Hydrophobic and Ionic Interactions in Nanosized Water Droplets

Ultrafast C-C and C-N bond formation reactions in water microdroplets facilitated by the spontaneous generation of carbocations

Carbocations are important electrophilic intermediates in organic chemistry, but their formation typically requires harsh conditions such as extremely low pH, elevated temperature, strong oxidants and/or expensive noble-metal catalysts. Herein, we report the spontaneous generation of highly reactive carbocations in water microdroplets by simply spraying a diarylmethanol aqueous solution. The formation of transient carbocations as well as their ultrafast in-droplet transformations through carbocation-involved C-C and C-N bond formation reactions are directly characterized by mass spectrometry. The intriguing formation and stabilization of carbocations are attributed to the super acidity of the positively charged water microdroplets as well as the high electric fields at the water-air interfaces. Without the utilization of external acids as catalysts, we believe that these microdroplet reactions would pose a new and sustainable way for the construction of aryl-substituted compounds.

Rapid Characterization of Antibodies via Automated Flow Injection Coupled with Online Microdroplet Reactions and Native-pH Mass Spectrometry

Microdroplet reactions have aroused much interest due to significant reaction acceleration (e.g., ultrafast protein digestion in microdroplets could occur in less than 1 ms). This study integrated a microdroplet protein digestion technique with automated sample flow injection and online mass spectrometry (MS) analysis, to develop a rapid and robust method for structural characterization of monoclonal antibodies (mAbs) that is essential to assess the antibody drug's safety and quality. Automated sequential aspiration and mixing of an antibody and an enzyme (IdeS or IgdE) enabled rapid analysis with high reproducibility (total analysis time: 2 min per sample; reproducibility: ∼2% coefficient of variation). Spraying the sample in ammonium acetate buffer (pH 7) using a jet stream source allowed efficient digestion of antibodies and efficient ionization of resulting antibody subunits under native-pH conditions. Importantly, it also provided a platform to directly study specific binding of an antibody and an antigen (e.g., detecting the complexes mAb/RSFV antigen and F(ab')2/RSVF in this study). Furthermore, subsequent tandem MS analysis of a resulting subunit from microdroplet digestion enabled localizing post-translational modifications on particular domains of a mAb in a rapid fashion. In combination with IdeS digestion of an antibody, additional tris(2-carboxyethyl)phosphine (TCEP) reduction and N-glycosidase F (PNGase F) deglycosylation reactions that facilitate antibody analysis could be realized in "one-pot" spraying. Interestingly, increased deglycosylation yield in microdroplets was found, simply by raising the sample temperature. We expect that our method would have a high impact for rapid characterization of monoclonal antibodies.

Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids

Amide bond formation, the essential condensation reaction underlying peptide synthesis, is hindered in aqueous systems by the thermodynamic constraints associated with dehydration. This represents a key difficulty for the widely held view that prebiotic chemical evolution leading to the formation of the first biomolecules occurred in an oceanic environment. Recent evidence for the acceleration of chemical reactions at droplet interfaces led us to explore aqueous amino acid droplet chemistry. We report the formation of dipeptide isomer ions from free glycine or L-alanine at the air-water interface of aqueous microdroplets emanating from a single spray source (with or without applied potential) during their flight toward the inlet of a mass spectrometer. The proposed isomeric dipeptide ion is an oxazolidinone that takes fully covalent and ion-neutral complex forms. This structure is consistent with observed fragmentation patterns and its conversion to authentic dipeptide ions upon gentle collisions and for its formation from authentic dipeptides at ultra-low concentrations. It also rationalizes the results of droplet fusion experiments that show that the dipeptide isomer facilitates additional amide bond formation events, yielding authentic tri- through hexapeptides. We propose that the interface of aqueous microdroplets serves as a drying surface that shifts the equilibrium between free amino acids in favor of dehydration via stabilization of the dipeptide isomers. These findings offer a possible solution to the water paradox of biopolymer synthesis in prebiotic chemistry.

Droplet Flow Assisted Electrocatalytic Oxidation of Selected Alcohols under Ambient Condition

This study reports using a droplet flow assisted mechanism to enhance the electrocatalytic oxidation of benzyl alcohol, 2-phenoxyethanol, and hydroxymethylfurfural at room temperature. Cobalt phosphide (CoP) was employed as an active electrocatalyst to promote the oxidation of each of the individual substrates. Surface analysis of the CoP electrocatalyst using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), as well as electrochemical characterization, revealed that it had excellent catalytic activity for each of the substrates studied. The combined droplet flow with the continuous flow electrochemical oxidation approach significantly enhanced the conversion and selectivity of the transformation reactions. The results of this investigation show that at an electrolysis potential of 1.3 V and ambient conditions, both the selectivity and yield of aldehyde from substrate conversion can reach 97.0%.

Low Density Interior in Supercooled Aqueous Nanodroplets Expels Ions to the Subsurface

The interaction between water and ions within droplets plays a key role in the chemical reactivity of atmospheric and man-made aerosols. Here we report direct computational evidence that in supercooled aqueous nanodroplets a lower density core of tetrahedrally coordinated water expels the cosmotropic ions to the denser and more disordered subsurface. In contrast, at room temperature, depending on the nature of the ion, the radial distribution in the droplet core is nearly uniform or elevated toward the center. We analyze the spatial distribution of a single ion in terms of a reference electrostatic model. The energy of the system in the analytical model is expressed as the sum of the electrostatic and surface energy of a deformable droplet. The model predicts that the ion is subject to a harmonic potential centered at the droplet's center of mass. We name this effect "electrostatic confinement". The model's predictions are consistent with the simulation findings for a single ion at room temperature but not at supercooling. We anticipate this study to be the starting point for investigating the structure of supercooled (electro)sprayed droplets that are used to preserve the conformations of macromolecules originating from the bulk solution.

Unraveling the Interaction of Water-in-Oil Emulsion Droplets via Molecular Simulations and Surface Force Measurements

Water-in-oil emulsions widely exist in various chemical and petroleum engineering processes, and their stabilization and destabilization behaviors have attracted much attention. In this work, molecular dynamic (MD) simulations were conducted on the water-in-oil emulsion droplets with the presence of surface-active components, including a polycyclic aromatic compound (VO-79) and two nonionic surfactants: the PEO₅PPO₁₀PEO₅ triblock copolymer and Brij-93. At the surface of water droplets, films were formed by the adsorbate molecules that redistributed during the approaching of the droplets. The redistribution of PEO₅PPO₁₀PEO₅ was more pronounced than that of Brij-93 and VO-79, which contributed to lower repulsion during coalescence. The interaction forces during droplet coalescence were also measured using atomic force microscopy. Jump-in phenomenon and coalescence were observed for systems with VO-79, Brij-93, and a low concentration of Pluronic P123. The critical force before jump-in was lowest for the low concentration of Pluronic P123, consistent with the MD results. Adhesion was measured when separating water droplets with a high concentration of Pluronic P123. By correlating theoretical simulations and experimental force measurements, this work improves the fundamental understanding on the interaction behaviors of water droplets in an oil medium in the presence of interface-active species and provides atomic-level insights into the stabilization and destabilization mechanisms of water-in-oil emulsion.

Microdroplet Ultrafast Reactions Speed Antibody Characterization

Recently, microdroplet reactions have aroused much interest because the microdroplet provides a unique medium where organic reactions could be accelerated by a factor of 10³ or more. However, microdroplet reactions of proteins have been rarely studied. We report the occurrence of multiple-step reactions of a large protein, specifically, the digestion, reduction, and deglycosylation of an intact antibody, which can take place in microseconds with high reaction yields in aqueous microdroplets at room temperature. As a result, fast structural characterization of a monoclonal antibody, essential for assessing its quality as a therapeutic drug, can be enabled. We found that the IgG1 antibody can be digested completely by the IdeS protease in aqueous microdroplets in 250 microseconds, a 7.5 million-fold improvement in speed in comparison to traditional digestion in bulk solution (>30 min). Strikingly, inclusion of the reductant tris(2-carboxyethyl)phosphine in the spray solution caused simultaneous antibody digestion and disulfide bond reduction. Digested and reduced antibody fragments were either collected or analyzed online by mass spectrometry. Further addition of PNGase F glycosylase into the spray solution led to antibody deglycosylation, thereby producing reduced and deglycosylated fragments of analytical importance. In addition, glycated fragments of IgG1 derived from glucose modification were identified rapidly with this ultrafast digestion/reduction technique. We suggest that microdroplets can serve as powerful microreactors for both exploring large-molecule reactions and speeding their structural analyses.

Accelerated reactions of amines with carbon dioxide driven by superacid at the microdroplet interface

Microdroplets display distinctive interfacial chemistry, manifested as accelerated reactions relative to those observed for the same reagents in bulk. Carbon dioxide undergoes C–N bond formation reactions with amines at the interface of droplets to form carbamic acids. Electrospray ionization mass spectrometry displays the reaction products in the form of the protonated and deprotonated carbamic acid. Electrosonic spray ionization (ESSI) utilizing carbon dioxide as nebulization gas, confines reaction to the gas–liquid interface where it proceeds much faster than in the bulk. Intriguingly, trace amounts of water accelerate the reaction, presumably by formation of superacid or superbase at the water interface. The suggested mechanism of protonation of CO₂ followed by nucleophilic attack by the amine is analogous to that previously advanced for imidazole formation from carboxylic acids and diamines.

Microdroplets display distinctive interfacial chemistry, manifested as accelerated reactions relative to those observed for the same reagents in bulk.

Organic Reactions in Microdroplets: Reaction Acceleration Revealed by Mass Spectrometry

The striking finding that reaction acceleration occurs in confined-volume solutions sets up an apparent conundrum: Microdroplets formed by spray ionization can be used to monitor the course of bulk-phase reactions and also to accelerate reactions between the reagents in such a reaction. This Minireview introduces droplet and thin-film acceleration phenomena and summarizes recent methods applied to study accelerated reactions in confined-volume, high-surface-area solutions. Conditions that dictate either simple monitoring or acceleration are reconciled in the occurrence of discontinuous and complete desolvation as the endpoint of droplet evolution. The contrasting features of microdroplet and bulk-solution reactions are described together with possible mechanisms that drive reaction acceleration in microdroplets. Current applications of droplet microreactors are noted as is reaction acceleration in confined volumes and possible future scale-up.

Microdroplets Accelerate Ring Opening of Epoxides

The nucleophilic opening of an epoxide is a classic organic reaction that has widespread utility in both academic and industrial applications. We have studied the reaction of limonene oxide with morpholine to form 1-methyl-2-morpholino-4-(prop-1-en-2-yl) cyclohexan-1-ol in bulk solution and in electrosprayed microdroplets with a 1:1 v/v water/methanol solvent system. We find that even after 90 min at room temperature, there is no product detected by nuclear magnetic resonance spectroscopy in bulk solution whereas in room-temperature microdroplets (2-3 μm in diameter), the yield is already 0.5% in a flight time of 1 ms as observed by mass spectrometry. This constitutes a rate acceleration of ~ 10⁵ in the microdroplet environment, if we assume that as much as 5% of product is formed in bulk after 90 min of reaction time. We examine how the reaction rate depends on droplet size, solvent composition, sheath gas pressure, and applied voltage. These factors profoundly influence the extent of reaction. This dramatic acceleration is not limited to just one system. We have also found that the nucleophilic opening of cis-stilbene oxide by morpholine is similarly accelerated. Such large acceleration factors in reaction rates suggest the use of microdroplets for ring opening of epoxides in other systems, which may have practical significance if such a procedure could be scaled. Graphical Abstract This graphical image is distorted.  It is too extended in the vertical direction.  Please fix.ᅟ.

Controlling the Growth Modes of Femtoliter Sessile Droplets Nucleating on Chemically Patterned Surfaces

Femtoliter droplet arrays on immersed substrates are essential elements in a broad range of advanced droplet-based technologies, such as light manipulation, sensing, and high throughput diagnosis. Solvent exchange is a bottom-up approach for producing those droplets from a pulse of oil oversaturation when a good solvent of the droplet liquid is displaced by a poor solvent. The position and arrangement of the droplets are regulated by chemical micropatterns on the substrate. Here we show experimentally and theoretically that the growth modes of droplets confined in planar micropatterns on the surface can be manipulated through the laminar flow of the solvent exchange. The control parameters are the area size of the micropatterns and the flow rate, and the observables are the contact angle and the final droplet volume. For a given pattern size, the Peclet number of the flow determines whether the growing droplets switch from an initial constant contact angle mode to a subsequent constant contact radius mode. Good agreement is achieved between the experimental results and our theoretical model that describes the dependence of the final droplet size on Pe.

Entropy and enthalpy of interaction between amino acid side chains in nanopores

Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.

A nucleation-based method to study hydrophobic interactions under confinement: enhanced hydrophobic association driven by energetic contributions

A novel simulation approach was developed and applied to the study of hydrophobic interactions for a small hydrophobic solute pair under confinement. In this method, the aggregation-volume-bias Monte Carlo algorithm, developed originally for nucleation studies, is used to evaluate the association free energy with water molecules for a methane pair through the gradual addition of water molecules into a nanometer-sized sphere. Through a thermodynamic cycle, this method allows for a convenient examination of the free energy difference between two different solvated configurations without sampling any of the configurations in between. The potential of mean force (PMF) for a methane pair under confinement obtained from this method reveals that the stability of the contact pair configuration can be enhanced compared to that in bulk water, which is in agreement with previous studies. Also, constraining the center of this methane pair at the center of this confined volume yields a PMF with a metastable solvent separated configuration, resembling more closely the PMF from the bulk-phase system compared to previous studies in which this solvent-separated minimum was found to be completely absent. A combination with histogram reweighting enables the study of this association behavior at different thermodynamic conditions without additional simulations. From a comprehensive thermodynamic analysis, it is evident that such hydrophobic association, known to be entropically driven in the bulk-phase system at ambient conditions, is entropically favorable only when a suitable range of solvent molecules is added to the confined system. More importantly, the energetic contributions are a favorable factor that explains the enhanced hydrophobic association toward the high number of solvent molecules.

Self-assembly of proteins into a three-dimensional multilayer system: investigation of the surface of the human fungal pathogen Aspergillus fumigatus

Hydrophobins are small surface active proteins that fulfil a wide spectrum of functions in fungal growth and development. The human fungal pathogen Aspergillus fumigatus expresses RodA hydrophobins that self-assemble on the outer conidial surface into tightly organized nanorods known as rodlets. AFM investigation of the conidial surface allows us to evidence that RodA hydrophobins self-assemble into rodlets through bilayers. Within bilayers, hydrophilic domains of hydrophobins point inward, thus making a hydrophilic core, while hydrophobic domains point outward. AFM measurements reveal that several rodlet bilayers are present on the conidial surface thus showing that proteins self-assemble into a complex three-dimensional multilayer system. The self-assembly of RodA hydrophobins into rodlets results from attractive interactions between stacked β-sheets, which conduct to a final linear cross-β spine structure. A Monte Carlo simulation shows that anisotropic interactions are the main driving forces leading the hydrophobins to self-assemble into parallel rodlets, which are further structured in nanodomains. Taken together, these findings allow us to propose a mechanism, which conducts RodA hydrophobins to a highly ordered rodlet structure. The mechanism of hydrophobin assembly into rodlets offers new prospects for the development of more efficient strategies leading to disruption of rodlet formation allowing a rapid detection of the fungus by the immune system.

Adsorption of solutes at liquid-vapor interfaces: insights from lattice gas models

The adsorption behavior of ions at liquid-vapor interfaces exhibits several unexpected yet generic features. In particular, energy and entropy are both minimum when the solute resides near the surface, for a variety of ions in a range of polar solvents, contrary to predictions of classical theories. Motivated by this generality, and by the simple physical ingredients implicated by computational studies, we have examined interfacial solvation in highly schematic models, which resolve only coarse fluctuations in solvent density and cohesive energy. Here we show that even such lattice gas models recapitulate surprising thermodynamic trends observed in detailed simulations and experiments. Attention is focused on the case of two dimensions, for which approximate energy and entropy profiles can be calculated analytically. Simulations and theoretical analysis of the lattice gas highlight the role of capillary wave-like fluctuations in mediating adsorption. They further point to ranges of temperature and solute-solvent interaction strength where surface propensity is expected to be strongest.

Role of water in protein aggregation and amyloid polymorphism

A variety of neurodegenerative diseases are associated with amyloid plaques, which begin as soluble protein oligomers but develop into amyloid fibrils. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Mechanisms of in vivo amyloid formation involve a number of coconspirators and complex interactions with membranes. Nevertheless, understanding the biophysical basis of simpler in vitro amyloid formation is considered important for discovering ligands that preferentially bind regions harboring amyloidogenic tendencies. The determination of the fibril structure of many peptides has set the stage for probing the dynamics of oligomer formation and amyloid growth through computer simulations. Most experimental and simulation studies, however, have been interpreted largely from the perspective of proteins: the role of solvent has been relatively overlooked in oligomer formation and assembly to protofilaments and amyloid fibrils. In this Account, we provide a perspective on how interactions with water affect folding landscapes of amyloid beta (Aβ) monomers, oligomer formation in the Aβ16-22 fragment, and protofilament formation in a peptide from yeast prion Sup35. Explicit molecular dynamics simulations illustrate how water controls the self-assembly of higher order structures, providing a structural basis for understanding the kinetics of oligomer and fibril growth. Simulations show that monomers of Aβ peptides sample a number of compact conformations. The formation of aggregation-prone structures (N*) with a salt bridge, strikingly similar to the structure in the fibril, requires overcoming a high desolvation barrier. In general, sequences for which N* structures are not significantly populated are unlikely to aggregate. Oligomers and fibrils generally form in two steps. First, water is expelled from the region between peptides rich in hydrophobic residues (for example, Aβ16-22), resulting in disordered oligomers. Then the peptides align along a preferred axis to form ordered structures with anti-parallel β-strand arrangement. The rate-limiting step in the ordered assembly is the rearrangement of the peptides within a confining volume. The mechanism of protofilament formation in a polar peptide fragment from the yeast prion, in which the two sheets are packed against each other and create a dry interface, illustrates that water dramatically slows self-assembly. As the sheets approach each other, two perfectly ordered one-dimensional water wires form. They are stabilized by hydrogen bonds to the amide groups of the polar side chains, resulting in the formation of long-lived metastable structures. Release of trapped water from the pore creates a helically twisted protofilament with a dry interface. Similarly, the driving force for addition of a solvated monomer to a preformed fibril is water release; the entropy gain and favorable interpeptide hydrogen bond formation compensate for entropy loss in the peptides. We conclude by offering evidence that a two-step model, similar to that postulated for protein crystallization, must also hold for higher order amyloid structure formation starting from N*. Distinct water-laden polymorphic structures result from multiple N* structures. Water plays multifarious roles in all of these protein aggregations. In predominantly hydrophobic sequences, water accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow fibril growth rates in hydrophilic sequences.

Interactions between ionizable amino acid side chains at a lipid bilayer-water interface

Potentials of mean force (PMF) between ionizable amino acid side chains (Arg, Lys, His, Glu) in the headgroup area of a palmitoyl oleoyl phosphatidylcholine lipid bilayer were obtained from all-atom molecular dynamics simulations and the adaptive biasing force method. Simulations in bulk water were also performed for comparison. Side chains were constrained in collinear, stacking, and orthogonal (T-shaped) orientations. The most structured and attractive PMFs were observed for hydrogen-bonded side chains. Contact minima occurred at a distance of 2.6-3.1 Å between selected atoms or centers of mass with the most attractive interaction (-9.6 kcal/mol) observed between Arg(+) and Glu(-). Hydrogen bonds play a significant role in stabilizing these interactions. Interactions between like charged side chains can also be very attractive if the charges are screened by surrounding molecules or groups (e.g., the PMF value at the contact minimum for Arg(+)···Arg(+) is -7.6 kcal/mol). Like charged side chains can have contact minima as close as 3.6 Å. The PMFs depend strongly on the relative orientation of the side chains. In agreement with experimental studies and other simulations, we found the stacking arrangement of like charged side chains to be the most favorable orientation. Interaction energies and Lennard-Jones energies between side chains, headgroups, and water molecules were analyzed in order to rationalize the observed PMFs and their dependence on orientation. In general, the results cannot be explained by simple dielectric arguments.

Probing solvation decay length in order to characterize hydrophobicity-induced bead-bead attractive interactions in polymer chains

In this paper, we quantitatively demonstrate that exponentially decaying attractive potentials can effectively mimic strong hydrophobic interactions between monomer units of a polymer chain dissolved in aqueous solvent. Classical approaches to modeling hydrophobic solvation interactions are based on invariant attractive length scales. However, we demonstrate here that the solvation interaction decay length may need to be posed as a function of the relative separation distances and the sizes of the interacting species (or beads or monomers) to replicate the necessary physical interactions. As an illustrative example, we derive a universal scaling relationship for a given solute-solvent combination between the solvation decay length, the bead radius, and the distance between the interacting beads. With our formalism, the hydrophobic component of the net attractive interaction between monomer units can be synergistically accounted for within the unified framework of a simple exponentially decaying potential law, where the characteristic decay length incorporates the distinctive and critical physical features of the underlying interaction. The present formalism, even in a mesoscopic computational framework, is capable of incorporating the essential physics of the appropriate solute-size dependence and solvent-interaction dependence in the hydrophobic force estimation, without explicitly resolving the underlying molecular level details.

Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework

Water permeates all life, and mediates forces that are essential to the process of macromolecular self-assembly. Predicting these forces in a given biological context is challenging, since water organizes itself differently next to charged and hydrophobic surfaces, both of which are typically at play on the nanoscale in vivo. In this work, we present a simple statistical mechanical model for the forces water mediates between different confining surfaces, and demonstrate that the model qualitatively unifies a wide range of phenomena known in the simulation literature, including several cases of protein folding under confinement.

Quasichemical and structural analysis of polarizable anion hydration

Quasichemical theory is utilized to analyze the relative roles of solute polarization and size in determining the structure and thermodynamics of bulk anion hydration for the Hofmeister series Cl(-), Br(-), and I(-). Excellent agreement with experiment is obtained for whole salt hydration free energies using the polarizable AMOEBA force field. The total hydration free energies display a stronger dependence on ion size than on polarizability. The quasichemical approach exactly partitions the solvation free energy into inner-shell, outer-shell packing, and outer-shell long-ranged contributions by means of a hard-sphere condition. The inner-shell contribution becomes slightly more favorable with increasing ion polarizability, indicating electrostriction of the nearby waters. Small conditioning radii, even well inside the first maximum of the ion-water(oxygen) radial distribution function, result in Gaussian behavior for the long-ranged contribution that dominates the ion hydration free energy. This in turn allows for a mean-field treatment of the long-ranged contribution, leading to a natural division into first-order electrostatic, induction, and van der Waals terms. The induction piece exhibits the strongest ion polarizability dependence, while the larger-magnitude first-order electrostatic piece yields an opposing but weaker polarizability dependence. The van der Waals piece is small and positive, and it displays a small ion specificity. The sum of the inner-shell, packing, and long-ranged van der Waals contributions exhibits little variation along the anion series for the chosen conditioning radii, targeting electrostatic effects (influenced by ion size) as the largest determinant of specificity. In addition, a structural analysis is performed to examine the solvation anisotropy around the anions. As opposed to the hydration free energies, the solvation anisotropy depends more on ion polarizability than on ion size: increased polarizability leads to increased anisotropy. The water dipole moments near the ion are similar in magnitude to bulk water, while the ion dipole moments are found to be significantly larger than those observed in quantum mechanical studies. Possible impacts of the observed over-polarization of the ions on simulated anion surface segregation are discussed.

Hydrophobic interactions of hexane in nanosized water droplets

We use all-atomistic molecular dynamics simulations to study hydrophobic interactions of hexane in nanosized water droplets where the hydrogen bonding network of water molecules is disrupted at the surface. As a result of the competition between the energetics of a hexane molecule and the distribution of water molecules that lost the ability to form hydrogen bonds at the boundary, all-trans-hexane molecules are statistically favored at the surface of a nanosized water droplet and such a statistical trend increases as the size of a nano water droplet decreases. Changes in the radial distribution and the orientation of water molecules surrounding hexane in nanosized water droplets over bulk water are indicative of the finite-size effects on the structural distribution of a short, topologically complex hydrocarbon chain.

Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study

The single mutation effect on the binding affinity of H3N2 viral protein hemagglutinin (HA) with the monoclonical antibody fragment (Fab) is studied in this paper using the free energy perturbation (FEP) simulations. An all-atom protein model with explicit solvents is used to perform an aggregate of several microsecond FEP molecular dynamics simulations. A recent experiment shows that a single mutation in H3N2 HA, T131I, increases the antibody-antigen dissociation constant Kd by a factor of approximately 4000 (equivalent to a binding affinity decrease of approximately 5 kcal/mol), thus introducing an escape of the antibody (Ab) neutralization. Our FEP result confirms this experimental finding by estimating the HA-Ab binding affinity decrease of 5.2 +/- 0.9 kcal/mol but with a somewhat different molecular mechanism from the experimental findings. Detailed analysis reveals that this large binding affinity decrease in the T131I mutant is mainly due to the displacement of two bridge water molecules otherwise present in the wild-type HA/Ab interface. The decomposition of the binding free energy supports this observation, as the major contribution to the binding affinity is from the electrostatic interactions. In addition, we find that the loss of the binding affinity is also related to the large conformational distortion of one loop (loop 155-161) in the unbound state of the mutant. We then simulate all other possible mutations for this specific mutation site T131, and predict a few more mutations with even larger decreases in the binding affinity (i.e., better candidates for antibody neutralization), such as T131W, T131Y, and T131F. As for further validation, we have also modeled another mutation, S157L, with experimental binding affinity available (Kd increasing approximately 500 times), and found a binding affinity decrease of 4.1 +/- 1.0 kcal/mol, which is again in excellent agreement with experiment. These large scale simulations might provide new insights into the detailed physical interaction, possible future escape mutation, and antibody-antigen coevolution relationship between influenza virus and human antibodies.

Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores

We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between the nonpolar solutes and completely eliminates the solvent separated minimum (SSM) that is seen in bulk water. The free energy profiles show that the methane molecules are either in contact or at separations corresponding to the diameter and the length of the cylindrical pore. Analytic calculations that estimate the entropy of the solutes, which are solvated at the pore surface, qualitatively explain the shape of the free energy profiles. Adding charges of opposite sign and magnitude 0.4e or e (where e is the electronic charge) to the methane molecules decreases their tendency for surface solvation and restores the SSM. We show that confinement induced ion-pair formation occurs whenever l(B)/D approximately O(1), where l(B) is the Bjerrum length and D is the pore diameter. The extent of stabilization of the SSM increases with ion charge density as long as l(B)/D<1. In pores with D<or=1.2 nm, in which the water is strongly layered, increasing the charge magnitude from 0.4e to e reduces the stability of the SSM. As a result, ion-pair formation that occurs with negligible probability in the bulk is promoted. In larger diameter pores that can accommodate a complete hydration layer around the solutes, the stability of the SSM is enhanced.

Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability

Confinement effects on protein stability are relevant in a number of biological applications ranging from encapsulation in the cylindrical cavity of a chaperonin, translocation through pores, and structure formation in the exit tunnel of the ribosome. Consequently, free energies of interaction between amino acid side chains in restricted spaces can provide insights into factors that control protein stability in nanopores. Using all-atom molecular dynamics simulations, we show that 3 pair interactions between side chains--hydrophobic (Ala-Phe), polar (Ser-Asn) and charged (Lys-Glu)--are substantially altered in hydrophobic, water-filled nanopores, relative to bulk water. When the pore holds water at bulk density, the hydrophobic pair is strongly destabilized and is driven to large separations corresponding to the width and the length of the cylindrical pore. As the water density is reduced, the preference of Ala and Phe to be at the boundary decreases, and the contact pair is preferred. A model that accounts for the volume accessible to Phe and Ala in the solvent-depleted region near the pore boundary explains the simulation results. In the pore, the hydrogen-bonded interactions between Ser and Asn have an enhanced dependence on their relative orientations, as compared with bulk water. When the side chains of Lys and Glu are restrained to be side by side, parallel to each other, then salt bridge formation is promoted in the nanopore. Based on these results, we argue and demonstrate that for a generic amphiphilic sequence, cylindrical confinement is likely to enhance thermodynamic stability relative to the bulk.

Polar confinement modulates solvation behavior of methane molecules

Polar confinement induces an amorphous solidlike state of water characterized by an orientational correlation time longer than hundreds of picoseconds and significant structural disorder. Solvation behavior of methane molecules is dramatically modulated under polar confinement. Moreover our simulations indicate that the charges equivalent to those borne by atoms of amino acids could generate an electric field which is strong enough to stimulate the phase transition of water. In our results, polar confinement is found to be more capable of aggregating hydrophobic molecules. This study raises an interesting mechanism by which the cagelike structure of the Escherichia coli chaperonin GroEL and the cochaperonin GroES complex helps protein folding.

Potential for modulation of the hydrophobic effect inside chaperonins

Despite the spontaneity of some in vitro protein-folding reactions, native folding in vivo often requires the participation of barrel-shaped multimeric complexes known as chaperonins. Although it has long been known that chaperonin substrates fold upon sequestration inside the chaperonin barrel, the precise mechanism by which confinement within this space facilitates folding remains unknown. We examine the possibility that the chaperonin mediates a favorable reorganization of the solvent for the folding reaction. We discuss the effect of electrostatic charge on solvent-mediated hydrophobic forces in an aqueous environment. Based on these physical arguments, we construct a simple, phenomenological theory for the thermodynamics of density and hydrogen-bond order fluctuations in liquid water. Within the framework of this model, we investigate the effect of confinement inside a chaperonin-like cavity on the configurational free energy of water by calculating solvent free energies for cavities corresponding to the different conformational states in the ATP-driven catalytic cycle of the prokaryotic chaperonin GroEL. Our findings suggest that one function of chaperonins may involve trapping unfolded proteins and subsequently exposing them to a microenvironment in which the hydrophobic effect, a crucial thermodynamic driving force for folding, is enhanced.

Rattling the cage: computational models of chaperonin-mediated protein folding

Chaperonins are known to maintain the stability of the proteome by facilitating the productive folding of numerous misfolded or aggregation-prone proteins and are thus essential for cell viability. Despite their established importance, the mechanism by which chaperonins facilitate protein folding remains unknown. Computer simulation techniques are now being employed to complement experimental ones in order to shed light on this mystery. Here we review previous computational models of chaperonin-mediated protein folding in the context of the two main hypotheses for chaperonin function: iterative annealing and landscape modulation. We then discuss new results pointing to the importance of solvent (a previously neglected factor) in chaperonin activity. We conclude with our views on the future role of simulation in studying chaperonin activity as well as protein folding in other biologically relevant confined contexts.

Enhancing the hydrophobic effect in confined water nanodrops

The distribution of hydrophobic solutes, such as methane, enclosed in a nanosized water droplet contained in a reverse micelle of diameter 2.82 nm is investigated using Monte Carlo simulations. The effect of the hydrophobic solute's atomic diameter on the solute-solute potential of mean force is also studied. The study reveals that confinement has a strong influence on the solute's tendency to associate. The potential of mean force exhibits only a single minimum, indicating that the contact pair is the only stable configuration between solutes. The solvent-separated pair that is universally observed for small solutes in bulk water is conspicuously absent. This enhanced hydrophobic effect is attributed to the lack of sufficient water to completely hydrate and stabilize the solvent-separated configurations. The study is expected to be important in understanding the role of hydrophobic forces during protein folding and nucleation under confinement.

Macromolecular crowding increases structural content of folded proteins

Here we show that increased amount of secondary structure is acquired in the folded states of two structurally-different proteins (alpha-helical VlsE and alpha/beta flavodoxin) in the presence of macromolecular crowding agents. The structural content of flavodoxin and VlsE is enhanced by 33% and 70%, respectively, in 400 mg/ml Ficoll 70 (pH 7, 20 degrees C) and correlates with higher protein-thermal stability. In the same Ficoll range, there are only small effects on the unfolded-state structures of the proteins. This is the first in vitro assessment of crowding effects on the native-state structures at physiological conditions. Our findings imply that for proteins with low intrinsic stability, the functional structures in vivo may differ from those observed in dilute buffers.