Showing papers in "The Journal of Physical Chemistry in 2015"

Microfluidic Mixing: A General Method for Encapsulating Macromolecules in Lipid Nanoparticle Systems B

Abstract: Previous work has shown that lipid nanoparticles (LNP) composed of an ionizable cationic lipid, a poly(ethylene glycol) (PEG) lipid, distearoylphosphatidylcholine (DSPC), cholesterol, and small interfering RNA (siRNA) can be efficiently manufactured employing microfluidic mixing techniques. Cryo-transmission electron microscopy (cryo-TEM) and molecular simulation studies indicate that these LNP systems exhibit a nanostructured core with periodic aqueous compartments containing siRNA. Here we examine first how the lipid composition influences the structural properties of LNP–siRNA systems produced by microfluidic mixing and, second, whether the microfluidic mixing technique can be extended to macromolecules larger than siRNA. It is shown that LNP–siRNA systems can exhibit progressively more bilayer structure as the proportion of bilayer DSPC lipid is increased, suggesting that the core of LNP–siRNA systems can exhibit a continuum of nanostructures depending on the proportions and structural preferences of component lipids. Second, it is shown that the microfluidic mixing technique can also be extended to encapsulation of much larger negatively charged polymers such mRNA (1.7 kb) or plasmid DNA (6 kb). Finally, as a demonstration of the generality of the microfluidic mixing encapsulation process, it is also demonstrated that negatively charged gold nanoparticles (5 nm diameter) can also be efficiently encapsulated in LNP containing cationic lipids. Interestingly, the nanostructure of these gold-containing LNP reveals a “currant bun” morphology as visualized by cryo-TEM. This structure is fully consistent with LNP–siRNA structure predicted by molecular modeling.

Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases B

Abstract: In nature, polysaccharide glycosidic bonds are cleaved by hydrolytic enzymes for a vast array of biological functions. Recently, a new class of enzymes that utilize an oxidative mechanism to cleave glycosidic linkages was discovered; these enzymes are called lytic polysaccharide monooxygenases (LPMO). These oxidative enzymes are synergistic with cocktails of hydrolytic enzymes and are thought to act primarily on crystalline regions, in turn providing new sites of productive attachment and detachment for processive hydrolytic enzymes. In the case of cellulose, the homopolymer of β-1,4-d-glucose, enzymatic oxidation occurs at either the reducing end or the nonreducing end of glucose, depending on enzymatic specificity, and results in the generation of oxidized chemical substituents at polymer chain ends. LPMO oxidation of cellulose is thought to produce either a lactone at the reducing end of glucose that can spontaneously or enzymatically convert to aldonic acid or 4-keto-aldose at the nonreducing end that may further oxidize to a geminal diol. Here, we use molecular simulation to examine the effect of oxidation on the structure of crystalline cellulose. The simulations highlight variations in behaviors depending on the chemical identity of the oxidized species and its location within the cellulose fibril, as different oxidized species introduce steric effects that disrupt local crystallinity and in some cases reduce the work needed for polymer decrystallization. Reducing-end oxidations are easiest to decrystallize when located at the end of the fibril, whereas nonreducing end oxidations readily decrystallize from internal cleavage sites despite their lower solvent accessibility. The differential in decrystallization free energy suggests a molecular mechanism consistent with experimentally observed LPMO/cellobiohydrolase synergy. Additionally, the soluble oxidized cellobiose products released by hydrolytic cellulases may bind to the active sites of cellulases with different affinities relative to cellobiose itself, which potentially affects hydrolytic turnover through product inhibition. To examine the effect of oxidation on cello–oligomer binding, we use thermodynamic integration to compute the relative change in binding free energy between the hydrolyzed and oxidized products in the active site of Family 7 and Family 6 processive glycoside hydrolases, Trichoderma reesei Cel7A and Cel6A, which are key industrial cellulases and commonly used model systems for fungal cellulases. Our results suggest that the equilibrium between the two reducing end oxidized products, favoring the linear aldonic acid, may increase product inhibition, which would in turn reduce processive substrate turnover. In the case of LMPO action at the nonreducing end, oxidation appears to lower affinity with the nonreducing end specific cellulase, reducing product inhibition and potentially promoting processive cellulose turnover. Overall, this suggests that oxidation of recalcitrant polysaccharides by LPMOs accelerates degradation not only by increasing the concentration of chain termini but also by reducing decrystallization work, and that product inhibition may be somewhat reduced as a result.

Multiscale Modeling of Four-Component Lipid Mixtures: Domain Composition, Size, Alignment, and Properties of the Phase Interface

Abstract: Simplified lipid mixtures are often used to model the complex behavior of the cell plasma membrane. Indeed, as few as four componentsa high-melting lipid, a nandomain-inducing low-melting lipid, a macrodomain-inducing low-melting lipid, and cholesterol (chol)can give rise to a wide range of domain sizes and patterns that are highly sensitive to lipid compositions. Although these systems are studied extensively with experiments, the molecular-level details governing their phase behavior are not yet known. We address this issue by using molecular dynamics simulations to analyze how phase separation evolves in a four-component system as it transitions from small domains to large domains. To do so, we fix concentrations of the high-melting lipid 16:0,16:0-phosphatidylcholine (DPPC) and chol, and incrementally replace the nanodomain-inducing low-melting lipid 16:0,18:2-PC (PUPC) by the macrodomain-inducing low-melting lipid 18:2,18:2-PC (DUPC). Coarse-grained simulations of this four-component system reveal that lipid demixing increases as the amount of DUPC increases. Additionally, we find that domain size and interleaflet alignment change sharply over a narrow range of replacement of PUPC by DUPC, indicating that intraleaflet and interleaflet behaviors are coupled. Corresponding united atom simulations show that only lipids within ∼2 nm of the phase interface are significantly perturbed regardless of domain composition or size. Thus, whereas the fraction of interface-perturbed lipids is negligible for large domains, it is significant for smaller ones. Together, these results reveal characteristic traits of bilayer thermodynamic behavior in four-component mixtures, and provide a baseline for investigation of the effects of proteins and other lipids on membrane phase properties.

Kirkwood–Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields B

Abstract: Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein–water over protein–protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood–Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood–Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.

Molecular Structures of Fluid Phosphatidylethanolamine Bilayers Obtained from Simulation-to-Experiment Comparisons and Experimental Scattering Density Profiles B

Abstract: Following our previous efforts in determining the structures of commonly used PC, PG, and PS bilayers, we continue our studies of fully hydrated, fluid phase PE bilayers. The newly designed parsing scheme for PE bilayers was based on extensive MD simulations, and is utilized in the SDP analysis of both X-ray and neutron (contrast varied) scattering measurements. Obtained experimental scattering form factors are directly compared to our simulation results, and can serve as a benchmark for future developed force fields. Among the evaluated structural parameters, namely, area per lipid A, overall bilayer thickness DB, and hydrocarbon region thickness 2DC, the PE bilayer response to changing temperature is similar to previously studied bilayers with different headgroups. On the other hand, the reduced hydration of PE headgroups, as well as the strong hydrogen bonding between PE headgroups, dramatically affects lateral packing within the bilayer. Despite sharing the same glycerol backbone, a markedly smaller area per lipid distinguishes PE from other bilayers (i.e., PC, PG, and PS) studied to date. Overall, our data are consistent with the notion that lipid headgroups govern bilayer packing, while hydrocarbon chains dominate the bilayer’s response to temperature changes.

Investigation of the Structure of Ethanol–Water Mixtures by Molecular Dynamics Simulation I: Analyses Concerning the Hydrogen-Bonded Pairs B

Abstract: Series of molecular dynamics simulations for ethanol–water mixtures with 20–80 mol % ethanol content, pure ethanol, and water were performed. In each mixture, for ethanol the OPLS force field was used, combined with three different water force fields, the SPC/E, the TIP4P-2005, and the SWM4-DP. Water potential models were distinguished on the basis of deviations between calculated and measured total scattering X-ray structure factors aided by ethanol–water pair binding energy comparison. No single water force field could provide the best agreement with experimental data at all concentrations: at the ethanol content of 80% the SWM-DP, for 60 mol % the SWM4-DP and the TIP4P-2005, whereas for the 40 and 20 mol % mixtures TIP4P-2005 water force field provided the closest match. Coordination numbers and hydrogen bonds/molecule values were calculated, revealing that the oxygen–oxygen first coordination numbers strongly overestimate the average number of hydrogen bonds/molecule. The center-of-molecule distributions indicate that the ethanol–ethanol first coordination sphere expands with increasing water concentration while the size of the first water–water coordination sphere does not change. Various two and three-dimensional distributions were calculated that reveal the differences between simulations with different water force fields. Detailed conformational analyses of the hydrogen–bonded pairs were performed; drawings of the characteristic molecular arrangements are provided.

Designing Nanoparticle Translocation through Cell Membranes by Varying Amphiphilic Polymer Coatings B

Abstract: Nanoparticle (NP)-assisted drug delivery has been emerging as an active research area. Understanding and controlling the interaction of the coated NPs with cell membranes is key to the development of the efficient drug delivery technologies and to the management of nanoparticle-related health and safety issues. Cellular uptake of nanoparticles coated with mixed hydrophilic/hydrophobic polymer ligands is known to be strongly influenced by the polymer pattern on the NP surface and remains open for further exploration. To unravel the physical mechanism behind this intriguing phenomenon, here we perform dissipative particle dynamics simulations to analyze the forces and efficacy time as the copolymer-coated NPs pass through the lipid bilayer so as to provide better design of coated NPs for future drug delivery applications. Four characteristic copolymer ligands are constructed to perform the simulations: hydrophilic–hydrophobic (AB), hydrophobic–hydrophilic (BA), hydrophobic–hydrophilic–hydrophobic–hydrophilic (BABA), and a random pattern with hydrophilic and hydrophobic beads. We mainly study the critical force and potential of mean force required for entering inside of the lipid bilayer and penetration force to pass all the way through the cell membrane as well as the translocation time for these patterned NPs across the bilayer. Through copolymer ligand pattern designing, we find a suitable nanoparticle candidate with a specific polymer coating pattern for drug delivery. These findings provide useful guidelines for the molecular design of patterned NPs for controllable cell penetrability and help establish qualitative rules for the organization and optimization of copolymer ligands for desired drug delivery.

Atomistic Modeling of Two-Dimensional Electronic Spectra and Excited-State Dynamics for a Light Harvesting 2 Complex B

Abstract: The Light Harvesting 2 (LH2) complex is a vital part of the photosystem of purple bacteria. It is responsible for the absorption of light and transport of the resulting excitations to the reaction center in a highly efficient manner. A general description of the chromophores and the interaction with their local environment is crucial to understand this highly efficient energy transport. Here we include this interaction in an atomistic way using mixed quantum-classical (molecular dynamics) simulations of spectra. In particular, we present the first atomistic simulation of nonlinear optical spectra for LH2 and use it to study the energy transport within the complex. We show that the frequency distributions of the pigments strongly depend on their positions with respect to the protein scaffold and dynamics of their local environment. Furthermore, we show that although the pigments are closely packed the transition frequencies of neighboring pigments are essentially uncorrelated. We present the simulated linear absorption spectra for the LH2 complex and provide a detailed explanation of the states responsible for the observed two-band structure. Finally, we discuss the energy transfer within the complex by analyzing population transfer calculations and 2D spectra for different waiting times. We conclude that the energy transfer from the B800 ring to the B850 ring is mediated by intermediate states that are delocalized over both rings, allowing for a stepwise downhill energy transport.

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models

Abstract: We develop a systematic procedure for obtaining rate and transition matrices that optimally describe the dynamics of aggregated superstates formed by combining (clustering or lumping) microstates. These reduced dynamical models are constructed by matching the time-dependent occupancy-number correlation functions of the superstates in the full and aggregated systems. Identical results are obtained by using a projection operator formalism. The reduced dynamic models are exact for all times in their full non-Markovian formulation. In the approximate Markovian limit, we derive simple analytic expressions for the reduced rate or Markov transition matrices that lead to exact auto- and cross-relaxation times. These reduced Markovian models strike an optimal balance between matching the dynamics at short and long times. We also discuss how this approach can be used in a hierarchical procedure of constructing optimal superstates through aggregation of microstates. The results of the general reduced-matrix theory are illustrated with applications to simple model systems and a more complex master-equation model of peptide folding derived previously from atomistic molecular dynamics simulations. We find that the reduced models faithfully capture the dynamics of the full systems, producing substantial improvements over the common local-equilibrium approximation.

MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers B

Abstract: Commercial-scale biofuel production requires a deep understanding of the structure and dynamics of its principal target: cellulose. However, an accurate description and modeling of this carbohydrate structure at the mesoscale remains elusive, particularly because of its overwhelming length scale and configurational complexity. We have derived a set of MARTINI coarse-grained force field parameters for the simulation of crystalline cellulose fibers. The model is adapted to reproduce different physicochemical and mechanical properties of native cellulose Iβ. The model is able not only to handle a transition from cellulose Iβ to another cellulose allomorph, cellulose IIII, but also to capture the physical response to temperature and mechanical bending of longer cellulose nanofibers. By developing the MARTINI model of a solid cellulose crystalline fiber from the building blocks of a soluble cellobiose coarse-grained model, we have provided a systematic way to build MARTINI models for other crystalline biopolymers.

Proteins at Interfaces Probed by Chiral Vibrational Sum Frequency Generation Spectroscopy B

Abstract: Characterizations of protein structures at interfaces are important in solving an array of fundamental and engineering problems, including understanding transmembrane signal transduction and molecular transport processes and development of biomaterials to meet the needs of biomedical and energy research. However, in situ and real-time characterization of protein secondary structures is challenging because it requires physical methods that are selective to both interface and secondary structures. Here, we summarize recent experimental developments in our laboratory of chiral vibrational sum frequency generation spectroscopy (SFG) for analyzing protein structures at interfaces. We showed that chiral SFG provides vibrational optical signatures of the peptide N–H stretch and amide I modes that can distinguish various protein secondary structures. Using these signatures, we further applied chiral SFG to probe orientations and folding kinetics of proteins at interfaces. Our results show that chiral SFG is a background-free, label-free, in situ, and real-time vibrational method for studying proteins at interfaces. This recent progress demonstrates the potential of chiral SFG in solving problems related to proteins and other chiral biopolymers at interfaces.

Cooperative or Anticooperative: How Noncovalent Interactions Influence Each Other B

Abstract: This computational study examines the key factors that control the structures and energetics of the coexistence of multiple noncovalent interactions. 4-Amino-2-iodophenol is taken as a model that exhibits nine different kinds of noncovalent interactions, viz., cation−π (CP), hydrogen bond (HB) through O (OHB), HB through N (NHB), halogen bond (XB), π–π (PP), metal ion–lone pair (ML) through O (OML), ML through N (NML), charge assisted hydrogen bond (CHB) through O (OCHB), and CHB through N (NCHB). Through all possible combinations of these noncovalent interactions, based on energy, geometry, charge, and atoms in molecules (AIM) analysis, we have systematically analyzed the cooperativity among 40 ternary systems and 105 quaternary systems. We have observed that CP–HB, CP–XB, CP–PP, HB–HB, HB–XB, HB–PP, HB–ML, HB–CHB, XB–PP, XB–ML, XB–CHB, PP–ML, and PP–OCHB can form cooperative ternary systems. While studying the quaternary systems, we have observed that HB, XB, and PP work together by enhancing each other’s strength. The study highlights that the positively charged species enhances HB–HB and HB–PP interactions and forms cooperative HB–HB–CHB, HB–HB–ML, HB–PP–ML, and HB–PP–CHB systems. Surprisingly, OHB–OML–NML, OHB–OML–OCHB, OHB–OML–NCHB, OHB–NML–OCHB, NHB–OML–NML, NHB–OML–NCHB, and NHB–NML–OCHB are also cooperative in nature despite the electrostatic repulsion between two positive charge species. The current study shows the widespread presence of cooperativity as well as anticooperativity in supramolecular assembles.

Surface Adsorption of Oppositely Charged SDS:C12TAB Mixtures and the Relation to Foam Film Formation and Stability B

Abstract: The complexation, surface adsorption, and foam film stabiliztation of the oppositely charged surfactants, sodium dodecyl sulfate (SDS) and dodecyl trimethylammonium bromide (C₁₂TAB), is analyzed. The SDS:C₁₂TAB mixing ratio is systematically varied to investigate whether the adsorption of equimolar or irregular catanionic surfactant complexes, and thus a variation in surface charge (i.e., surface excess of either SDS or C₁₂TAB), governs foam film properties. Surface tension measurements indicate that SDS and C₁₂TAB interact electrostatically in order to form stoichometric catanionic surfactant complexes and enhance surface adsorption. On the other hand it can be demonstrated that the SDS:C₁₂TAB mixing ratio and, thus, a change in surface charge and composition plays a decisive role in foam film stabilization. The present study demonstrates that varying the mixing ratio between SDS and C₁₂TAB offers a tool for tailoring surface composition and foam film properties, which are therefore not exclusively mediated by the presence of equimolar catanionic surfactant complexes. The SDS:C₁₂TAB net amount and mixing ratio determine the type, stability, and thinning behavior of the corresponding foam film. These observations indicate the formation of a mixed surface layer, composed of the catanionic surfactant species surrounded by either free SDS or C₁₂TAB molecules in excess. Furthermore, a systematic variation in CBF–NBF transition kinetics is rationalized on the basis of a microscopic phase transition within the foam films. Fundamental knowlegde gained from this research gives insight into the surface adsorption and foam film formation of catanionic surfactant mixtures. The study helps researchers to understand basic mechanisms of foam film stabilization and to use resources more efficiently.

Energy Propagation and Network Energetic Coupling in Proteins B

Abstract: Understanding how allosteric proteins respond to changes in their environment is a major goal of current biological research. We show that these responses can be quantified by analyzing protein energy networks using a method recently developed in our group. On the basis of this method, we introduce here a quantity named energetic coupling, which we show is able to discriminate allosterically active mutants of the lactose repressor (LacI) protein, and of the catabolite activator protein (CAP), a dynamically driven allosteric protein. Our method assumes that allostery and signal transmission can be more accurately described as efficient energy propagation, and not as the more widely used atomic motion correlations. We demonstrate the validity of this assumption by performing energy-propagation simulations. Finally, we present results from energy-propagation simulations performed on folded and fully extended conformations of the postsynaptic density protein 95 (PSD-95). They show that the protein backbone provides a more efficient route for energy transfer, when compared to secondary or tertiary contacts. On the basis of this, we propose energy propagation through the backbone as a possible explanation for the observation that intrinsically disordered proteins can efficiently transmit signals while lacking a well-defined tertiary structure.

A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar Couplings B

Abstract: Residual dipolar couplings (RDCs) are parameters measured in nuclear magnetic resonance spectroscopy that can provide exquisitely detailed information about the structure and dynamics of biological macromolecules. We describe here a method of using RDCs for the structural and dynamical refinement of proteins that is based on the observation that the RDC between two atomic nuclei depends directly on the angle ϑ between the internuclear vector and the external magnetic field. For every pair of nuclei for which an RDC is available experimentally, we introduce a structural restraint to minimize the deviation from the value of the angle ϑ derived from the measured RDC and that calculated in the refinement protocol. As each restraint involves only the calculation of the angle ϑ of the corresponding internuclear vector, the method does not require the definition of an overall alignment tensor to describe the preferred orientation of the protein with respect to the alignment medium. Application to the case of ubiquitin demonstrates that this method enables an accurate refinement of the structure and dynamics of this protein to be obtained.

Glass Transitions of Poly(methyl methacrylate) Confined in Nanopores: Conversion of Three- and Two-Layer Models B

Abstract: The glass transitions of poly(methyl methacrylate) (PMMA) oligomer confined in alumina nanopores with diameters much larger than the polymer chain dimension were investigated. Compared with the case of 80 nm nanopores, PMMA oligomer confined in 300 nm nanopores shows three glass transition temperatures (from from low to high, denoted as Tg,ₗₒ, Tg,ᵢₙₜₑᵣ, and Tg,ₕᵢ). Such phenomenon can be interpreted by a three-layer model: there exists an interphase between the adsorbed layer and core volume called the interlayer, which has an intermediate Tg. The behavior of multi-Tg parameters is ascribed to the propagation of the interfacial interaction during vitrifaction process. Besides, because of the nonequilibrium effect in the adsorbed layer, the cooling rate plays an important role in the glass transitions: the fast cooling rate generates a single Tg; the intermediate cooling rate induces three Tg values, while the ultraslow cooling rate results in two Tg values. With decreasing the cooling rate, the thickness of interlayer would continually decrease, while those of the adsorbed layer and core volume gradually increase; meanwhile, the Tg,ₗₒ gradually increases, Tg,ᵢₙₜₑᵣ almost stays constant, and the Tg,ₕᵢ value keeps decreasing. In such a process, the dynamic exchanges between the interlayer and adsorbed layer, core volume should be dominant.

Cysteine-Specific Cu2+ Chelating Tags Used as Paramagnetic Probes in Double Electron Electron Resonance

Abstract: Double electron electron resonance (DEER) is an attractive technique that is utilized for gaining insight into protein structure and dynamics via nanometer-scale distance measurements. The most commonly used paramagnetic tag in these measurements is a nitroxide spin label, R1. Here, we present the application of two types of high-affinity Cu²⁺ chelating tags, based on the EDTA and cyclen metal-binding motifs as alternative X-band DEER probes, using the B1 immunoglobulin-binding domain of protein G (GB1) as a model system. Both types of tags have been incorporated into a variety of protein secondary structure environments and exhibit high spectral sensitivity. In particular, the cyclen-based tag displays distance distributions with comparable distribution widths and most probable distances within 1–3 A when compared to homologous R1 distributions. The results display the viability of the cyclen tag as an alternative to the R1 side chain for X-band DEER distance measurements in proteins.

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model

Abstract: A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2–20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model.

Light Induced H2 Evolution from a Biophotocathode Based on Photosystem 1 – Pt Nanoparticles Complexes Integrated in Solvated Redox Polymers Films B

Abstract: We report on a biophotocathode based on photosystem 1 (PS1)–Pt nanoparticle complexes integrated in a redox hydrogel for photoelectrocatalytic H₂ evolution at low overpotential. A poly(vinyl)imidazole Os(bispyridine)₂Cl polymer serves as conducting matrix to shuttle the electrons from the electrode to the PS1-Pt complexes embedded within the hydrogel. Light induced charge separation at the PS1-Pt complexes results in the generation of photocurrents (4.8 ± 0.4 μA cm–²) when the biophotocathodes are exposed to anaerobic buffer solutions. Under these conditions, the protons are the sole possible electron acceptors, suggesting that the photocurrent generation is associated with H₂ evolution. Direct evidence for the latter process is provided by monitoring the H₂ production with a Pt microelectrode in scanning electrochemical microscopy configuration over the redox hydrogel film containing the PS1-Pt complexes under illumination.

Insights on the Isotropic-to-Smectic A Transition in Ionic Liquid Crystals from Coarse-Grained Molecular Dynamics Simulations: The Role of Microphase Segregation B

Abstract: We have investigated the role of microphase segregation as the driving force in the stabilization of thermotropic ionic liquid crystals of smectic type. To this end we have applied the heterogeneity order parameter, initially proposed for ionic liquids, to the coarse-grained molecular dynamics simulation results for a model system of an imidazolium nitrate ionic liquid crystal, [C₁₆mim][NO₃], whose phase diagram was recently studied. We have found that the heterogeneity order parameters become larger when the system goes through the transition from the isotropic phase to the smectic A phase as the temperature decreases. This can be understood by considering that, in the smectic A phase, the layered structure allows the tail groups to have a degree of aggregation larger than that in the isotropic phase. Our results highlight the role of microsegregation in the stabilization of ionic liquid crystals, which cannot be revealed by the commonly used translational and orientational order parameters used to describe liquid crystal phases.

Membrane Environment Modulates the pKa Values of Transmembrane Helices

Abstract: In this work, we apply the recently developed constant pH molecular dynamics technique to study protonation equilibria of titratable side chains in the context of simple transmembrane (TM) helices and explore the effect of pH on their configurations in membrane bilayers. We observe that, despite a significant shift toward neutral states, considerable population of different side chains stay in the charged state that give rise to pKₐ values around 9.6 for Asp and Glu and 4.5 to 6 for His and Lys side chains, respectively. These charged states are highly stabilized by favorable interactions between head groups, water molecules, and the charged side chains that are facilitated by substantial changes in the configuration of the peptides. The pH dependent configurations and the measured pKₐ values are in good agreement with relatively recent solid state NMR measurements. Our results presented here demonstrate that all-atom constant pH molecular dynamics can be applied to membrane proteins and peptides to obtain reliable pKₐ values and pH dependent behavior for these systems.

Electrostatic Interactions between OmpG Nanopore and Analyte Protein Surface Can Distinguish between Glycosylated Isoforms

Abstract: The flexible loops decorating the entrance of OmpG nanopore move dynamically during ionic current recording. The gating caused by these flexible loops changes when a target protein is bound. The gating is characterized by parameters including frequency, duration, and open-pore current, and these features combine to reveal the identity of a specific analyte protein. Here, we show that OmpG nanopore equipped with a biotin ligand can distinguish glycosylated and deglycosylated isoforms of avidin by their differences in surface charge. Our studies demonstrate that the direct interaction between the nanopore and analyte surface, induced by the electrostatic attraction between the two molecules, is essential for protein isoform detection. Our technique is remarkably sensitive to the analyte surface, which may provide a useful tool for glycoprotein profiling.

Oxygen Diffusion in Mayenite

Abstract: Oxygen transport in mayenite single crystals was studied by means of 18O/16O isotope exchange experiments and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Oxygen tracer diffusion coefficients D* and oxygen surface exchange coefficients k* were determined as a function of temperature, 773 ≤ T/K ≤ 1273, at an oxygen activity of aO2 = 0.1, and as a function of oxygen activity, 0.01 ≤ aO2 ≤ 0.9, at a temperature of T = 1123 K. Two diffusion processes were observed: a fast diffusion process that is attributed to the interstitialcy diffusion of free oxygen ions (O2–) and a slow diffusion process that is attributed to the interstitialcy diffusion of superoxide ions (O2–).

Pharmacophore-Based Similarity Scoring for DOCK

Abstract: Pharmacophore modeling incorporates geometric and chemical features of known inhibitors and/or targeted binding sites to rationally identify and design new drug leads. In this study, we have encoded a three-dimensional pharmacophore matching similarity (FMS) scoring function into the structure-based design program DOCK. Validation and characterization of the method are presented through pose reproduction, crossdocking, and enrichment studies. When used alone, FMS scoring dramatically improves pose reproduction success to 93.5% (∼20% increase) and reduces sampling failures to 3.7% (∼6% drop) compared to the standard energy score (SGE) across 1043 protein–ligand complexes. The combined FMS+SGE function further improves success to 98.3%. Crossdocking experiments using FMS and FMS+SGE scoring, for six diverse protein families, similarly showed improvements in success, provided proper pharmacophore references are employed. For enrichment, incorporating pharmacophores during sampling and scoring, in most cases, also yield improved outcomes when docking and rank-ordering libraries of known actives and decoys to 15 systems. Retrospective analyses of virtual screenings to three clinical drug targets (EGFR, IGF-1R, and HIVgp41) using X-ray structures of known inhibitors as pharmacophore references are also reported, including a customized FMS scoring protocol to bias on selected regions in the reference. Overall, the results and fundamental insights gained from this study should benefit the docking community in general, particularly researchers using the new FMS method to guide computational drug discovery with DOCK.

Interaction Forces and Aggregation Rates of Colloidal Latex Particles in the Presence of Monovalent Counterions B

Abstract: Force profiles and aggregation rates involving positively and negatively charged polystyrene latex particles are investigated in monovalent electrolyte solutions, whereby the counterions are varied within the Hofmeister series. The force measurements are carried out with the colloidal probe technique, which is based on the atomic force microscope (AFM), while the aggregation rates are measured with time-resolved multiangle light scattering. The interaction force profiles cannot be described by classical DLVO theory, but an additional attractive short-ranged force must be included. An exponential force profile with a decay length of about 0.5 nm is consistent with the measured forces. Furthermore, the Hamaker constants extracted from the measured force profiles are substantially smaller than the theoretical values calculated from dielectric spectra. The small surface roughness of the latex particles (below 1 nm) is probably responsible for this deviation. Based on the measured force profiles, the aggregation rates can be predicted without adjustable parameters. The measured absolute aggregation rates in the fast regime are somewhat lower than the calculated ones. The critical coagulation concentration (CCC) agrees well with the experiment, including the respective shifts of the CCC within the Hofmeister series. These shifts are particularly pronounced for the positively charged particles. However, the consideration of the additional attractive short-ranged force is essential to quantify these shifts correctly. In the slow regime, the calculated rates are substantially smaller than the experimental ones. This disagreement is probably related to surface charge heterogeneities.

Explicit Correlated Exciton-Vibrational Dynamics of the FMO Complex B

Abstract: The coupled exciton-vibrational dynamics of a three-site model of the Fenna–Matthews–Olson complex is investigated using the numerically exact multilayer multiconfiguration time-dependent Hartree approach. Thereby the specific coupling of the vibrational modes to local electronic transitions is adapted from a discretized experimental spectral density. The solution of the resulting time-dependent Schrodinger equation including three electronic and 450 vibrational degrees of freedom is analyzed in terms of excitonic populations and coherences. Emphasis is put onto the role of specific ranges of vibrational frequencies. It is observed that modes between 160 and 300 cm–¹ are responsible for the sub-picosecond population and coherence decay. Further, it is found that a mean-field approach with respect to the vibrational degrees of freedom is not applicable.

Interaction of the Nonsteroidal Anti-inflammatory Drug Indomethacin with Micelles and Its Release B

Abstract: In this study, we have reported the binding interaction and photophysics of a nonsteroidal anti-inflammatory drug (NSAID) indomethacin (IMC) in the presence of different micelles. We have used several spectroscopic techniques such as UV–vis absorption, steady state fluorescence and time-resolved fluorescence emission spectroscopy. The spectral properties of IMC were modulated in the presence of micelles compared to that in neat water. The weak emitting drug molecule (IMC) becomes highly fluorescent after binding with the micelles. The fluorescence quantum yield and fluorescence lifetime increase in the presence of micelles compared to those in neat water. The isothermal titration calorimetry (ITC) method was used to study the binding interaction of IMC with different micelles. The thermodynamic parameters and the nature of binding between IMC and different micelles have been estimated. Moreover, addition of KCl salt in the respective micelles releases IMC molecule from the micelles to the aqueous medium. This study will help elicidate the binding behavior of IMC in the presence of different micelles for possible use as potential drug delivery systems.

Chemiexcitation Induced Proton Transfer: Enolate Oxyluciferin as the Firefly Bioluminophore B

Abstract: Firefly bioluminescence is a phenomenon that attracts attention from the research community because of complex challenges for fundamental investigation, as well as diverse opportunities for practical application. Here we have studied the potential deprotonation of firefly oxyluciferin by using a theoretical approach in an enzymatic-like microenvironment in chemiexcited proton transfer involving adenosine 5′-monophosphate. We have uncovered a reaction route that links the evidence that the light-emitter is an anionic molecule while it is chemiexcited in its neutral form. Moreover, the results indicated that the anionic bioluminophore is the enolate anion and not the ketonic one. Further calculations supported this identification of the light-emitter: the spectrum of resulting enolate anion covers the entire yellow-green/red bioluminescence range, which is in line with the experimental findings regarding firefly multicolor bioluminescence.

Impact of Lipid Oxidization on Biophysical Properties of Model Cell Membranes B

Abstract: The oxidization of glycerophospholipids in cell membranes due to aging and environmental stresses may cause a variety of pathological and physiological consequences. A variety of oxidized phospholipid products (OxPl) are produced by the chemical oxidization of unsaturated hydrocarbon chains, which would significantly change the physicochemical properties of cell membranes. In this work, we constructed cell membrane models in the absence and presence of two stable oxidized lipid products and investigated their impact on physical properties of supported membranes using quartz crystal microbalance with dissipation (QCM-D) and high-energy X-ray reflectivity (XRR). Our experimental findings suggest that the lipid oxidization up to 20 mol % leads to the rupture of vesicles right after the adsorption. Our XRR analysis unravels the membrane thinning and the decrease in the lateral ordering of lipids, which can be explained by the decrease in the lateral packing of hydrocarbon chains. Further studies on mechanics of membranes incorporating oxidized lipids can be attributed to the decrease in the bending rigidity and the increase in the permeability.

Effects of Natural Osmolytes on the Protein Structure in Supercritical CO2: Molecular Level Evidence B

Abstract: Protein instability in supercritical CO₂ limits the application of this green solvent in enzyme-catalyzed reactions. CO₂ molecules act as a protein denaturant at high pressure under supercritical conditions. Here, for the first time, we show that natural osmolytes could stabilize protein conformation in supercritical CO₂. Molecular dynamics simulation is used to monitor the effects of adding different natural osmolytes on the conformation and dynamics of chymotrypsin inhibitor 2 (CI2) in supercritical CO₂. Simulations showed that CI2 is denatured at 200 bar in supercritical CO₂, which is in agreement with experimental observations. Interestingly, the protein conformation remains native after addition of ∼1 M amino acid- and sugar-based osmolyte models. These molecules stabilize protein through the formation of supramolecular self-assemblies resulting from macromolecule–osmolyte hydrogen bonds. Nevertheless, trimethylamine N-oxide, which is known as a potent osmolyte for protein stabilization in aqueous solutions, amplifies protein denaturation in supercritical CO₂. On the basis of our structural analysis, we introduce a new mechanism for the osmolyte effect in supercritical CO₂, an “inclusion mechanism”. To the best of our knowledge, this is the first study that introduces the application of natural osmolytes in a supercritical fluid and describes mechanistic insights into osmolyte action in nonaqueous media.