Showing papers in "Journal of Physical Chemistry B in 2023"

Promoting Effect of Common Marine Cations on Hydrate Dissociation and Structural Evolution under a Static Electric Field.

Abstract: Natural gas hydrate, a potential energy resource, is attracting worldwide attention. In this study, we propose a new method of hydrate dissociation which uses seawater and electrostatic fields (SE method) cooperatively. The hydrate molecular dissociation mechanism of gas hydrate is a key issue in studying the kinetic properties of gas hydrate using the SE method. Therefore, molecular dynamics simulations were used to investigate the thermodynamic properties and structural changes of methane hydrate (MH) in multiple kinds of salt solutions under an electrostatic field. The results show that the electric field can drive cations into the MH phase to form a series of random semiopen cages, which are essentially temporary and metastable. The variation in free energy indicates that it is more difficult for divalent cations to enter the hydrate phase than monovalent cations, meaning that the hydrate structures formed with divalent cations are more unstable. Then, the ion current occurred in the hydrate phase (called ion migration in this study), which greatly accelerated hydrate dissociation. In contrast, the promotion effect of cations with the same charge on MH dissociation is as follows: Sr2+ > K+ ≈ Na+ > Ca2+ ≈ Mg2+. In general, the presence of common marine cations enhanced the promotion effect of the electric field on gas hydrate dissociation.

Characterization of the Binding Properties of Sorafenib to c-MYC G-Quadruplexes: Evidence for Screening Potential Ligands.

Abstract: Sorafenib (Sor) is a multitarget kinase inhibitor used clinically to treat hepatocellular carcinoma and renal cancer. In this study, the interaction mechanism of Sor with c-MYC G-quadruplexes (G4) was investigated at the molecular level by computer-aided means and experiments. Molecular docking results predicted the binding of Sor to the groove of G4. Molecular dynamics (MD) simulations were used to evaluate the effect of ligand binding to G4. Ultraviolet (UV), fluorescence spectroscopy, and viscosity experiments showed that the binding site was in the groove. The UV and fluorescence titration results showed that compared with traditional G4 ligands represented by compound meso-tetra (N-methyl-4-pyridyl) porphine (TmPyP4), Sor has a lower affinity for G4. Likewise, results from fluorescence resonance energy transfer (FRET) experiments suggested that Sor could have a limited ability to stabilize G4, but it was not as prominent as that of TmPyP4. Time-resolved fluorescence spectroscopy again supported the results from steady-state fluorescence spectroscopy, indicating that a static quenching mechanism mainly drove the process. Studying the interaction mechanism of Sor and c-MYC may inspire the screening of new, selective c-MYC G4 ligands and provide ideas for the design of drugs with good stability, low toxicity, and specific targeting of G4.

Dynamics of Aqueous Electrolyte Solutions: Challenges for Simulations.

Abstract: This Perspective article focuses on recent simulation work on the dynamics of aqueous electrolytes. It is well-established that full-charge, nonpolarizable models for water and ions generally predict solution dynamics that are too slow in comparison to experiments. Models with reduced (scaled) charges do better for solution diffusivities and viscosities but encounter issues describing other dynamic phenomena such as nucleation rates of crystals from solution. Polarizable models show promise, especially when appropriately parametrized, but may still miss important physical effects such as charge transfer. First-principles calculations are starting to emerge for these properties that are in principle able to capture polarization, charge transfer, and chemical transformations in solution. While direct ab initio simulations are still too slow for simulations of large systems over long time scales, machine-learning models trained on appropriate first-principles data show significant promise for accurate and transferable modeling of electrolyte solution dynamics.

Machine Learning-Boosted Design of Ionic Liquids for CO2 Absorption and Experimental Verification

Abstract: Efficient CO2 capture is indispensable for achieving a carbon-neutral society while maintaining a high quality of life. Since the discovery that ionic liquids (ILs; room-temperature molten salts) can absorb CO2, various solvents composed of molecular ions have been studied. However, it is challenging to observe the properties of each isolated ion component to control the function of ILs as they are mixtures of ions. Finding the optimal cation–anion combination for the CO2 absorbent from their enormous chemical space had been impossible in a practical sense. This study applied electronic structure informatics to explore ILs with high CO2 solubility from 402,114 IL candidates. The feature variables were determined by a set of cheap quantum chemistry calculations for isolated small-ion fragments, and the importance of molecular geometries and electronic states governing molecular interactions was identified via the wrapper method. As a result, it was clearly shown that the electronic states of ionic species must have essential roles in the CO2 physisorption capacity of ILs. Considering synthetic easiness for the candidates narrowed by the machine learning model, trihexyl(tetradecyl)phosphonium perfluorooctanesulfonate was synthesized. Using a magnetic suspension balance, it was experimentally confirmed that this IL has higher CO2 solubility than trihexyl(tetradecyl)phosphonium bis(trifluoromethanesulfonyl)amide, which is the previous best IL for CO2 absorption.

Advances in the Spectroscopic and Structural Characterization of Core Light-Harvesting Complexes from Purple Phototrophic Bacteria.

Abstract: Purple phototrophic bacteria are ancient anoxygenic phototrophs and attractive research tools because they capture light energy in the near-infrared (NIR) region of the spectrum and transform it into chemical energy by way of uphill energy transfers. The heart of this reaction occurs in light-harvesting 1-reaction center (LH1-RC) complexes, which are the simplest model systems for understanding basic photosynthetic reactions within type-II (quinone-utilizing) reaction centers. In this Perspective, we highlight structure-function relationships concerning unresolved fundamental processes in purple bacterial photosynthesis, including the diversified light-harvesting capacity of LH1-associated BChl molecules, energies necessary for photoelectric conversion in the RC special pairs, and quinone transport mechanisms. Based on recent progress in the spectroscopic and structural analysis of LH1-RC complexes from a variety of purple phototrophs, we discuss several key factors for understanding how purple bacteria resource light energy in the inherently energy-poor NIR region of the electromagnetic spectrum.

Advances in Molecular Design and Photophysical Engineering of Perylene Bisimide-Containing Polyads and Multichromophores for Film-Based Fluorescent Sensors.

Abstract: Film-based fluorescent sensors (FFSs) represent an important chemistry technology for meeting the urgent needs of on-site and real-time analysis, thereby enabling significant applications in environmental and health monitoring. As the core of FFSs, innovative design of sensing fluorophores and their intrinsic excited-state-related response nature endow FFSs with superior sensing performances in an endless expansion. In this Perspective, we specifically focus on perylene bisimide (PBI)-containing polyads and multichromophores with rigid configuration and notable photochemical stability for developing high-performance FFSs. These nonplanar structures mitigate aggregation and create abundant gaps for the sake of mass transfer and availability of the sensing units in the adlayer of the sensing films. We also comprehensively discuss how to adjust electronic coupling governing the excited-state events by appropriate functionalization strategies, thus providing a plethora of valuable insights for the exploration of the structure-property relationships in these orchestrated molecular systems. Throughout this Perspective, we also identify opportunities for FFSs in the future developments.

Molecular Dynamics-Assisted Interaction of Vanadium Complex-AMPK: From Force Field Development to Biological Application for Alzheimer's Treatment.

Abstract: A large part of the world's population is affected by Alzheimer's disease (AD) and diabetes mellitus type 2, which cause both social and economic impacts. These two conditions are associated with one protein, AMPK. Studies have shown that vanadium complexes, such as bis(N',N'-dimethylbiguanidato)-oxovanadium(IV), VO(metf)2·H2O, are potential agents against AD. A crucial step in drug design studies is obtaining information about the structure and interaction of these complexes with the biological targets involved in the process through molecular dynamics (MD) simulations. However, MD simulations depend on the choice of a good force field that could present reliable results. Moreover, general force fields are not efficient for describing the properties of metal complexes, and a VO(metf)2·H2O-specific force field does not yet exist; thus, the proper development of a parameter set is necessary. Furthermore, this investigation is essential and relevant given the importance for both the scientific community and the population that is affected by this neurodegenerative disease. Therefore, the present work aims to develop and validate the AMBER force field parameters for VO(metf)2·H2O since the literature lacks such information on metal complexes and investigate through classical molecular dynamics the interactions made by the complex with the protein. The proposed force field proved to be effective for describing the vanadium complex (VC), supported by different analyses and validations. Moreover, it had a great performance when compared to the general AMBER force field. Beyond that, MD findings provided an in-depth perspective of vanadium complex-protein interactions that should be taken into consideration in future studies.

Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles

Abstract: The reshuffling mobility of molecular building blocks in self-assembled micelles is a key determinant of many their interesting properties, from emerging morphologies and surface compartmentalization, to dynamic reconfigurability and stimuli-responsiveness. However, the microscopic details of such complex structural dynamics are typically nontrivial to elucidate, especially in multicomponent assemblies. Here we show a machine-learning approach that allows us to reconstruct the structural and dynamic complexity of mono- and bicomponent surfactant micelles from high-dimensional data extracted from equilibrium molecular dynamics simulations. Unsupervised clustering of smooth overlap of atomic position (SOAP) data enables us to identify, in a set of multicomponent surfactant micelles, the dominant local molecular environments that emerge within them and to retrace their dynamics, in terms of exchange probabilities and transition pathways of the constituent building blocks. Tested on a variety of micelles differing in size and in the chemical nature of the constitutive self-assembling units, this approach effectively recognizes the molecular motifs populating them in an exquisitely agnostic and unsupervised way, and allows correlating them to their composition in terms of constitutive surfactant species.

Comparison of Force Fields for the Prediction of Thermophysical Properties of Long Linear and Branched Alkanes.

Abstract: The prediction of thermophysical properties at extreme conditions is an important application of molecular simulations. The quality of these predictions primarily depends on the quality of the employed force field. In this work, a systematic comparison of classical transferable force fields for the prediction of different thermophysical properties of alkanes at extreme conditions, as they are encountered in tribological applications, was carried out using molecular dynamics simulations. Nine transferable force fields from three different classes were considered (all-atom, united-atom, and coarse-grained force fields). Three linear alkanes (n-decane, n-icosane, and n-triacontane) and two branched alkanes (1-decene trimer and squalane) were studied. Simulations were carried out in a pressure range between 0.1 and 400 MPa at 373.15 K. For each state point, density, viscosity, and self-diffusion coefficient were sampled, and the results were compared to experimental data. The Potoff force field yielded the best results.

Personal Perspective on Strain-Induced Polymer Crystallization.

Abstract: Semicrystalline polymer materials are commonly strong yet tough after processed through fiber spinning, film stretching (or blowing), and plastic molding (or foaming), which are fundamentally related with strain-induced crystallization. This paper provides a personal perspective on thermodynamics and kinetics aspects of strain-induced polymer crystallization, mainly based on the author's recent research experience. The thermodynamic studies include homopolymers, random copolymers, solution polymers, and blend polymers. The kinetic studies cover three sequential crystallization stages, i.e., crystal nucleation, crystal growth, and postgrowth. The thermodynamic driving forces join with the kinetic barriers to determine the crystal nucleation mechanisms and the structure evolution at the molecular level, which yield unique polymer crystal morphologies from lamellar crystals to shish-kebab crystals and eventually fibril crystals. The resulting semicrystalline structures were discussed with their implications for the mechanical properties of products. Some future studies were briefly proposed.

Protein Dynamics and Enzymatic Catalysis.

Abstract: This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.

Physical Properties and Low-Frequency Polarizability Anisotropy and Dipole Responses of Phosphonium Bis(fluorosulfonyl)amide Ionic Liquids with Pentyl, Ethoxyethyl, or 2-(Ethylthio)ethyl Group.

Abstract: This study compared the physical properties, e.g., glass transition temperature, melting point, viscosity, density, surface tension, and electrical conductivity, and the low-frequency spectra under 200 cm-1 of three synthesized ionic liquids (ILs), triethylpentylphosphonium bis(fluorosulfonyl)amide ([P2225][NF2]), ethoxyethyltriethylphosphonium bis(fluorosulfonyl)amide ([P222(2O2)][NF2]), and triethyl[2-(ethylthio)ethyl]phosphonium bis(fluorosulfonyl)amide ([P222(2S2)][NF2]), at various temperatures using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES) and terahertz time-domain spectroscopy (THz-TDS). The [P222(2S2)][NF2] had the highest viscosity and glass transition temperature, whereas the [P222(2O2)][NF2] had the lowest. Among the three ILs, the [P222(2S2)][NF2] had the highest density and surface tension, and the [P222(2O2)][NF2] had the highest electrical conductivity. The RIKES and THz-TDS spectral line shapes for the three ILs varied significantly. For the [P2225][NF2], molecular dynamics simulations successfully reproduced the line shapes of the experimental spectra and indicated that the RIKES spectrum was mainly due to the cation and cross-term and their rotational motions, whereas the THz-TDS spectrum was mainly due to the anion and its translational motion. This shows that it is desirable to utilize both fs-RIKES and THz-TDS methods to reveal molecular motions at the low-frequency domain. The [P222(2S2)][NF2] had higher frequency peaks and broader bands in the low-frequency spectra via fs-RIKES and THz-TDS than those for the [P2225][NF2] and [P222(2O2)][NF2].

Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins

Abstract: iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin’s C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin’s N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation results in a slight change in absorption and a 4–8 nm red shift in the fluorescence relative to iLOV, in good agreement with the computational predictions. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red shifting may be achieved by bringing the side chain closer to the cofactor.

NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins

Abstract: Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale “breathing” motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.

Role of Strong Localized vs Weak Distributed Interactions in Disordered Protein Phase Separation

Abstract: Interaction strength and localization are critical parameters controlling the single-chain and condensed-state properties of intrinsically disordered proteins (IDPs). Here, we decipher these relationships using coarse-grained heteropolymers comprised of hydrophobic (H) and polar (P) monomers as model IDPs. We systematically vary the fraction of P monomers XP and employ two distinct particle-based models that include either strong localized attractions between only H–H pairs (HP model) or weak distributed attractions between both H–H and H–P pairs (HP+ model). To compare different sequences and models, we first carefully tune the attraction strength for all sequences to match the single-chain radius of gyration. Interestingly, we find that this procedure produces similar conformational ensembles, nonbonded potential energies, and chain-level dynamics for single chains of almost all sequences in both models, with some deviations for the HP model at large XP. However, we observe a surprisingly rich phase behavior for the sequences in both models that deviates from the expectation that similarity at the single-chain level will translate to a similar phase-separation propensity. Coexistence between dilute and dense phases is only observed up to a model-dependent XP, despite the presence of favorable interchain interactions, which we quantify using the second virial coefficient. Instead, the limited number of attractive sites (H monomers) leads to the self-assembly of finite-sized clusters of different sizes depending on XP. Our findings strongly suggest that models with distributed interactions favor the formation of liquid-like condensates over a much larger range of sequence compositions compared to models with localized interactions.

Atomistic Insights into Organization of RNA-Loaded Lipid Nanoparticles.

Abstract: RNA-based therapies have shown promise in a wide range of applications, from cancer therapy, treatment of inherited diseases to vaccination. Encapsulation of RNA into ionizable lipid (IL) containing lipid nanoparticles (LNPs) has enabled its safe and targeted delivery. We present here the simulations of the self-assembly process of pH-sensitive RNA-carrying LNPs and their internal morphology. At low pH, the simulations confirm a lipid core encapsulating RNA in the hexagonal phase. Our all-atom and coarse-grained simulations show that an RNA molecule inside an LNP is protected from interactions with ions by being enveloped in the charged ILs. At neutral pH, representing the environment after LNP administration into human tissues, LNPs expelled most of the encapsulated RNA and water and formed separate bulk IL-rich and ordered the helper-lipid-rich phase. Helper lipids arranged themselves to be in contact with RNA or water. The presented models provide atomistic understanding of the LNP structure and open a way to investigate them in silico, varying the LNP composition or interacting with other biostructures aiming at increasing the efficiency of RNA-based medicine.

Molecular Rotations, Multiscale Order, Hyperuniformity, and Signatures of Metastability during the Compression/Decompression Cycles of Amorphous Ices.

Abstract: We model, via large-scale molecular dynamics simulations, the isothermal compression of low-density amorphous ice (LDA) to generate high-density amorphous ice (HDA) and the corresponding decompression extending to negative pressures to recover the low-density amorphous phase (LDAHDA). Both LDA and HDA are nearly hyperuniform and are characterized by a dynamical HBN, showing that amorphous ices are nonstatic materials and implying that nearly hyperuniformity can be accommodated in dynamical networks. In correspondence with both the LDA-to-HDA and the HDA-to-LDAHDA phase transitions, the (partial) activation of rotational degrees of freedom activates a cascade effect that induces a drastic change in the connectivity and a pervasive reorganization of the HBN topology which, ultimately, break the samples' hyperuniform character. Key to this effect is the rapid rate at which changes occur, and not their magnitude. The inspection of structural properties from the short- to the long-range shows that signatures of metastability are present at all length-scales, hence providing further solid evidence in support of the liquid-liquid critical point scenario. LDA and LDAHDA differ in terms of HBN and structural properties, implying that they are distinct low-density glasses. Our work unveils the role of molecular rotations in the phase transitions between amorphous ices and shows how the unfreezing of rotational degrees of freedom generates a cascade effect that propagates over multiple length-scales. Our findings greatly improve our basic understanding of water and amorphous ices and can potentially impact the field of molecular network-forming materials at large.

Design of an Electrostatic Frequency Map for the NH Stretch of the Protein Backbone and Application to Chiral Sum Frequency Generation Spectroscopy.

Abstract: We develop an electrostatic map for the vibrational NH stretch (amide A) of the protein backbone with a focus on vibrational chiral sum frequency generation spectroscopy (chiral SFG). Chiral SFG has been used to characterize protein secondary structure at interfaces using the NH stretch and to investigate chiral water superstructures around proteins using the OH stretch. Interpretation of spectra has been complicated because the NH stretch and OH stretch overlap spectrally. Although an electrostatic map for water OH developed by Skinner and co-workers was used previously to calculate the chiral SFG response of water structures around proteins, a map for protein NH that is directly responsive to biological complexity has yet to be developed. Here, we develop such a map, linking the local electric field to vibrational frequencies and transition dipoles. We apply the map to two protein systems and achieve much better agreement with experiment than was possible in our previous studies. We show that couplings between NH and OH vibrations are crucial to the line shape, which informs the interpretation of chiral SFG spectra, and that the chiral NH stretch response is sensitive to small differences in structure. This work increases the utility of the NH stretch in biomolecular spectroscopy.

Protein Stability—Analysis of Heat and Cold Denaturation without and with Unfolding Models

Abstract: Protein stability is important in many areas of life sciences. Thermal protein unfolding is investigated extensively with various spectroscopic techniques. The extraction of thermodynamic properties from these measurements requires the application of models. Differential scanning calorimetry (DSC) is less common, but is unique as it measures directly a thermodynamic property, that is, the heat capacity Cp(T). The analysis of Cp(T) is usually performed with the chemical equilibrium two-state model. This is not necessary and leads to incorrect thermodynamic consequences. Here we demonstrate a straightforward model-independent evaluation of heat capacity experiments in terms of protein unfolding enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T)). This now allows the comparison of the experimental thermodynamic data with the predictions of different models. We critically examined the standard chemical equilibrium two-state model, which predicts a positive free energy for the native protein, and diverges distinctly from the experimental temperature profiles. We propose two new models which are equally applicable to spectroscopy and calorimetry. The ΘU(T)-weighted chemical equilibrium model and the statistical-mechanical two-state model provide excellent fits of the experimental data. They predict sigmoidal temperature profiles for enthalpy and entropy, and a trapezoidal temperature profile for the free energy. This is illustrated with experimental examples for heat and cold denaturation of lysozyme and β-lactoglobulin. We then show that the free energy is not a good criterion to judge protein stability. More useful parameters are discussed, including protein cooperativity. The new parameters are embedded in a well-defined thermodynamic context and are amenable to molecular dynamics calculations.

How Does Electronic Polarizability or Scaled-Charge Affect the Interfacial Properties of Room Temperature Ionic Liquids?

Abstract: The room temperature ionic liquid (RTIL) air-liquid interface plays an important role in many applications. Herein, we present molecular dynamics simulation results for the air-liquid interface of a common RTIL, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, [C4mim][NTf2]. To elucidate the effects of electronic polarizability and scaled-charge ions on the properties of the RTIL air-liquid interface, we employ three different kinds of force fields: a nonpolarizable force field (FF) with united ion charges (FixQ), a nonpolarizable FF with scaled-charge by 0.8 (ScaleQ), and a polarizable FF (Drude). To identify whether the ions reside at the interface or not, the method of identification of the truly interfacial molecules is used. The structural and dynamical properties in the interfacial, subinterfacial, and central layers are evaluated. In general for bulk liquids, the FixQ model predicts too-ordered structures and too-sluggish dynamics, while the ScaleQ model can serve as a simple cure. However, the ScaleQ model cannot reproduce the results of the Drude model at the interface, due to an inappropriate scaled-down charge near the interface.

Equation of State of Liquid Water Written by Simple Experimental Polynomials and the Liquid-Liquid Critical Point.

Abstract: Experimental and theoretical evidence has been accumulating to support the liquid-liquid critical point (LLCP) hypothesis for water. However, no agreement has yet been reached on the pressure and temperature of LLCP. Here we made simple experimental equations that reproduced the volume of liquid water measured over a wide pressure-temperature range. They were polynomials that calculate pressure using volume and temperature as variables, and coefficients were determined by the method of least-squares. We analyzed the polynomials by changing the volume data and the number of terms in the polynomials and extrapolated them slightly to low temperatures. Consequently, the available experimental volume of liquid water indicated (but did not prove) the existence of LLCP at low temperature. Representative polynomials suggested that LLCP locates around 105 ± ∼ 9 MPa, 207 ± ∼ 5 K, and 0.993 ± ∼ 0.009 cm3/g.

Light-Induced Forward and Reverse Intersystem Crossing in Green Fluorescent Proteins at Cryogenic Temperatures.

Abstract: Combining fluorescence and phosphorescence kinetics, we characterize forward and reverse intersystem crossing (FISC and RISC, respectively) between the singlet and triplet manifolds S ↔ T in photoswitchable (rsEGFP2) and non-photoswitchable (EGFP) green fluorescent proteins upon continuous 488 nm laser excitation at cryogenic temperatures (CTs). Both proteins behave very similarly, with T1 absorption spectra showing a visible peak at 490 nm (10 mM-1 cm-1) and a vibrational progression in the near-infrared (720 to 905 nm). The dark lifetime of T1 is 21-24 ms at 100 K and very weakly temperature-dependent up to 180 K. Above 180 K, T1 lifetimes reduce rapidly to few milliseconds as found at room temperature (RT). FISC and RISC quantum yields are 0.3 and 0.1%, respectively, for both proteins. The light-induced RISC channel becomes faster than the dark reversal at power densities as low as 20 W cm-2. We discuss implications for fluorescence (super resolution-) microscopy at CT and RT.

Characterizing Experimental Monoclonal Antibody Interactions and Clustering Using a Coarse-Grained Simulation Library and a Viscosity Model.

Abstract: Attractive protein-protein interactions in concentrated monoclonal antibody (mAb) solutions may lead to the formation of clusters that increase viscosity. Here, we propose an analytical model that relates mAb solution viscosity to clustering by accounting for the contributions of suboptimal mAb packing within a cluster and cluster fractal dimension. The influence of short-range, anisotropic attractions and long-range Coulombic repulsion on cluster properties is investigated by analyzing the cluster-size distributions, cluster fractal dimensions, radial distribution functions, and static structure factors from a library of coarse-grained molecular dynamics simulations. The library spans a vast range of mAb charges and attractive interactions in solutions of varying ionic strength. We present a framework for combining the viscosity model and simulation library to successfully characterize the attraction, repulsion, and clustering of an experimental mAb in three different pH and cosolute conditions by fitting the measured viscosity or structure factor from small-angle X-ray scattering. At low ionic strength, the cluster-size distribution is impacted by strong charges, and both the viscosity and net charge or structure factor and net charge must be considered to deconvolute the effects of short-range attraction and long-range repulsion.

Self-Quenching Behavior of a Fluorescent Probe Incorporated within Lipid Membranes Explored Using Electrophoresis and Fluorescence Lifetime Imaging Microscopy

Abstract: Fluorescent probes are useful in biophysics research to assess the spatial distribution, mobility, and interactions of biomolecules. However, fluorophores can undergo “self-quenching” of their fluorescence intensity at high concentrations. A greater understanding of concentration-quenching effects is important for avoiding artifacts in fluorescence images and relevant to energy transfer processes in photosynthesis. Here, we show that an electrophoresis technique can be used to control the migration of charged fluorophores associated with supported lipid bilayers (SLBs) and that quenching effects can be quantified with fluorescence lifetime imaging microscopy (FLIM). Confined SLBs containing controlled quantities of lipid-linked Texas Red (TR) fluorophores were generated within 100 × 100 μm corral regions on glass substrates. Application of an electric field in-plane with the lipid bilayer induced the migration of negatively charged TR-lipid molecules toward the positive electrode and created a lateral concentration gradient across each corral. The self-quenching of TR was directly observed in FLIM images as a correlation of high concentrations of fluorophores to reductions in their fluorescence lifetime. By varying the initial concentration of TR fluorophores incorporated into the SLBs from 0.3% to 0.8% (mol/mol), the maximum concentration of fluorophores reached during electrophoresis could be modulated from 2% up to 7% (mol/mol), leading to the reduction of fluorescence lifetime down to 30% and quenching of the fluorescence intensity down to 10% of their original levels. As part of this work, we demonstrated a method for converting fluorescence intensity profiles into molecular concentration profiles by correcting for quenching effects. The calculated concentration profiles have a good fit to an exponential growth function, suggesting that TR-lipids can diffuse freely even at high concentrations. Overall, these findings prove that electrophoresis is effective at producing microscale concentration gradients of a molecule-of-interest and that FLIM is an excellent approach to interrogate dynamic changes to molecular interactions via their photophysical state.

Surface Affinity of Tetramethylammonium Iodide in Aqueous Solutions: A Combined Experimental and Computer Simulation Study.

Abstract: The surface affinity of tetramethylammonium iodide (TMAI) in aqueous solutions is investigated by surface tension measurements and molecular dynamics computer simulations. Experiments, performed in the entire composition range of solubility using the pendant drop method with two different setups, clearly reveal that TMAI is a weakly capillary active salt. Computer simulations performed with the AMBER force field reproduce the experimental data very well, while two other major force fields (i.e., CHARMM and OPLS) can still reproduce the experimental trend qualitatively; however, even qualitative reproduction of the experimental trend requires scaling down the ion charges according to the Leontyev-Stuchebrukhov correction. On the other hand, the GROMOS force field fails in reproducing the experimentally confirmed capillary activity of TMAI. Molecular dynamics simulation results show that, among the two ions, iodide has a clearly larger surface affinity than tetramethylammonium (TMA+). Further, the adsorption of the I- anions is strictly limited to the first molecular layer beneath the liquid-vapor interface, which is followed by several layers of their depletion. On the other hand, the net negative charge of the surface layer, caused by the excess amount of I- with respect to TMA+, is compensated by a diffuse layer of adsorbed TMA+ cations, extending to or beyond the fourth molecular layer beneath the liquid surface.

Identifying Protein-Ligand Interactions via a Novel Distance Self-Feedback Biomolecular Interaction Network.

Abstract: Efficient and accurate characterizations of protein-ligand interactions are key to understanding biology at the molecular level. They are particularly useful in pharmaceutical industry applications. They are usually computationally demanding for those widely applied dynamics-based methods in identifying important residues or calculating ligand binding free energy. In this work, we proposed a graph deep learning (DL) framework, namely, the distance self-feedback biomolecular interaction network (DSBIN), in which the relationship between the complex structure and binding affinity can be established by means of a carefully designed distance self-feedback module and interaction layer. Our model can directly provide a quantitative evaluation of inhibitor binding affinities (pKd). More importantly, the DSBIN model efficiently identifies key interactions for inhibitor binding and thus intrinsically bears the interpretability. Its generalization performance was further verified using 1405 unseen structures. The predicted binding free energies' deviations were calculated to be less than 1.37 kcal/mol for more than 55% structures. Moreover, we also compared the DSBIN model with a commonly used theoretical method in calculating the substrate binding free energy, MM/GBSA. Our results show that the current DL model has generally better performance in predicting the binding free energy. For a specific complex system, mannopentaose/TmCBM27, the DSBIN predicted binding free energy is -8.21 kcal/mol, which is very close to experimentally measured -7.76 kcal/mol and MM/GBSA calculated -7.16 kcal/mol. Meanwhile, all important aromatic residues around the binding pocket can be identified by our DL model. Considering the accuracy and efficiency of the newly developed DL model, it may be very helpful in the field of drug design and molecular recognition.

Dynamic Heterogeneity of Solvent Motion and Ion Transport in Concentrated Electrolytes.

Abstract: Molecular-level understanding of the cation transference number t+0, an important property that characterizes the transport of working cations, is critical to the bottom-up design of battery electrolytes. We quantify t+0 in a model tetraglyme-based electrolyte using molecular dynamics simulation and the Onsager approach. t+0 exhibits a concentration dependence in three distinct regimes: dilute, intermediate, and concentrated. The cluster approximation uncovers dominant correlations and dynamic heterogeneity in each regime. In the dilute regime, t+0 decreases sharply as increasing numbers of solvent molecules become coordinated with Li+. The crossover to the intermediate regime, t+0 ≈ 0, occurs when all solvent molecules become coordinated, and a plateau is obtained because anions enter the Li+ solvation shell, resulting in ion pairs that do not contribute to t+0. Transference in concentrated electrolytes is dominated by the presence of cations in a variety of negatively charged and solvent-excluded clusters, resulting in t+0 < 0.

Composition Effect on Interfacial Reactions of Sodium Aluminosilicate Glasses in Aqueous Solution.

Abstract: Understanding the underlying reaction mechanisms responsible for aluminosilicate glass dissolution in aqueous environments is crucial for designing glasses for technological applications ranging from architecture windows and touch screens to nuclear waste disposal. This study investigated the glass composition effect on the interfacial reactions of sodium aluminosilicate (NAS) glasses using molecular dynamics (MD) simulations with recently developed reactive potentials. Glass-water interfacial models of six NAS glasses with varying Al2O3/Na2O ratios were investigated for up to 4 nanoseconds (ns) to elucidate the interfacial reaction mechanisms at ambient temperature. The results showed that the coordination defects, such as undercoordinated Si and Al, as well as non-bridging oxygens (NBOs) accumulated at the glass surfaces, play a crucial role in the initial hydration reaction process of the glasses. They promote the formation of silanol (Si-OH) and aluminol (Al-OH) species together with the Na+⇔ H+ ion-exchange reactions. The z-density profiles of H2O and H+ ions affirmed the water/H+ propagation into the glass up to 2 nanometers after 4 ns reactions. The penetration depth depends on the composition and shows a nonlinear dependence, suggesting that the subsequent water penetration, particularly into the bulk glass, is supported by the availability of random channels. Aluminol formations, including Al-OH or Al-OH2 near the surface, were found to form mainly through the hydrolysis of Al-O-Al bonds and hydration of Al+-NBO- units. While water molecules are involved in initial interfacial reactions, water penetration into the bulk glass region is primarily achieved by proton transfer. Compared to highly mobile proton transfer involving silanol groups, proton transfer associated with [AlO4]- species is much more limited, particularly in the bulk glass region. These new insights into the role of aluminum in interfacial reactions of the NAS glasses can help to understand the initial dissolution mechanisms and in designing more durable glasses.

Functional Protein Dynamics Directly from Sequences

Abstract: The sequence correlations within a protein multiple sequence alignment are routinely being used to predict contacts within its structure, but here we point out that these data can also be used to predict a protein’s dynamics directly. The elastic network protein dynamics models rely directly upon the contacts, and the normal modes of motion are obtained from the decomposition of the inverse of the contact map. To make the direct connection between sequence and dynamics, it is necessary to apply coarse-graining to the structure at the level of one point per amino acid, which has often been done, and protein coarse-grained dynamics from elastic network models has been highly successful, particularly in representing the large-scale motions of proteins that usually relate closely to their functions. The interesting implication of this is that it is not necessary to know the structure itself to obtain its dynamics and instead to use the sequence information directly to obtain the dynamics.

Full-Spectrum CARS Microscopy of Cells and Tissues with Ultrashort White-Light Continuum Pulses

Abstract: Coherent anti-Stokes Raman scattering (CARS) microscopy is an emerging nonlinear vibrational imaging technique that delivers label-free chemical maps of cells and tissues. In narrowband CARS, two spatiotemporally superimposed picosecond pulses, pump and Stokes, illuminate the sample to interrogate a single vibrational mode. Broadband CARS (BCARS) combines narrowband pump pulses with broadband Stokes pulses to record broad vibrational spectra. Despite recent technological advancements, BCARS microscopes still struggle to image biological samples over the entire Raman-active region (400–3100 cm–1). Here, we demonstrate a robust BCARS platform that answers this need. Our system is based on a femtosecond ytterbium laser at a 1035 nm wavelength and a 2 MHz repetition rate, which delivers high-energy pulses used to produce broadband Stokes pulses by white-light continuum generation in a bulk YAG crystal. Combining such pulses, pre-compressed to sub-20 fs duration, with narrowband pump pulses, we generate a CARS signal with a high (<9 cm–1) spectral resolution in the whole Raman-active window, exploiting both the two-color and three-color excitation mechanisms. Aided by an innovative post-processing pipeline, our microscope allows us to perform high-speed (≈1 ms pixel dwell time) imaging over a large field of view, identifying the main chemical compounds in cancer cells and discriminating tumorous from healthy regions in liver slices of mouse models, paving the way for applications in histopathological settings.