Showing papers in "The Journal of Physical Chemistry in 2017"

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

Abstract: For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein–protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein–water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.

Immobilization of Enzymes in Mesoporous Silica Particles: Protein Concentration and Rotational Mobility in the Pores B

Abstract: Enzyme immobilization in porous silica particles is used to improve enzyme function in biocatalytic applications. Here, we study the effective protein concentration and rotational mobility of lipase and bovine serum albumin in the pores, when confined in five types of mesoporous silica particles with different pore and particle sizes, exploiting the intrinsic UV–vis absorption and fluorescence anisotropy of the tryptophan residues. For all investigated combinations of proteins and particles, the steady-state anisotropy is higher than for the same protein in free solution, indicating a slower protein rotation inside the pores. The retardation is stronger in more narrow pores, but the proteins can still move, and there is no dependence on the particle size. The average number of proteins per particle, Nₚᵣₒₜ, varies with the particle diameter, D, as Nₚᵣₒₜ ∼ D².⁹⁵±⁰.⁰² for both proteins, which is close to the scaling D³.⁰±⁰.¹ for the available pore volume. This observation indicates that both proteins are distributed evenly throughout the particles and rules out that the proteins are only externally bound to the particle surface. Secondly, the concentration of the protein in the pores depends on the pore and protein size but not on the particle size and corresponds to volume fractions in the range of 20–60%.

Covalently Bonded MoS2–Borocarbonitride Nanocomposites Generated by Using Surface Functionalities on the Nanosheets and Their Remarkable HER Activity C

Abstract: In the light of the recent discovery that carbon-rich borocarbonitrides show electrocatalytic activity for generating hydrogen from water, we have synthesized nanocomposites by covalently cross-linking BC₇N with MoS₂ sheets to explore whether the HER activity can be significantly enhanced. In order to cross-link BC₇N and MoS₂ sheets, we have exploited the presence of different functional groups on the surfaces of BN (NH₂) and graphene (COOH) domains of the borocarbonitride, as quantitatively determined by FLOSS. We have thus obtained two nanocomposites differing in the location of the cross-linking and these are designated as BN/BCN–MoS₂ and G/BCN–MoS₂, depending on which domains in the borocarbonitride participate in cross-linking. These nanocomposites were characterized by various spectroscopic methods including fluorescence labeling and their electrochemical and photochemical HER activity investigated. The composite where the graphene domains are cross-linked to MoS₂ nanosheets, G/BCN–MoS₂ (1:2), exhibits outstanding electrochemical HER activity with an onset potential of −30 mV (vs RHE) and a current density of 10 mA cm–² at an overpotential of −35 mV. This performance is closely comparable to that of Pt. The composite where the BN domains were cross-linked show somewhat lower activity. The physical mixture of BCN and MoS₂, on the other hand, does not display any notable HER activity. The BCN–MoS₂ composites also exhibit good photochemical activity. It is noteworthy that 2H-MoS₂, which does not exhibit significant catalytic activity, can be rendered highly active by cross-linking with BCN.

Wettability of Complex Fluids and Surfactant Capped Nanoparticle-Induced Quasi-Universal Wetting Behavior B

Abstract: Even though there are quite large studies on wettability of aqueous surfactants and a few studies on effects of nanoparticles on wettability of colloids, to the best of authors’ knowledge, there is no study reported on the combined effect of surfactant and nanoparticles in altering the wettability. The present study, for the first time, reports an extensive experimental and theoretical study on the combined effect of surfactants and nanoparticles on the wettability of complex fluids such as nanocolloids on different substrates, ranging from hydrophilic with a predominantly polar surface energy component (silicon wafer and glass) to near hydrophobic range with a predominantly dispersive component of surface energy (aluminum and copper substrates). Systematically planned experiments are carried out to segregate the contributing effects of surfactants, particles, and combined particle and surfactants in modulating the wettability. The mechanisms and the governing parameters behind the interactions of nanocolloids alone and of surfactant capped nanocolloids with different surfaces are found to be grossly different. The article, for the first time, also analyzes the interplay of the nature of surfaces, surfactant and particle concentrations on contact angle, and contact angle hysteresis (CAH) of particle and surfactant impregnated colloidal suspensions. In the case of nanoparticle suspensions, the contact angle is observed to decrease for the hydrophobic system and increase for the hydrophilic systems considered. On the contrary, the combined particle and surfactant colloidal system shows a quasi-unique wetting behavior of decreasing contact angle with particle concentration on all substrates. Also interestingly, the combined particle surfactant system at all particle concentrations shows a wetting angle much lower than that of the only-surfactant case at the same surfactant concentration. Such counterintuitive observations have been explained based on the near-surface interactivity of the particle, fluid, and surfactant molecules based on effective slip length considerations. The CAH analyses of colloidal suspensions at varying surfactant and particle concentrations reveal in-depth physical insight into contact line pinning, and a unique novel relationship is established between the contact angle and differential energy for distorting the instantaneous contact angle for a pinned sessile droplet. A detailed theoretical analysis of the governing parameters influencing the wettability has been presented invoking the principles of DLVO (Derjaguin–Landau–Verwey–Overbeek), surface energy and interaction parameters influencing at the molecular scale, and the theoretical framework is found to support the experimental observations.

Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids B

Abstract: Locked nucleic acids (LNAs) are conformationally restricted RNA nucleotides. Their increased thermal stability and selectivity toward their complements make them well-suited for diagnostic and therapeutic applications. Although the structural and thermodynamic properties of LNA–LNA, LNA–RNA, and LNA–DNA hybridizations are known, the kinetic effects of incorporating LNA nucleotides into DNA strand displacement systems are not. Here, we thoroughly studied the strand displacement kinetics as a function of the number and position of LNA nucleotides in DNA oligonucleotides. When compared to that of an all-DNA control, with an identical sequence, the leakage rate constant was reduced more than 50-fold, to an undetectable level, and the invasion rate was preserved for a hybrid DNA/LNA system. The total performance enhancement ratio also increased more than 70-fold when calculating the ratio of the invading rate to the leakage rate constants for a hybrid system. The rational substitution of LNA nucleotides for DNA nucleotides preserves sequence space while improving the signal-to-noise ratio of strand displacement systems. Hybrid DNA/LNA systems offer great potential for high-performance chemical reaction networks that include catalyzed hairpin assemblies, hairpin chain reactions, motors, walkers, and seesaw gates.

Apparent Anomalous Diffusion in the Cytoplasm of Human Cells: The Effect of Probes’ Polydispersity B

Abstract: This work, based on in vivo and in vitro measurements, as well as in silico simulations, provides a consistent analysis of diffusion of polydisperse nanoparticles in the cytoplasm of living cells. Using the example of fluorescence correlation spectroscopy (FCS), we show the effect of polydispersity of probes on the experimental results. Although individual probes undergo normal diffusion, in the ensemble of probes, an effective broadening of the distribution of diffusion times occurs—similar to anomalous diffusion. We introduced fluorescently labeled dextrans into the cytoplasm of HeLa cells and found that cytoplasmic hydrodynamic drag, exponentially dependent on probe size, extraordinarily broadens the distribution of diffusion times across the focal volume. As a result, the in vivo FCS data were effectively fitted with the anomalous subdiffusion model while for a monodisperse probe the normal diffusion model was most suitable. Diffusion time obtained from the anomalous diffusion model corresponds to a probe whose size is determined by the weight-average molecular weight of the polymer. The apparent anomaly exponent decreases with increasing polydispersity of the probes. Our results and methodology can be applied in intracellular studies of the mobility of nanoparticles, polymers, or oligomerizing proteins.

Dissolution Kinetics of Hot Compressed Oxide Glasses

Abstract: The chemical durability of oxide glasses is an important property for a wide range of applications and can in some cases be tuned through composition optimization. However, these possibilities are relatively limited because around 3/5 of the atoms in most oxide glasses are oxygens. An alternative approach involves post-treatment of the glass. In this work, we focus on the effect of hot compression on dissolution kinetics because it is known to improve, for example, elastic moduli and hardness, whereas its effect on chemical durability is poorly understood. Specifically, we study the bulk glass dissolution rate of phosphate, silicophosphate, borophosphate, borosilicate, and aluminoborosilicate glasses, which have been compressed at 0.5, 1.0, and 2.0 GPa at the glass transition temperature (Tg). We perform weight loss and supplementary modifier leaching measurements of bulk samples immersed in acid (pH 2) and neutral (pH 7) solutions. Compression generally improves the chemical durability as measured from weight loss, but the effect is highly composition- and pressure-dependent. As such, we show that the dissolution mechanisms depend on the topological changes induced by permanent densification, which in turn are a function of the changes in the number of nonbridging oxygens and the network cross-linking. We also demonstrate a direct relationship between the chemical durability and the number of chemical topological constraints per atom (nc) acting within the molecular network.

Size-Dependent Relationships between Protein Stability and Thermal Unfolding Temperature Have Important Implications for Analysis of Protein Energetics and High-Throughput Assays of Protein–Ligand Interactions B

Abstract: Changes in protein stability are commonly reported as changes in the melting temperature, ΔTM, or as changes in unfolding free energy at a particular temperature, ΔΔG°. Using data for 866 mutants from 16 proteins, we examine the relationship between ΔΔG° and ΔTM. A linear relationship is observed for each protein. The slopes of the plots of ΔTM vs ΔΔG° for different proteins scale as N–¹, where N is the number of residues in the protein. Thus, a given change in ΔG° causes a much larger change in TM for a small protein relative to the effect observed for a large protein. The analysis suggests that reasonable estimates of ΔΔG° for a mutant can be obtained by interpolating measured values of TM. The relationship between ΔΔG° and ΔTM has implications for the design and interpretation of high-throughput assays of protein–ligand binding. So-called thermal shift assays rely upon the increase in stability which results from ligand binding to the folded state. Quantitative relationships are derived which show that the observed thermal shift, ΔTM, scales as N–¹. Hence, thermal shift assays are considerably less sensitive for ligand binding to larger proteins.

Improved Solution-State Properties of Monoclonal Antibodies by Targeted Mutations

Abstract: Monoclonal antibody (mAb)-based therapeutics often require high-concentration formulations. Unfortunately, highly concentrated antibody solutions often have biophysical properties that are disadvantageous for therapeutic development, such as high viscosity, solubility limitations, precipitation issues, or liquid–liquid phase separation. In this work, we present a computational rational design principle for improving the thermodynamic stability of mAb solutions through targeted point mutations. Two publicly available IgG1 monoclonal antibodies that exhibit high viscosity at high concentrations were used as model systems. Guided by a computationally efficient approach that combines molecular dynamics simulations with three-dimensional reference interaction site model theory, point mutations of charged residues were introduced in the variable Fv regions in such a manner that the hydration free energy was optimized. Two selected point mutants were then produced by transient expression and characterized experimentally. Both engineered mAbs have reduced viscosity at high concentration, less negative second virial coefficient, and improved solubility compared to the respective wild-types. The results obtained with the suggested straightforward design principle underline the relevance of solvation effects for understanding, and ultimately optimizing, the properties of highly concentrated mAb solutions, with possible implications also for other biomolecular systems.

Molecular Simulations of Melittin-Induced Membrane Pores

Abstract: Membrane-active peptides (MAPs) are able to induce pores in cell membranes via molecular mechanisms, which are still subject to ongoing research. In this work, we present molecular dynamics simulations that suggest a precursor membrane defect plays an important role in the pore-inducing activity of the prototypical antimicrobial peptide melittin. The simulations reveal that the hydrophobic N-terminus of melittin is able to recognize and insert into the membrane defect in the lipid bilayer and that this leads to a cascading transfer of adsorbed peptides to the membrane defect, leading to peptide aggregation in the pore. We show that this mechanism also acts in the case of a melittin mutant without the flexible central proline hinge, thus indicating the latter is not crucial to the activity of melittin, which is consistent with experiments.

Proton-Detected NMR Spectroscopy of Nanodisc-Embedded Membrane Proteins: MAS Solid-State vs Solution-State Methods B

Abstract: The structural and dynamical characterization of membrane proteins in a lipid bilayer at physiological pH and temperature and free of crystal constraints is crucial for the elucidation of a structure/dynamics–activity relationship. Toward this aim, we explore here the properties of the outer-membrane protein OmpX embedded in lipid bilayer nanodiscs using proton-detected magic angle spinning (MAS) solid-state NMR at 60 and 110 kHz. [¹H,¹⁵N]-correlation spectra overlay well with the corresponding solution-state NMR spectra. Line widths as well as line intensities in solid and solution both depend critically on the sample temperature and, in particular, on the crossing of the lipid phase transition temperature. MAS (110 kHz) experiments yield well-resolved NMR spectra also for fully protonated OmpX and both below and above the lipid phase transition temperature.

Binding of Thioflavin T and Related Probes to Polymorphic Models of Amyloid-β Fibrils

Abstract: Alzheimer’s disease is a challenge of the utmost importance for contemporary society. An early diagnosis is essential for the development of treatments and for establishing a network of support for the patient. In this light, the deposition in the brain of amyloid-β fibrillar aggregates, which is a distinctive feature of Alzheimer, is key for an early detection of this disease. In this work we propose an atomistic study of the interaction of amyloid tracers with recently published polymorphic models of amyloid-β 1–40 and 1–42 fibrils, highlighting the relationship between marker architectures and binding affinity. This work uncovers the importance of quaternary structure, and in particular of junctions between amyloid-β protofilaments, as the key areas for marker binding.

Insight into the Complexation of Actinides and Lanthanides with Diglycolamide Derivatives: Experimental and Density Functional Theoretical Studies

Abstract: Extraction of actinide (Pu⁴⁺, UO₂²⁺, Am³⁺) and lanthanide (Eu³⁺) ions was carried out using different diglycolamide (DGA) ligands with systematic increase in the alkyl chain length from n-pentyl to n-dodecyl. The results show a monotonous reduction in the metal ion extraction efficiency with increasing alkyl chain length and this reduction becomes even more prominent in case of the branched alkyl (2-ethylhexyl) substituted DGA (T2EHDGA) for all the metal ions studied. Steric hindrance provided by the alkyl groups has a strong influence in controlling the extraction behavior of the DGAs. The distribution ratio reduction factor, defined as the ratio of the distribution ratio values of different DGAs to that of T2EHDGA, in n-dodecane follows the order UO₂²⁺ > Pu⁴⁺ > Eu³⁺ > Am³⁺. Complexation of Nd³⁺ was carried out with the DGAs in methanol by carrying out UV–vis spectrophotometric titrations. The results indicate a significant enhancement in the complexation constants upon going from methyl to n-pentyl substituted DGAs. They decreased significantly for DGAs containing alkyl substituents beyond the n-pentyl group, which corresponds to the observed trend from the solvent extraction studies. DFT-based calculations were performed on the free and the Nd³⁺ complexes of the DGAs both in the gas and the solvent (methanol) phase and the results were compared the experimental observations. Luminescence spectroscopic investigations were carried out to understand the complexation of Eu³⁺ with the DGA ligands and to correlate the nature of the alkyl substituents on the photophysical properties of the Eu(III)-DGA complexes. The monoexponential nature of the decay profiles of the complex revealed the predominant presence of single species, while no water molecules were present in the inner coordination sphere of the Eu³⁺ ion.

Predicting Accurate Solvation Free Energy in n-Octanol Using 3D-RISM-KH Molecular Theory of Solvation: Making Right Choices

Abstract: Molecular theory of solvation, a.k.a., three-dimensional reference interaction site model theory of solvation with Kovalenko–Hirata closure relation (3D-RISM-KH), is an accurate and fast theory predicting solvation free energy and structure. Here we report a benchmark study of n-octanol solvation free energy calculations using this theory. The choice of correct force field parameters is quintessential for the success of 3D-RISM theory, and we present a guideline to obtain them for n-octanol solvent. Our best prediction of the solvation free energy on a set of 205 small organic molecules supplemented with the so-called “universal correction” scheme yields relative mean unsigned error of 0.94 kcal/mol against the reported database. The best agreement is obtained with the united atom (UA) type force field parametrization of n-octanol with the van der Waals parameters of hydroxyl hydrogen reported by Kobryn et al. [Kobryn, A. E.; Kovalenko, A. J. Chem. Phys. 2008, 129, 134701].

Lattice Model of an Ionic Liquid at an Electrified Interface B

Abstract: We study ionic liquids interacting with electrified interfaces. The ionic fluid is modeled as a Coulomb lattice gas. We compare the ionic density profiles calculated using a popular modified Poisson–Boltzmann equation with the explicit Monte Carlo simulations. The modified Poisson–Boltzmann theory fails to capture the structural features of the double layer and is also unable to correctly predict the ionic density at the electrified interface. The lattice Monte Carlo simulations qualitatively capture the coarse-grained structure of the double layer in the continuum. We propose a convolution relation that semiquantitatively relates the ionic density profiles of a continuum ionic liquid and its lattice counterpart near an electrified interface.

The Dynamical Transition of Lipid Multilamellar Bilayers as a Matter of Cooperativity B

Abstract: The present study is the application of a two-state model formerly developed by Bicout and Zaccai [Bicout, D. J. and Zaccai, G. Biophys. J. 2001, 80 (3), 1115−1123] to describe the dynamical transition exhibited in the atomic mean square displacements of biological samples in terms of dynamic and thermodynamic parameters. Data were obtained by elastic incoherent neutron scattering on 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes in various hydration states and on one partially per-deuterated lipid membrane. Fitting the data with the model allowed investigating which parts of lipid molecules were mainly involved in the dynamical transition, heads, tails, or both. Clear differences were found between the fully protonated and partially deuterated membranes. These findings shed light on the question of what is the degree of dynamical cooperativity of the atoms during the transition. Whereas the level of hydration does not significantly affect it, as the dry, the intermediate dry, and fully hydrated membranes all undergo a rather broad transition, the transition of the lipid tails is much sharper and sets in at much lower temperature than that of the heads. Therefore, the dynamical cooperativity appears high among the particles in the tails. Moreover, the transition of the lipid tails has to be completed first before the one of the head groups starts.

Membrane Binding and Pore Formation by a Cytotoxic Fragment of Amyloid β Peptide

Abstract: Amyloid β (Aβ) peptide contributes to Alzheimer's disease by a yet unidentified mechanism. In the brain tissue, Aβ occurs in various forms, including an undecapeptide Aβ25-35, which exerts a neurotoxic effect through the mitochondrial dysfunction and/or Ca2+-permeable pore formation in cell membranes. This work was aimed at the biophysical characterization of membrane binding and pore formation by Aβ25-35. Interaction of Aβ25-35 with anionic and zwitterionic membranes was analyzed by microelectrophoresis. In pore formation experiments, Aβ25-35 was incubated in aqueous buffer to form oligomers and added to Quin-2-loaded vesicles. Gradual increase in Quin-2 fluorescence was interpreted in terms of membrane pore formation by the peptide, Ca2+ influx, and binding to intravesicular Quin-2. The kinetics and magnitude of this process were used to evaluate the rate constant of pore formation, peptide-peptide association constants, and the oligomeric state of the pores. Decrease in membrane anionic charge and high ionic strength conditions significantly suppressed membrane binding and pore formation, indicating the importance of electrostatic interactions in these events. Circular dichroism spectroscopy showed that Aβ25-35 forms the most efficient pores in β-sheet conformation. The data are consistent with an oligo-oligomeric pore model composed of up to eight peptide units, each containing 6-8 monomers.

Computational Insight into the Interaction of Cytochrome C with Wet and PVP-Coated Ag Surfaces

Abstract: In this work, the adsorption of cytochrome C (CytC) on wet {100}, {111}, {110}, and {120} silver surfaces has been investigated by computational simulations. The effect of polyvinylpyrrolidone (PVP) coating has also been studied. The main results obtained can be summarized as follow: (a) CytC strongly interacts with wet bare high index facets, while the adsorption over the {100} surface is disfavored due to the strong water structuring at the surface; (b) a nonselective protein adsorption mechanism is highlighted; (c) the native structure of CytC is well preserved during adsorption; (d) the heme group of CytC is never found to interact directly with the surface; (e) the interactions with the PVP-capped {100} surface is weak and specific. These results can be exploited to better control biological responses at engineered nanosurface, allowing the development of improved diagnostic tools.

Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials

Abstract: We introduce a computational framework that is able to describe general many-body coarse-grained (CG) interactions of molecules and use it to model the free energy surface of molecular liquids as a cluster expansion in terms of monomer, dimer, and trimer terms. The contributions to the free energy due to these terms are inferred from all-atom molecular dynamics (MD) data using Gaussian Approximation Potentials, a type of machine-learning model that employs Gaussian process regression. The resulting CG model is much more accurate than those possible using pair potentials. Though slower than the latter, our model can still be faster than all-atom simulations for solvent-free CG models commonly used in biomolecular simulations.

Role of Water Solidification Concepts in Designing Nano-Textured Anti-Icing Surfaces B

Abstract: Creating anti-icing surfaces has proven to be a challenging task. With such a wide range of impacting parameters it is important to quantify ones with a large effect. Water solidification mechanisms play a fundamental role in designing anti-icing surfaces. In this Review Article, we will consider the effects of surface roughening on the mechanisms of nucleation and ice growth to show how surface roughening can be an alternative to overcome the limitations of icing of superhydrophobic coatings and surfaces. The results from various studies of anti-icing properties of superhydrophobic surfaces are reviewed and expanded to incorporate water solidification mechanisms to provide a more comprehensive approach to the design of anti-icing surfaces. The literature within this review shows that by applying the necessary roughness to either hydrophilic or hydrophobic surfaces and adjusting the surface topography, we can significantly suppress ice nucleation on various surfaces.

The Role of the Hydroxyl Group in Propofol–Protein Target Recognition: Insights from ONIOM Studies B

Abstract: Propofol (PFL, 1-hydroxyl-2,6-diisopropylbenzene) is currently used widely as one of the most well-known intravenous anesthetics to relieve surgical suffering, but its mechanism of action is not yet clear. Previous experimental studies have demonstrated that the hydroxyl group of PFL plays a dominant role in the molecular recognition of PFL with receptors that lead to hypnosis. To further explore the mechanism of anesthesia induced by PFL in the present work, the exact binding features and interaction details of PFL with three important proteins, human serum albumin (HSA), the pH-gated ion channel from Gloeobacter violaceus (GLIC), and horse spleen apoferritin (HSAF), were investigated systematically by using a rigorous three-layer ONIOM (M06-2X/6-31+G*:PM6:AMBER) method. Additionally, to further characterize the possible importance of such hydroxyl interactions, a similar set of calculations was carried out on the anesthetically inactive fropofol (FFL, 1-fluoro-2,6-diisopropylbenzene) in which the fluorine was substituted for the hydroxyl. According to the ONIOM calculations, atoms in molecules (AIM) analyses, and electrostatic potential (ESP) analyses, the significance of hydrogen bond, halogen bond, and hydrophobic interactions in promoting proper molecular recognition was revealed. The binding interaction energies of PFL with different proteins were generally larger than FFL and are a significant determinant of their differential anesthetic efficacies. Interestingly, although the hydrogen-bonding effect of the hydroxyl moiety was prominent in propofol, the substitution of the 1-hydroxyl by a fluorine atom did not prevent FFL from binding to the protein via a halogen-bonding interaction. It therefore became clear that multiple specific interactions rather than just hydrogen or halogen bonds must be taken into account to explain the different anesthesia endpoints caused by PFL and FFL. The contributions of key residues in ligand–receptor binding were also quantified, and the calculated results agreed with many available experimental observations. This work will provide complementary insights into the molecular mechanisms of anesthetic action for PFL from a robust theoretical point of view. This will not only assist in interpreting experimental observations but will also help to develop working hypotheses for further experiments and future drug design.

Position-Specific 13C Fractionation during Liquid–Vapor Transition Correlated to the Strength of Intermolecular Interaction in the Liquid Phase B

Abstract: The relationship between the strength of the intermolecular interaction in liquid and the position-specific ¹³C fractionation observed during distillation was investigated. A range of molecules showing different intermolecular interactions in terms of mode and intensity were incorporated in the study. Although it had previously been suggested that during evaporation the diffusive ¹³C isotope effect in the thin liquid layer interfaced with vapor is not position-specific, herein we show that this is not the case. In particular, the position-specific effect was demonstrated for a series of alcohols. Our hypothesis is that intermolecular interactions in the liquid phase are the source of position-specific ¹³C fractionation observed on the molecule. A clear trend is observed between the ¹³C isotope effect of the carbon bearing the heteroatom of chemical function and the relative permittivity, the solvent hydrogen bond acidity, and the solvent hydrogen bond basicity, while only a weak trend was observed when using the ¹³C content of the whole molecule. Furthermore, two families of products appeared when using the hydrogen bond acidity parameter for the correlation by distinguishing H-acceptor and H-donor molecules from those H-acceptors only. This strongly reinforces the hypothesis of an important role of the ¹³C positioned close to the interaction center.

Concentration Dependent Self-Assembly of TrK-NGF Receptor Derived Tripeptide: New Insights from Experiment and Computer Simulations B

Abstract: Early research has shown that many neurodegenerative diseases are associated with the absence of a short and natural tripeptide sequence, Lys-Phe-Gly (KFG). Herein we report results of both experiments and extensive MD simulations of this tripeptide to understand the self-assembly and morphology as a function of its concentration. Morphologies of the aggregates formed by the tripeptide at low concentration (vesicles), and at high concentration (nanotubes) are studied by several independent 3 μs long Martini coarse-graining MD simulation runs. Further, prediction from MD at still higher concentrations about the formation of rectangular blocks, reported for the first time, has been verified through laboratory experiments. Thus, the computational studies performed are in agreement with the experimental findings observed in our laboratory and a complete control over the formation of various nanostructures is achieved simply by changing the concentration of a short and naturally conserved tripeptide.

Surface Propensity of Atmospherically Relevant Amino Acids Studied by XPS B

Abstract: Amino acids constitute an important fraction of the water-soluble organic nitrogen (WSON) compounds in aerosols and are involved in many processes in the atmosphere. In this work, we applied X-ray photoelectron spectroscopy (XPS) to study aqueous solutions of four amino acids, glycine, alanine, valine, and methionine, in their zwitterionic forms. We found that amino acids with hydrophilic side chains and smaller size, GLY and ALA, tend to stay in the bulk of the liquid, while the hydrophobic and bigger amino acids, VAL and MET, are found to concentrate more on the surface. We found experimental evidence that the amino acids have preferential orientation relative to the surface, with the hydrophobic side chain being closer to the surface than the hydrophilic carboxylate group. The observed amino acid surface propensity has implications in atmospheric science as the surface interactions play a central role in cloud droplet formation, and they should be considered in climate models.

Swelling of Random Copolymer Networks in Pure and Mixed Solvents: Multi-Component Flory–Rehner Theory B

Abstract: A generalized extension of Flory–Rehner (FR) theory is derived to describe equilibrium swelling of polymer networks, including copolymers with two or more chemically distinct repeat units, in either pure or mixed solvents. The model is derived by equating the chemical potential of each solvent in the liquid and gel phases at equilibrium, while assuming the deformation of the network chains is affine. Simplifications of the model are derived for specific cases involving homopolymer networks, copolymer networks, pure solvents, and binary solvent mixtures. With reasonable assumptions, the number of polymer–solvent interaction parameters that must be determined by experiments can be reduced to two effective parameters (θ₁ and θ₂), which describe the net interactions between water/copolymer (θ₁) and ethanol/copolymer (θ₂), respectively. Experimental measurements of the swelling of random copolymer networks of n-butyl acrylate and 2-hydroxyethyl acrylate in water, ethanol, and a 100 g/L ethanol/water mixture are utilized to validate the model. For a random copolymer network, θ₁ and θ₂ can be obtained by fitting the three-component FR model to equilibrium swelling data obtained in the pure solvents. Predicted solvent volume fractions for swelling in water–ethanol mixtures obtained by inserting fitted values of θ₁ and θ₂ into the four-component FR model are in reasonable agreement with experimental measurements.

Field-Theoretic Simulations of the Distribution of Nanorods in Diblock Copolymer Thin Films

Abstract: Using block copolymer microphases to guide the self-assembly of nanorods in thin films can give rise to polymeric materials with unique optical, thermal, and mechanical properties beyond those found in neat block copolymers. Often the design and manufacture of these materials require exquisite control of the nanorod distribution, which is experimentally challenging due to the large parameter space spanned by this class of materials. Simulation approaches, on the other hand, can access the thermodynamics that contribute to the nanorod distribution and hence offer valuable guidance toward the design and manufacture of the materials. In this work, we employ complex Langevin field-theoretic simulations to examine the thermodynamic forces that govern the assembly of nanorods in thin films of block copolymers with a particular focus on vertically oriented cylindrical and lamellar domains. Our simulations show that the nanorod geometry, the substrate selectivity for the distinct blocks of the copolymer, and the film thickness all play important roles in engineering both the nanorod orientation and spatial distribution in diblock copolymer thin films. In addition, we employ thermodynamic integration to examine how the nanorods alter the stability of vertical and horizontal domains in thin films, where we find that the tendency of the nanorods to stabilize a vertical orientation depends on both the film thickness and the nanorod concentration.

Insoluble Off-Pathway Aggregates as Crowding Agents during Amyloid Fibril Formation B

Abstract: The study of drug candidates for the treatment of amyloidosis and neurodegenerative diseases frequently involves in vitro measurements of amyloid fibril formation. Macromolecular crowding and off-pathway aggregation (OPA) are, by different reasons, two important phenomena affecting the scalability of amyloid inhibitors and their successful application in vivo. On the one hand, the cellular milieu is crowded with macromolecules that drastically increase the effective (thermodynamic) concentration of the amyloidogenic protein. On the other hand, off-pathway aggregates, rather than amyloid fibrils, are increasingly appointed as causative agents of toxicity. The present contribution reveals that insoluble off-pathway aggregates of hen egg-white lysozyme (HEWL) are a peculiar type of crowding agents that, unlike classical macromolecular crowders, decrease the thermodynamic concentration of protein. Illustrating this effect, OPA is shown to resume after lowering the fraction of insoluble aggregates at a constant soluble HEWL concentration. Protein depletion and thioflavin-T fluorescence progress curves indicate that OPA rebirth is not accompanied by additional amyloid fibril formation. The crystallization-like model extended to account for OPA and time-dependent activity coefficients is able to fit multiple kinetic results using a single set of three parameters describing amyloid nucleation, autocatalytic growth, and off-pathway nucleation. The list of fitted results notably includes the cases of aggregation rebirth and all types of progress curves measured for different HEWL concentrations. The quantitative challenges posed by macromolecular crowding and OPA find here a unified response with broader implications for the development of on- and off-pathway inhibitors.

Molecular Mechanism of Self-Assembly of Aromatic Oligoamides into Interlocked Double-Helix Foldamers

Abstract: Foldamer, inspired by the structures and functions of biopolymers, is defined as an artificial molecular architecture that can fold into a three-dimensional structure in solution and has been a growing and active field in supramolecular chemistry. The central issue in foldamer science is to understand how the primary sequence of oligomer folds into conformationally ordered structures as well as how individual subunits self-associate into assembly. For duplex structures, these two issues are always interrelated and inseparable with each other. Although the emergence of new foldamer keeps growing, the detailed mechanism remains elusive. On the basis of an artificially synthesized arylamide oligoamide foldamer with its crystal structure available, we constructed a set of four foldamers with a similar backbone but different substituents and aimed at dissecting the folding and self-association mechanisms of a double-helical foldamer with computations. Using molecular simulations at a microsecond time scale, we observed very consistent processes of the spontaneous self-assembly of two single-helical motifs into an entwined complex. Our results reveal that aggregation of two single-helical motifs driven by extensive π-π interactions is energetically favorable and that this spontaneous self-assembly proceeds through an \"unwinding-threading-rewinding\" mechanism. The detailed mechanisms about the folding and self-assembly in an aromatic oligoamide foldamer we present here disclose how the sequence is associated with a well-ordered three-dimensional structure at atomic level and therefore may have implications for designing new foldamers with versatile functions.

Molecular Dynamics–Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit B

Abstract: Conformational selection and induced fit are well-known contributors to ligand binding and allosteric effects in proteins. Molecular dynamics (MD) simulations now enable the theoretical study of protein–ligand binding in terms of ensembles of interconverting microstates and the population shifts characteristic of “dynamical allostery.” Here we investigate protein–ligand binding and allostery based on a Markov state model (MSM) with states and rates obtained from all-atom MD simulations. As an exemplary case, we consider the single domain protein par-6 PDZ with and without ligand and allosteric effector. This is one of the smallest proteins in which allostery has been experimentally observed. In spite of the increased complexity intrinsic to a statistical ensemble perspective, we find that conformational selection and induced fit mechanisms can be readily identified in the analysis. In the nonallosteric pathway, MD-MSM shows that PDZ binds ligand via conformational selection. However, the allosteric pathway requires an activation step that involves a conformational change induced by the allosteric effector Cdc42. Once in the allosterically activated state, we find that ligand binding can proceed by conformational selection. Our MD-MSM model predicts that allostery in this and possibly other systems involves both induced fit and conformational selection, not just one or the other.