsulation, allowing for simple and cost-effective sterilization of the drug-free microspheres before encapsulation of the peptide.

Simple two-dimensional models of alcohols

Alcohols are organic compounds characterized by one or more hydroxyl groups attached to a carbon atom of an alkyl group. They can be considered as organic derivatives of water in which one of the hydrogen atoms is replaced by an alkyl group. In this work, the Mercedes-Benz model of water is used to design simple two-dimensional (2D) models of lower alcohols. The structural and thermodynamic properties of the constructed simple models are studied by conducting Monte Carlo simulations in the isothermal-isobaric ensemble. We show that 2D models display similar trends in structuring and thermodynamics as in experiments. The present work on the smallest amphiphilc organic solutes provides a simple testing ground to study the competition between polar and non-polar effects within the molecule and physical properties.

Isothermal-isobaric algorithm to study the effects of rotational degrees of freedom-Benz water model

We have developed isothermal-isobaric algorithm for non-equilibrium Monte Carlo simulations. As first we have shown that the new method correctly predict density by comparing it to the density determined in canonical Monte Carlo simulations through the virial pressure. The new method was then used to study the effect of translational and rotational degrees of freedom on the structural and thermodynamic properties of the simple Mercedes-Benz water model. By holding one of the temperatures constant and varying the other one, we investigated how the position of the density maxima changes. We have observed that upon increase of rotational temperature the fluid become more Lennard-Jones like and the density maxima disappears.

Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation

In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation. We achieve this goal by interfacing our recently developed divide-and-conquer approach for semiclassical initial value representation molecular dynamics with the polarizable AMOEBABIO18 force field. The method is applied to the study of solvation of the thymidine nucleoside in two different polar solvents, water and N,N-dimethylformamide. Such systems are made of up to 2476 atoms. Experimental evidence concerning the different behavior of thymidine in the two solvents is well reproduced by our study, even though quantitative estimates are hampered by the limited accuracy of the classical force field employed. Overall, this study shows that semiclassically approximate quantum dynamical studies of explicitly solvated biological systems are both computationally affordable and insightful.

Anion-cation contrast of small molecule solvation in salt solutions

The contributions from anions and cations from salt are inseparable in their perturbation of molecular systems by experimental and computational methods, rendering it difficult to dissect the effects exerted by the anions and cations individually. Here we investigate the solvation of a small molecule, caffeine, and its perturbation by monovalent salts from various parts of the Hofmeister series. Using molecular dynamics and the energy-representation theory of solvation, we estimate the solvation free energy of caffeine and decompose it into the contributions from anions, cations, and water. We also decompose the contributions arising from the solute-solvent and solute-ions interactions and that from excluded volume, enabling us to pin-point the mechanism of salt. Anions and cations revealed high contrast in their perturbation of caffeine solvation, with the cations salting-in caffeine via binding to the polar ketone groups, while the anions were found to be salting-out via perturbations of water. In agreement with previous findings, the perturbation by salt is mostly anion dependent, with the magnitude of the excluded-volume effect found to be the governing mechanism. The free-energy decomposition as conducted in the present work can be useful to understand ion-specific effects and the associated Hofmeister series.

Effects of Salts on the Solvation of Hydrophobic Objects in Water

The solvation of large, hydrophobic objects in water is facilitated by the formation of a low-density region surrounding the solute that is separated from the bulk liquid by an interface, which has a structure that resembles that between a liquid and its vapor. We study the effect of dissolved sodium chloride on the thermodynamics of solvation and on the solvent structure surrounding hydrophobic solutes in the size regime where this interface is not yet fully formed. Using biased Molecular Dynamics computer simulations, we calculate solvation free energies and orientational distributions of water molecules at different salt concentrations and solute sizes. We find that while the effects of sodium chloride on thermodynamic properties are small, the ions' response to the presence of a hydrophobic solute differs significantly from that of the water. Our findings provide mechanistic insight into how our understanding of hydrophobic solvation in water can be extended to electrolyte solutions.

Spatially resolved free-energy contributions of native fold and molten-globule-like Crambin

The folding stability of a protein is governed by the free-energy difference between its folded and unfolded states, which results from a delicate balance of much larger but almost compensating enthalpic and entropic contributions. The balance can therefore easily be shifted by an external disturbance, such as a mutation of a single amino acid or a change of temperature, in which case the protein unfolds. Effects such as cold denaturation, in which a protein unfolds because of cooling, provide evidence that proteins are strongly stabilized by the solvent entropy contribution to the free-energy balance. However, the molecular mechanisms behind this solvent-driven stability, their quantitative contribution in relation to other free-energy contributions, and how the involved solvent thermodynamics is affected by individual amino acids are largely unclear. Therefore, we addressed these questions using atomistic molecular dynamics simulations of the small protein Crambin in its native fold and a molten-globule-like conformation, which here served as a model for the unfolded state. The free-energy difference between these conformations was decomposed into enthalpic and entropic contributions from the protein and spatially resolved solvent contributions using the nonparametric method Per|Mut. From the spatial resolution, we quantified the local effects on the solvent free-energy difference at each amino acid and identified dependencies of the local enthalpy and entropy on the protein curvature. We identified a strong stabilization of the native fold by almost 500 kJ mol-1 due to the solvent entropy, revealing it as an essential contribution to the total free-energy difference of (53 ± 84) kJ mol-1. Remarkably, more than half of the solvent entropy contribution arose from induced water correlations.

A Complex of LaoA and LaoB Acts as a Tat-Dependent Dehydrogenase for Long-Chain Alcohols in Pseudomonas aeruginosa

The opportunistic pathogen Pseudomonas aeruginosa can utilize unusual carbon sources, like sodium dodecyl sulfate (SDS) and alkanes. Whereas the initiating enzymatic steps of the corresponding degradation pathways have been characterized in detail, the oxidation of the emerging long-chain alcohols has received little attention. Recently, the genes for the Lao (long-chain-alcohol/aldehyde oxidation) system were discovered to be involved in the oxidation of long-chain alcohols derived from SDS and alkane degradation. In the Lao system, LaoA is predicted to be an alcohol dehydrogenase/oxidase; however, according to genetic studies, efficient long-chain-alcohol oxidation additionally required the Tat-dependent protein LaoB. In the present study, the Lao system was further characterized. In vivo analysis revealed that the Lao system complements the substrate spectrum of the well-described Exa system, which is required for growth with ethanol and other short-chain alcohols. Mutational analysis revealed that the Tat site of LaoB was required for long-chain-alcohol oxidation activity, strongly suggesting a periplasmic localization of the complex. Purified LaoA was fully active only when copurified with LaoB. Interestingly, in vitro activity of the purified LaoAB complex also depended on the presence of the Tat site. The copurified LaoAB complex contained a flavin cofactor and preferentially oxidized a range of saturated, unbranched primary alcohols. Furthermore, the LaoAB complex could reduce cytochrome c₅₅₀-type redox carriers like ExaB, a subunit of the Exa alcohol dehydrogenase system. LaoAB complex activity was stimulated by rhamnolipids in vitro. In summary, LaoAB constitutes an unprecedented protein complex with specific properties apparently required for oxidizing long-chain alcohols. IMPORTANCE Pseudomonas aeruginosa is a major threat to public health. Its ability to thrive in clinical settings, water distribution systems, or even jet fuel tanks is linked to detoxification and degradation of diverse hydrophobic substrates that are metabolized via alcohol intermediates. Our study illustrates a novel flavoprotein long-chain-alcohol dehydrogenase consisting of a facultative two-subunit complex, which is unique among related enzymes, while the homologs of the corresponding genes are found in numerous bacterial genomes. Understanding the catalytic and compartmentalization processes involved is of great interest for biotechnological and hygiene research, as it may be a potential starting point for rationally designing novel antibacterial substances with high specificity against this opportunistic pathogen.

Development of nano affinity columns for the study of ligand (including SARS-CoV-2 related proteins) binding to heparan sulfate proteoglycans

The interactions of heparan sulfate proteoglycans (HSPGs) present on the cell surface with target proteins lead to cell signaling and they are considered as viral receptors. The analysis of the recognition mechanism between HSPG and its potential ligands and high-throughput screening in drug discovery thus remain important challenges. Glycidyl methacrylate-based monoliths were thus prepared in situ in miniaturized capillary columns (internal diameter 75 μm) and HSPG was grafted onto them by the use of the Schiff base method. The quantity of grafted HSPG was in the nanogram range (11 nanograms per cm of capillary length). This is of significant importance when working with less available or expensive biological material. Other advantages of our miniaturized capillary column are as follows: (i) the immobilization process of HSPG onto the organic monolithic support was reliable and reproducible. (ii) The resultant affinity capillary column showed a strong resistance to changes in temperature and pH and a negligible non-specific interaction. So as to confirm the proper functioning of our miniaturized capillary column, the molecular recognition by HSPG of five selected compounds including three ligands of interest related to SARS-CoV-2 was studied.

Identifying hydrophobic protein patches to inform protein interaction interfaces

Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.

Stable Display of Artificially Long Foreign Antigens on Chimeric Bamboo mosaic virus Particles

Plant viruses can be genetically modified to generate chimeric virus particles (CVPs) carrying heterologous peptides fused on the surface of coat protein (CP) subunits as vaccine candidates. However, some factors may be especially significant in determining the properties of chimeras. In this study, peptides from various sources and of various lengths were inserted into the Bamboo mosaic virus-based (BaMV) vector CP N-terminus to examine the chimeras infecting and accumulating in plants. Interestingly, it was found that the two different strains Foot-and-mouth disease virus (FMDV) VP1 antigens with flexible linker peptides (77 or 82 amino acids) were directly expressed on the BaMV CP, and the chimeric particles self-assembled and continued to express FMDV antigens. The chimeric CP, when directly fused with a large foreign protein (117 amino acids), can self-fold into incomplete virus particles or disks. The physicochemical properties of heterologus peptides N-terminus, complex strand structures of heterologus peptides C-terminus and different flexible linker peptides, can affect the chimera accumulation. Based on these findings, using plant virus-based chimeras to express foreign proteins can increase their length limitations, and engineered plant-made CVP-based vaccines have increasing potential for further development as novel vaccines.

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model

Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution. To leverage both the computational efficiency of the CG simulation and the inclusion of higher-order interactions, we propose a new statistical mechanical theory that effectively projects many-body interactions onto pairwise basis sets. The many-body projection theory presented in this work shares similar physics from liquid state theory, providing an efficient approach to account for higher-order interactions within the reduced model. We apply this theory to project the widely used Stillinger-Weber three-body interaction onto a pairwise (two-body) interaction for water. Based on the projected interaction with the correct long-range behavior, we denote the new CG water model as the Bottom-Up Many-Body Projected Water (BUMPer) model, where the resultant CG interaction corresponds to a prior model, the iteratively force-matched model. Unlike other pairwise CG models, BUMPer provides high-fidelity recapitulation of pair correlation functions and three-body distributions, as well as N-body correlation functions. BUMPer extensively improves upon the existing bottom-up CG water models by extending the accuracy and applicability of such models while maintaining a reduced computational cost.

Different phosphorylation and farnesylation patterns tune Rnd3-14-3-3 interaction in distinct mechanisms

Protein posttranslational modifications (PTMs) are often involved in the mediation or inhibition of protein-protein interactions (PPIs) within many cellular signaling pathways. Uncovering the molecular mechanism of PTM-induced multivalent PPIs is vital to understand the regulatory factors to promote inhibitor development. Herein, Rnd3 peptides with different PTM patterns as the binding epitopes and 14-3-3ζ protein were used as models to elucidate the influences of phosphorylation and farnesylation on binding thermodynamics and kinetics and their molecular mechanism. The quantitative thermodynamic results indicate that phosphorylated residues S210 and S218 (pS210 and pS218) and farnesylated C241 (fC241) enhance Rnd3-14-3-3ζ interactions in the presence of the essential pS240. However, distinct PTM patterns greatly affect the binding process. Initial association of pS240 with the phosphate-binding pocket of one monomer of the 14-3-3ζ dimer triggers the binding of pS210 or pS218 to another monomer, whereas the binding of fC241 to the hydrophobic groove on one 14-3-3ζ monomer induces the subsequent binding of pS240 to the adjacent pocket on the same monomer. Based on the experimental and molecular simulation results, we estimate that pS210/pS218 and pS240 mediate the multivalent interaction through an additive mechanism, whereas fC241 and pS240 follow an induced fit mechanism, in which the cooperativity of these two adjacent PTMs is reflected by the index ε described in our established thermodynamic binding model. Besides, these proposed binding models have been further used for describing the interaction between 14-3-3ζ and other substrates containing adjacent phosphorylation and lipidation groups, indicating their potential in general applications. These mechanistic insights are significant for understanding the regulatory factors and the design of PPI modulators.

Molecular Recognition in Water Using Macrocyclic Synthetic Receptors

Molecular recognition in water using macrocyclic synthetic receptors constitutes a vibrant and timely research area of supramolecular chemistry. Pioneering examples on the topic date back to the 1980s. The investigated model systems and the results derived from them are key for furthering our understanding of the remarkable properties exhibited by proteins: high binding affinity, superior binding selectivity, and extreme catalytic performance. Dissecting the different effects contributing to the proteins' properties is severely limited owing to its complex nature. Molecular recognition in water is also involved in other appreciated areas such as self-assembly, drug discovery, and supramolecular catalysis. The development of all these research areas entails a deep understanding of the molecular recognition events occurring in aqueous media. In this review, we cover the past three decades of molecular recognition studies of neutral and charged, polar and nonpolar organic substrates and ions using selected artificial receptors soluble in water. We briefly discuss the intermolecular forces involved in the reversible binding of the substrates, as well as the hydrophobic and Hofmeister effects operating in aqueous solution. We examine, from an interdisciplinary perspective, the design and development of effective water-soluble synthetic receptors based on cyclic, oligo-cyclic, and concave-shaped architectures. We also include selected examples of self-assembled water-soluble synthetic receptors. The catalytic performance of some of the presented receptors is also described. The latter process also deals with molecular recognition and energetic stabilization, but instead of binding ground-state species, the targets become elusive counterparts: transition states and other high-energy intermediates.

Assessing the Effect of Hofmeister Anions on the Hydrogen-Bonding Strength of Water via Nitrile Stretching Frequency Shift

The temperature dependence of the peak frequency (ν_max) of the C≡N stretching vibrational spectrum of a hydrogen-bonded C≡N species is known to be a qualitative measure of its hydrogen-bonding strength. Herein, we show that within a two-state framework, this dependence can be analyzed in a more quantitative manner to yield the enthalpy and entropy changes (ΔH_HB and ΔS_HB) for the corresponding hydrogen-bonding interactions. Using this method, we examine the effect of ten common anions on the strength of the hydrogen-bond(s) formed between water and the C≡N group of an unnatural amino acid, p-cyanophenylalanine (Phe_CN). We find that based on the ΔH_HB values, these anions can be arranged in the following order: HPO₄^2- > OAc^- > F^- > SO₄^2- ≈ Cl^- ≈ (H₂O) ≈ ClO₄^- ≈ NO₃^- > Br^- > SCN^- ≈ I^-, which differs from the corresponding Hofmeister series. Because Phe_CN has a relatively small size, the finding that anions having very different charge densities (e.g., SO₄^2- and ClO₄^-) act similarly suggests that this ranking order is likely the result of specific ion effects. Since proteins contain different backbone and side-chain units, our results highlight the need to assess their individual contributions toward the overall Hofmeister effect in order to achieve a microscopic understanding of how ions affect the physical and chemical properties of such macromolecules. In addition, the analytical method described in the present study is applicable for analyzing the spectral evolution of any vibrational spectra composed of two highly overlapping bands.

Some thermodynamic effects of varying nonpolar surfaces in protein-ligand interactions

Understanding how making structural changes in small molecules affects their binding affinities for targeted proteins is central to improving strategies for rational drug design. To assess the effects of varying the nature of nonpolar groups upon binding entropies and enthalpies, we designed and prepared a set of Grb2-SH2 domain ligands, Ac-pTyr-Ac6c-Asn-(CH2)n-R, in which the size and electrostatic nature of R groups at the pTyr+3 site were varied. The complexes of these ligands with the Grb2-SH2 domain were evaluated in a series of studies in which the binding thermodynamics were determined using isothermal titration calorimetry, and binding interactions were examined in crystallographic studies of two different complexes. Notably, adding nonpolar groups to the pTyr+3 site leads to higher binding affinities, but the magnitude and energetic origins of these effects vary with the nature of the R substituent. For example, enhancements to binding affinities using aliphatic R groups are driven by more favorable changes in binding entropies, whereas aryl R groups improve binding free energies through a combination of more favorable changes in binding enthalpies and entropies. However, enthalpy/entropy compensation plays a significant role in these associations and mitigates against any significant variation in binding free energies, which vary by only 0.8 kcal•mol-1, with changes in the electrostatic nature and size of the R group. Crystallographic studies show that differences in ΔG° or ΔH° correlate with buried nonpolar surface area, but they do not correlate with the total number of polar or van der Waals contacts. The relative number of ordered water molecules and relative order in the side chains at pTyr+3 correlate with differences in -TΔS°. Overall, these studies show that burial of nonpolar surface can lead to enhanced binding affinities arising from dominating entropy- or enthalpy-driven hydrophobic effects, depending upon the electrostatic nature of the apolar R group.

Charge distributions for molecular dynamics simulations from self-consistent polarization method

Partial atomic charges are important force field parameters. They are usually computed by applying quantum-chemical calculations and the assumed population scheme. In this study polarization consistent scheme of deriving a charge distribution inside solute molecule is proposed. The environment effect is explicitly taken into account by distributing solvent molecules around the solute target. The performed analysis includes a few computational schemes (HF, MP2, B3LYP, and M026X), basis sets (cc-pvnz, n = 2, 3, …, 6), and electrostatically derived charge distributions (KS, CHELP, CHELPG, and HLY). It is demonstrated that the environment effect is very important and cannot be disregarded. The second solvation shell should be included to achieve the charge convergence. Huge corrections to charge distribution are due to induction and dispersion. The B3LYP/cc-pvqz level of theory is recommended for deriving the charges within self-consistent polarization scheme.

Influence of Ionic Strength on Hydrophobic Interactions in Water: Dependence on Solute Size and Shape

Hydrophobicity is a phenomenon of great importance in biology, chemistry, and biochemistry. It is defined as the interaction between nonpolar molecules or groups in water and their low solubility. Hydrophobic interactions affect many processes in water, for example, complexation, surfactant aggregation, and coagulation. These interactions play a pivotal role in the formation and stability of proteins or biological membranes. In the present study, we assessed the effect of ionic strength, solute size, and shape on hydrophobic interactions between pairs of nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene, ethane, propane, butane, hexane, octane, and decane were simulated by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P and TIP4PEW water models were used. Potential of mean force (PMF) plots of these dimers were determined at four values of ionic strength, 0, 0.04, 0.08, and 0.40 mol/dm³, to observe its impact on hydrophobic interactions. The characteristic shape of PMFs with three extrema (contact minimum, solvent-separated minimum, and desolvation maximum) was observed for most of the compounds for hydrophobic interactions. Ionic strength affected hydrophobic interactions. We observed a tendency to deepen contact minima with an increase in ionic strength value in the case of spherical and spheroidal molecules. Additionally, two-dimensional distribution functions describing water density and average number of hydrogen bonds between water molecules were calculated in both water models for adamantane and hexane. It was observed that the density of water did not significantly change with the increase in ionic strength, but the average number of hydrogen bonds changed. The latter tendency strongly depends on the water model used for simulations.

Solvation structure and dynamics of the dimethylammonium cation diluted in liquid water: A molecular dynamics approach

Classical molecular dynamics simulation techniques were employed to investigate the local solvation structure and related dynamics of the dimethylammonium cation diluted in liquid water at ambient conditions. The translational and orientational order around the dimethylammonium cation was investigated in terms of the corresponding radial and angular distribution functions. The results obtained revealed that the first solvation shell of the dimethylammonium consists mainly of two and, less frequently, three water molecules. The two nearest water neighbors form hydrogen bonds with the ammonium hydrogen atoms of the cation, whereas the third neighbor interacts with the methyl hydrogen atoms as well. The distribution of the trigonal order parameter exhibits a bimodal behavior, signifying the existence of local orientational heterogeneities in the solvation shell of the dimethylammonium cation. The calculated continuous and intermittent residence and hydrogen bond lifetimes for the cation-water pairs have also been found to be longer in comparison with the water-water ones. The very similar self-diffusion coefficients of the dimethylammonium cation and the water molecules in the bulk dilute solution indicate that the translational motions of the cation are mainly controlled by the translational mobility of the surrounding water molecules.

Interaction of Reactive-Dye Chromophores and DEG on Ink-Jet Printing Performance

Digital inkjet printing has been widely used in textile industry. The quality of dye solutions and ink-jet droplets limits the ink-jet printing performance, which is very important for obtaining high-quality ink-jet printing images on fabrics. In this paper, we introduced diethylene glycol (DEG) into the dye solutions of Reactive Blue 49 and Reactive Orange 13, respectively, and investigated the interaction between dye chromophores and DEG molecules. Results indicated that the dye chromophores were featured in the aggregation. Adding DEG into the dye solution could effectively disaggregate clusters of reactive dyes, and eliminate satellite ink droplets, thus improving the resolution of the ink-jet printing image on fabrics. Under the same DEG concentration, the disaggregation effect was more obvious in Orange 13 than in Reactive Blue 49. Higher DEG concentration was required in Reactive Orange 13 solution for creating complete and stable ink drops. The surface tension and viscosity of the dye solutions were measured, and printing performance on cotton fabrics was evaluated. The interaction mechanism between dye chromophores and DEG molecules was also investigated. Results from this work are useful for high-quality ink-jet printing images on fabrics.

Protein Supramolecular Structures: From Self-Assembly to Nanovaccine Design

Life-inspired protein supramolecular assemblies have recently attracted considerable attention for the development of next-generation vaccines to fight against infectious diseases, as well as autoimmune diseases and cancer. Protein self-assembly enables atomic scale precision over the final architecture, with a remarkable diversity of structures and functionalities. Self-assembling protein nanovaccines are associated with numerous advantages, including biocompatibility, stability, molecular specificity and multivalency. Owing to their nanoscale size, proteinaceous nature, symmetrical organization and repetitive antigen display, protein assemblies closely mimic most invading pathogens, serving as danger signals for the immune system. Elucidating how the structural and physicochemical properties of the assemblies modulate the potency and the polarization of the immune responses is critical for bottom-up design of vaccines. In this context, this review briefly covers the fundamentals of supramolecular interactions involved in protein self-assembly and presents the strategies to design and functionalize these assemblies. Examples of advanced nanovaccines are presented, and properties of protein supramolecular structures enabling modulation of the immune responses are discussed. Combining the understanding of the self-assembly process at the molecular level with knowledge regarding the activation of the innate and adaptive immune responses will support the design of safe and effective nanovaccines.

Modeling hydration-mediated ion-ion interactions in electrolytes through oscillating Yukawa potentials

Classical Poisson-Boltzmann theory represents a mean-field description of the electric double layer in the presence of only Coulomb interactions. However, aqueous solvents hydrate ions, which gives rise to additional hydration-mediated ion-ion interactions. Experimental and computational studies suggest damped oscillations to be a characteristic feature of these hydration-mediated interactions. We have therefore incorporated oscillating Yukawa potentials into the mean-field description of the electric double layer. This is accomplished by allowing the decay length of the Yukawa potential to be complex valued. Ion specificity emerges from assigning individual strengths and phases to the Yukawa potential for anion-anion, anion-cation, and cation-cation pairs as well as for anions and cations interacting with an electrode or macroion. Excluded volume interactions between ions are approximated by replacing the ideal gas entropy by that of a lattice gas. We derive mean-field equations for the Coulomb and Yukawa potentials and use their solutions to compute the differential capacitance for an isolated planar electrode and the pressure that acts between two planar, like-charged macroion surfaces. Attractive interactions appear if the surface charge density of the macroions is sufficiently small.