TEMPO-conjugated tobacco mosaic virus as a magnetic resonance imaging contrast agent for detection of superoxide production in the inflamed liver.

Superoxide, an anionic dioxygen molecule, plays a crucial role in redox regulation within the body but is implicated in various pathological conditions when produced excessively. Efforts to develop superoxide detection strategies have led to the exploration of organic-based contrast agents for magnetic resonance imaging (MRI). This study compares the effectiveness of two such agents, nTMV-TEMPO and kTMV-TEMPO, for detecting superoxide in a mouse liver model with lipopolysaccharide (LPS)-induced inflammation. The study demonstrates that kTMV-TEMPO, with a strategically positioned lysine residue for TEMPO attachment, outperforms nTMV-TEMPO as an MRI contrast agent. The enhanced sensitivity of kTMV-TEMPO is attributed to its more exposed TEMPO attachment site, facilitating stronger interactions with water protons and superoxide radicals. EPR kinetics experiments confirm kTMV-TEMPO's faster oxidation and reduction rates, making it a promising sensor for superoxide in inflamed liver tissue. In vivo experiments using healthy and LPS-induced inflamed mice reveal that reduced kTMV-TEMPO remains MRI-inactive in healthy mice but becomes MRI-active in inflamed livers. The contrast enhancement in inflamed livers is substantial, validating the potential of kTMV-TEMPO for detecting superoxide in vivo. This research underscores the importance of optimizing contrast agents for in vivo imaging applications. The enhanced sensitivity and biocompatibility of kTMV-TEMPO make it a promising candidate for further studies in the realm of medical imaging, particularly in the context of monitoring oxidative stress-related diseases.

Self-assembly of a fluorescent virus-like particle for imaging in tissues with high autofluorescence.

Virus-like particles (VLPs) are engineered nanoparticles that mimic the properties of viruses-like high tolerance to heat and proteases-but lack a viral genome, making them non-infectious. They are easily modified chemically and genetically, making them useful in drug delivery, enhancing vaccine efficacy, gene delivery, and cancer immunotherapy. One such VLP is Qß, which has an affinity towards an RNA hairpin structure found in its viral RNA that drives the self-assembly of the capsid. It is possible to usurp the native way infectious Qß self-assembles to encapsidate its RNA to place enzymes inside the VLP's lumen as a protease-resistant cage. Further, using RNA templates that mimic the natural self-assembly of the native capsid, fluorescent proteins (FPs) have been placed inside VLPs in a "one pot" expression system. Autofluorescence in tissues can lead to misinterpretation of results and unreliable science, so we created a single-pot expression system that uses the fluorescent protein smURFP, which avoids autofluorescence and has spectral properties compatible with standard commercial filter sets on confocal microscopes. In this work, we were able to simplify the existing "one-pot" expression system while creating high-yielding fluorescent VLP nanoparticles that could easily be imaged inside lung epithelial tissue.

Optical control of neuronal activities with photoswitchable nanovesicles.

Precise modulation of neuronal activity by neuroactive molecules is essential for understanding brain circuits and behavior. However, tools for highly controllable molecular release are lacking. Here, we developed a photoswitchable nanovesicle with azobenzene-containing phosphatidylcholine (azo-PC), coined 'azosome', for neuromodulation. Irradiation with 365 nm light triggers the trans-to-cis isomerization of azo-PC, resulting in a disordered lipid bilayer with decreased thickness and cargo release. Irradiation with 455 nm light induces reverse isomerization and switches the release off. Real-time fluorescence imaging shows controllable and repeatable cargo release within seconds (< 3 s). Importantly, we demonstrate that SKF-81297, a dopamine D1-receptor agonist, can be repeatedly released from the azosome to activate cultures of primary striatal neurons. Azosome shows promise for precise optical control over the molecular release and can be a valuable tool for molecular neuroscience studies.

The Stiffest and Strongest Predicted Material: C2 N Atomic Chains Approach the Theoretical Limits.

Though linear atomic chains exhibit extreme properties, it is presently unclear how these properties can be maximized by the choice of elemental composition. Considering that boron, carbon, and nitrogen can form high modulus and high strength atomic chains, here an algorithm is developed to construct 143 possible atomic chains of these elements with 6 or fewer atoms in the primitive cell and explore their stabilities and mechanical properties by first-principles calculations. It is found that the gravimetric modulus (1032 GPa g-1 cm3 ) and strength (108 GPa g-1 cm3 ) of the C2 N chain significantly exceed those of any known material, including the previously stiffest predicted material (C chain, 945 GPa g-1 cm3 ) and the previously strongest predicted material (BC chain, 92 GPa g-1 cm3 ), and also approach the theoretical limits of gravimetric modulus (1036 GPa g-1 cm3 ) and strength (130 GPa g-1 cm3 ). Mechanistic analyses demonstrate that the higher gravimetric modulus and strength of the C2 N chain, compared with the C and BC chains, originate from its short, stiff chemical bonding and the abnormal decrease in bond length alternation under tension. The likely ease of fabrication and potential synthesis routes for C2 N chains are discussed.

Exogenous Protein Delivery of Ionic Liquid-Mediated HMGB1 Coating on Titanium Implants.

Strategies for modifying titanium (Ti) implant surfaces are becoming increasingly popular to enhance osseointegration during acute and inflammatory healing stages. In this study, two dicationic imidazolium-based ionic liquids (IonLs) containing phenylalanine and methionine anions (IonL-Phe(1,10-bis(3-methylimidazolium-1-yl)decane diphenylalanine) and IonL-Met(1,10-bis(3-methylimidazolium-1-yl)decane dimethionine)) were investigated to stably deliver exogenous proteins on Ti to promote osseointegration. The protein selected for this study is High-Mobility Group Box 1 (HMGB1), which recruits inflammatory and mesenchymal stem cells to the implantation site, contributing to healing. To explore IonL-Ti interactions and HMGB1 stability on the IonL-coated surface, experimental characterization techniques including X-ray photoelectron spectroscopy, scanning electron microscopy, dynamic scanning calorimetry (DSC), and liquid chromatography mass spectrometry (LC-MS) were used along with molecular dynamics (MD) computer simulations to provide a detailed molecular level description. Results show well-structured IonL molecules on the Ti surface that impact protein crystallization and coating morphology. IonL cations and anions were found to bind strongly to oppositely charged residues of the protein. LC-MS/MS reveals that HMGB1 B-box lysine residues bind strongly to the IonLs. Stronger interactions of HMGB1 with Ion-Phe in contrast to IonL-Met results in greater retention capacity of HMGB1 in the IonL-Phe coating. Overall, this study provides evidence that the selected IonLs strongly interact with HMGB1, which can be a potential surface treatment for bone-implantable Ti devices.

Curvature and temperature-dependent thermal interface conductance between nanoscale gold and water.

Plasmonic gold nanoparticles (AuNPs) can convert laser irradiation into thermal energy for a variety of applications. Although heat transfer through the AuNP-water interface is considered an essential part of the plasmonic heating process, there is a lack of mechanistic understanding of how interface curvature and the heating itself impact interfacial heat transfer. Here, we report atomistic molecular dynamics simulations that investigate heat transfer through nanoscale gold-water interfaces. We simulated four nanoscale gold structures under various applied heat flux values to evaluate how gold-water interface curvature and temperature affect the interfacial heat transfer. We also considered a case in which we artificially reduced wetting at the gold surfaces by tuning the gold-water interactions to determine if such a perturbation alters the curvature and temperature dependence of the gold-water interfacial heat transfer. We first confirmed that interfacial heat transfer is particularly important for small particles (diameter ≤10 nm). We found that the thermal interface conductance increases linearly with interface curvature regardless of the gold wettability, while it increases nonlinearly with the applied heat flux under normal wetting and remains constant under reduced wetting. Our analysis suggests the curvature dependence of the interface conductance coincides with changes in interfacial water adsorption, while the temperature dependence may arise from temperature-induced shifts in the distribution of water vibrational states. Our study advances the current understanding of interface thermal conductance for a broad range of applications.

Biophysical and in silico characterization of NrtA: a protein-based host for aqueous nitrate and nitrite recognition.

Nitrate and nitrite are key components of the global nitrogen cycle. As such, Nature has evolved proteins as biological supramolecular hosts for the recognition, translocation, and transformation of both nitrate and nitrite. To understand the supramolecular principles that govern these anion-protein interactions, here, we employ a hybrid biophysical and in silico approach to characterize the thermodynamic properties and protein dynamics of NrtA from the cyanobacterium Synechocystis sp. PCC 6803 for the recognition of nitrate and nitrite.

Molecular-Level Understanding of the Influence of Ions and Water on HMGB1 Adsorption Induced by Surface Hydroxylation of Titanium Implants.

Due to its excellent chemical and mechanical properties, titanium has become the material of choice for orthopedic and dental implants to promote rehabilitation via bone anchorage and osseointegration. Titanium osseointegration is partially related to its capability to form a TiO2 surface layer and its ability to interact with key endogenous proteins immediately upon implantation, establishing the first bone-biomaterial interface. Surgical trauma caused by implantation results in the release of high-mobility group box 1 (HMGB1) protein, which is a prototypic DAMP (damage-associated molecular pattern) with multiple roles in inflammation and tissue healing. To develop different surface strategies that improve the clinical outcome of titanium-based implants by controlling their biological activity, a molecular-scale understanding of HMGB1-surface interactions is desired. Here, we use molecular dynamics (MD) computer simulations to provide direct insight into the HMGB1 interactions and the possible molecular arrangements of HMGB1 on fully hydroxylated and nonhydroxylated rutile (110) TiO2 surfaces. The results establish that HMGB1 is most likely to be adsorbed directly onto the surface regardless of surface hydroxylation, which is undesirable because it could affect its biological activity by causing structural changes to the protein. The hydroxylated TiO2 surface shows a greater affinity for HMGB1 than the nonhydroxylated surface. The water layer on the nonhydroxylated TiO2 surface prevents ions and the protein from directly contacting the surface. However, it was observed that if the ionic strength increases, the total number of ions adsorbed on the two surfaces increases and the protein's direct adsorption ability decreases. These findings will help to understand the HMGB1-TiO2 interactions upon implantation as well as the development of different surface strategies by introducing ions or ionic materials to the titanium implant surface to modulate its interactions with HMGB1 to preserve biological function.

An activity-based fluorescent sensor for the detection of the phenol sulfotransferase SULT1A1 in living cells.

Human phenol sulfotransferases mediate the transfer of a sulfuryl moiety from the activated sulfate donor PAPS to hydroxy-containing substrates, altering substrate solubility and charge to affect phase II metabolism and cell signaling. Here, we present the development, computational modeling, in vitro enzymology, and biological application of STS-3, an activity-based fluorescent sensor for the SULT1A1 isoform.

Molecular Dynamics Simulations of Water Condensation on Surfaces with Tunable Wettability.

Water condensation plays a major role in a wide range of industrial applications. Over the past few years, many studies have shown interest in designing surfaces with enhanced water condensation and removal properties. It is well known that heterogeneous nucleation outperforms homogeneous nucleation in the condensation process. Because heterogeneous nucleation initiates on a surface at a small scale, it is highly desirable to characterize water-surface interactions at the molecular level. Molecular dynamics (MD) simulations can provide direct insight into heterogeneous nucleation and advance surface designs. Existing MD simulations of water condensation on surfaces were conducted by tuning the solid-water van der Waals interaction energy as a substitute for modeling surfaces with different wettabilities. However, this approach cannot reflect the real intermolecular interactions between the surface and water molecules. Here, we report MD simulations of water condensation on realistic surfaces of alkanethiol self-assembled monolayers with different head group chemistries. We show that decreasing surface hydrophobicity significantly increases the electrostatic forces between water molecules and the surface, thus increasing the water condensation rate. We observe a strong correlation between our rate of condensation results and the results from other surface characterization metrics, such as the interfacial thermal conductance, contact angle, and the molecular-scale wettability metric of Garde and co-workers. This work provides insight into the water condensation process at the molecular scale on surfaces with tunable wettability.

Supramolecular and biomacromolecular enhancement of metal-free magnetic resonance imaging contrast agents.

Many contrast agents for magnetic resonance imaging are based on gadolinium, however side effects limit their use in some patients. Organic radical contrast agents (ORCAs) are potential alternatives, but are reduced rapidly in physiological conditions and have low relaxivities as single molecule contrast agents. Herein, we use a supramolecular strategy where cucurbit[8]uril binds with nanomolar affinities to ORCAs and protects them against biological reductants to create a stable radical in vivo. We further overcame the weak contrast by conjugating this complex on the surface of a self-assembled biomacromolecule derived from the tobacco mosaic virus.

Transient Photoinactivation of Cell Membrane Protein Activity without Genetic Modification by Molecular Hyperthermia.

Precise manipulation of protein activity in living systems has broad applications in biomedical sciences. However, it is challenging to use light to manipulate protein activity in living systems without genetic modification. Here, we report a technique to optically switch off protein activity in living cells with high spatiotemporal resolution, referred to as molecular hyperthermia (MH). MH is based on the nanoscale-confined heating of plasmonic gold nanoparticles by short laser pulses to unfold and photoinactivate targeted proteins of interest. First, we show that protease-activated receptor 2 (PAR2), a G-protein-coupled receptor and an important pathway that leads to pain sensitization, can be photoinactivated in situ by MH without compromising cell proliferation. PAR2 activity can be switched off in laser-targeted cells without affecting surrounding cells. Furthermore, we demonstrate the molecular specificity of MH by inactivating PAR2 while leaving other receptors intact. Second, we demonstrate that the photoinactivation of a tight junction protein in brain endothelial monolayers leads to a reversible blood-brain barrier opening in vitro. Lastly, the protein inactivation by MH is below the nanobubble generation threshold and thus is predominantly due to the nanoscale heating. MH is distinct from traditional hyperthermia (that induces global tissue heating) in both its time and length scales: nanoseconds versus seconds, nanometers versus millimeters. Our results demonstrate that MH enables selective and remote manipulation of protein activity and cellular behavior without genetic modification.

Non-Arrhenius Reaction-Diffusion Kinetics for Protein Inactivation over a Large Temperature Range.

Understanding protein folding and unfolding has been a long-standing fundamental question and has important applications in manipulating protein activity in biological systems. Experimental investigations of protein unfolding have been predominately conducted by small temperature perturbations (e.g., temperature jump), while molecular simulations are limited to small time scales (microseconds) and high temperatures to observe unfolding. Thus, it remains unclear how fast a protein unfolds irreversibly and loses function (i.e., inactivation) across a large temperature range. In this work, using nanosecond pulsed heating of individual plasmonic nanoparticles to create precise localized heating, we examine the protein inactivation kinetics at extremely high temperatures. Connecting this with protein inactivation measurements at low temperatures, we observe that the kinetics of protein unfolding is less sensitive to temperature change at the higher temperatures, which significantly departs from the Arrhenius behavior extrapolated from low temperatures. To account for this effect, we propose a reaction-diffusion model that modifies the temperature-dependence of protein inactivation by introducing a diffusion limit. Analysis of the reaction-diffusion model provides general guidelines in the behavior of protein inactivation (reaction-limited, transition, diffusion-limited) across a large temperature range from physiological temperature to extremely high temperatures. We further demonstrate that the reaction-diffusion model is particularly useful for designing optimal operating conditions for protein photoinactivation. The experimentally validated reaction-diffusion kinetics of protein unfolding is an important step toward understanding protein-inactivation kinetics over a large temperature range. It has important applications including molecular hyperthermia and calls for future studies to examine this model for other protein molecules.

Site-Selective Nucleation and Size Control of Gold Nanoparticle Photothermal Antennae on the Pore Structures of a Virus.

In this Article, we show that the surface of the bacteriophage Qß is equipped with natural ligands for the synthesis of small gold nanoparticles (AuNPs). By exploiting disulfides in the protein secondary structure and the geometry formed from the capsid quaternary structure, we find that we can produce regularly arrayed patterns of ∼6 nm AuNPs across the surface of the virus-like particle. Experimental and computational analyses provide insight into the formation and stability of this composite. We further show that the entrapped genetic material can hold upward of 500 molecules of the anticancer drug Doxorubicin without leaking and without interfering with the synthesis of the AuNPs. This direct nucleation of nanoparticles on the capsid allows for exceptional conduction of photothermal energy upon nanosecond laser irradiation. As a proof of principle, we demonstrate that this energy is capable of rapidly releasing the drug from the capsid without heating the bulk solution, allowing for highly targeted cell killing in vitro.

Hydrophilic directional slippery rough surfaces for water harvesting.

Multifunctional surfaces that are favorable for both droplet nucleation and removal are highly desirable for water harvesting applications but are rare. Inspired by the unique functions of pitcher plants and rice leaves, we present a hydrophilic directional slippery rough surface (SRS) that is capable of rapidly nucleating and removing water droplets. Our surfaces consist of nanotextured directional microgrooves in which the nanotextures alone are infused with hydrophilic liquid lubricant. We have shown through molecular dynamics simulations that the physical origin of the efficient droplet nucleation is attributed to the hydrophilic surface functional groups, whereas the rapid droplet removal is due to the significantly reduced droplet pinning of the directional surface structures and slippery interface. We have further demonstrated that the SRS, owing to its large surface area, hydrophilic slippery interface, and directional liquid repellency, outperforms conventional liquid-repellent surfaces in water harvesting applications.

Investigation of Controlled Growth of Metal-Organic Frameworks on Anisotropic Virus Particles.

Biomimetic mineralization with metal-organic frameworks (MOF), typically zeolitic imidazolate framework-8 (ZIF-8), is an emerging strategy to protect sensitive biological substances against denaturing environmental stressors such as heat and proteolytic agents. Additionally, this same biomimetic mineralization process has the potential of being used to create distinct core-shell architectures using genetically or chemically modified viral nanoparticles. Despite the proliferation of examples for ZIF-8 growth on biological or proteinaceous substrates, systematic studies of these processes are few and far between. Herein, we employed the tobacco mosaic virus (TMV) as a model biological template to investigate the biomimetic mineralization of ZIF-8, which has been proven to be a robust MOF for encasing and protecting inlaid biological substances. Our study shows a systematic dependence upon ZIF-8 crystallization parameters, e.g., ligand to metal molar ratio and metal concentration, which can yield several distinct morphologies of TMV@ZIF-8 composites and phases of ZIF-8. Further investigation using charged synthetic conjugates, time dependent growth analysis, and calorimetric analysis has shown that the TMV-Zn interaction plays a pivotal role in the final morphology of the TMV@ZIF-8, which can take the form of either core-shell bionanoparticles or large crystals of ZIF-8 with entrapped TMV located exclusively on the outer facets. The design rules outlined here, it is hoped, will provide guidance in biomimetic mineralization of MOFs on proteinaceous materials using ZIF-8.

Computational and Experimental Studies on the Effects of Monomer Planarity on Covalent Organic Framework Formation.

We report the synthesis of one new boronate ester-based covalent organic framework (COF) and two new covalent organic polymers (COPs) made with fluoranthene-containing monomers and hexahydroxytriphenylene. The structure of the monomer heavily influences whether this material forms a highly ordered mesoporous material (COF) or an amorphous, microporous material (COP). The synthesis of the fluoranthene monomers was carried out using a divergent strategy that allows for systematic structural variation and the ability to conduct a careful structure-function study. We found that small structural variations in the monomers dramatically affected the crystallinity, surface area, pore structure, and luminescence properties of the polymers. While each of the monomers contains the same fluoranthene core, the resultant pore sizes range from microporous (10 Å) to mesoporous (37 Å), with surface areas ranging from ∼500 to 1200 m2/g. To help explain how these small structural differences can have such a large effect, we carried out a series of molecular dynamics simulations on the polymers to obtain information with atomic-scale resolution on how the monomer structure affects non-covalent COF layer stacking.

Molecular Hyperthermia: Spatiotemporal Protein Unfolding and Inactivation by Nanosecond Plasmonic Heating.

Spatiotemporal control of protein structure and activity in biological systems has important and broad implications in biomedical sciences as evidenced by recent advances in optogenetic approaches. Here, this study demonstrates that nanosecond pulsed laser heating of gold nanoparticles (GNP) leads to an ultrahigh and ultrashort temperature increase, coined as "molecular hyperthermia", which causes selective unfolding and inactivation of proteins adjacent to the GNP. Protein inactivation is highly dependent on both laser pulse energy and GNP size, and has a well-defined impact zone in the nanometer scale. It is anticipated that the fine control over protein structure and function enabled by this discovery will be highly enabling within a number of arenas, from probing the biophysics of protein folding/unfolding to the nanoscopic manipulation of biological systems via an optical trigger, to developing novel therapeutics for disease treatment without genetic modification.

Nested sampling of isobaric phase space for the direct evaluation of the isothermal-isobaric partition function of atomic systems.

Nested Sampling (NS) is a powerful athermal statistical mechanical sampling technique that directly calculates the partition function, and hence gives access to all thermodynamic quantities in absolute terms, including absolute free energies and absolute entropies. NS has been used predominately to compute the canonical (NVT) partition function. Although NS has recently been used to obtain the isothermal-isobaric (NPT) partition function of the hard sphere model, a general approach to the computation of the NPT partition function has yet to be developed. Here, we describe an isobaric NS (IBNS) method which allows for the computation of the NPT partition function of any atomic system. We demonstrate IBNS on two finite Lennard-Jones systems and confirm the results through comparison to parallel tempering Monte Carlo. Temperature-entropy plots are constructed as well as a simple pressure-temperature phase diagram for each system. We further demonstrate IBNS by computing part of the pressure-temperature phase diagram of a Lennard-Jones system under periodic boundary conditions.

Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study.

In Förster resonance energy transfer (FRET) experiments, extracting accurate structural information about macromolecules depends on knowing the positions and orientations of donor and acceptor fluorophores. Several approaches have been employed to reduce uncertainties in quantitative FRET distance measurements. Fluorophore-position distributions can be estimated by surface accessibility (SA) calculations, which compute the region of space explored by the fluorophore within a static macromolecular structure. However, SA models generally do not take fluorophore shape, dye transition-moment orientation, or dye-specific chemical interactions into account. We present a detailed molecular-dynamics (MD) treatment of fluorophore dynamics for an ATTO donor/acceptor dye pair and specifically consider as case studies dye-labeled protein-DNA intermediates in Cre site-specific recombination. We carried out MD simulations in both an aqueous solution and glycerol/water mixtures to assess the effects of experimental solvent systems on dye dynamics. Our results unequivocally show that MD simulations capture solvent effects and dye-dye interactions that can dramatically affect energy transfer efficiency. We also show that results from SA models and MD simulations strongly diverge in cases where donor and acceptor fluorophores are in close proximity. Although atomistic simulations are computationally more expensive than SA models, explicit MD studies are likely to give more realistic results in both homogeneous and mixed solvents. Our study underscores the model-dependent nature of FRET analyses, but also provides a starting point to develop more realistic in silico approaches for obtaining experimental ensemble and single-molecule FRET data.