The Journal of Physical Chemistry B最新文献

Cathepsin B (CTSB) plays a key role in several processes that promote breast cancer progression, making its activity detection crucial for cancer analysis. In this study, we developed a surface-enhanced Raman scattering (SERS) and fluorescence seesaw nanosensor for probing CTSB activity in breast cancer cells. The nanosensor, termed Au-pep-TAMRA, was fabricated by conjugating carboxytetramethylrhodamine (TAMRA)-labeled peptide substrates (pep-TAMRA) to gold nanoparticles (Au NPs). The peptide substrates served dual functions: (1) as recognition units specifically cleavable by CTSB and (2) as linkers bridging the plasmonic Au NPs and TAMRA signal molecules. Upon CTSB-mediated proteolytic cleavage, the altered distance between Au NPs and TAMRA generated inversely correlated signal changes in the SERS (reduction) and fluorescence (recovery) channels. This dual-mode nanosensor exhibited an expanded detection range of 5-200 ng/mL (compared to the single-mode detection) while achieving a low limit of detection of 1.16 ng/mL. Cell experiment validated the nanosensor's capacity to precisely determine CTSB activity in MDA-MB-231 cell lysates. The SERS-fluorescence switchable nanosensor demonstrates potential for advancing accurate diagnosis and personalized therapeutic strategies for breast cancer in clinical settings.

Understanding how lipid bilayers respond to pressure is essential for interpreting the coupling between membrane proteins and their native environments. Here, we use all-atom molecular dynamics to examine the pressure-temperature behavior of model membranes composed of dimyristoylphosphatidylcholine (DMPC) or its cis-unsaturated analogue Δ9-cis-PC. Within the studied range (288-308 K, 1-2000 bar), DMPC undergoes a liquid-gel transition, while Δ9-cis-PC remains fluid due to unsaturation. The CHARMM36 force field reproduces experimental boundaries with high fidelity: simulated DMPC transitions fall within 5-10 K and 100-300 bar of experimental values, and Δ9-cis-PC exhibits no transition. Hysteresis is modest but most pronounced when starting from low-temperature gels; we propose a split-phase simulation protocol that alleviates the hysteresis problem. We identify the area per lipid, bilayer thickness, and acyl-chain gauche fractions as sensitive phase markers; among these, the gauche fraction provides the most robust signature. Simulations indicate that an interdigitated gel is the equilibrium structure under finite-size conditions, and we propose a novel metric to quantify the extent of this phenomenon. However, at low temperature and high pressure, interdigitation decreases, consistent with the experimental lamellar gel phase. This long-lived interdigitation critically impacts standard order parameters, specifically, area per lipid and membrane thickness. Finally, we discuss in detail how finite-size effects influence phase transition and interdigitation. Overall, these results underscore the accuracy of modern force fields and highlight how simulations are essential to mechanistically complement experimental studies of pressure-sensitive membranes.

This study prepared a composite hydrogel using polyethylene glycol diacrylate (PEGDA) and 2-acrylamido-2-methylpropanesulfonic acid (AMPS) as raw materials, aiming to investigate the relationship between its hydration lubrication mechanism and friction behavior. By adjusting the mass fractions of PEGDA and AMPS, the hydrogel's mechanical properties were matched to those of articular cartilage, achieving a compressive modulus of 3.63 MPa. Friction tests revealed that the hydrogel exhibited a low coefficient of friction, consistently maintained within the range of 0.01-0.03 under various frequencies and load conditions, while demonstrating excellent lubrication stability throughout 7200 cycles of testing. Wetting and swelling tests demonstrate that AMPS effectively enhances the hydrogel's hydrophilicity while suppressing swelling, simultaneously increasing the bound water content within the system. Molecular dynamics simulations validate the excellent compatibility between PEGDA and AMPS. Constrained shear simulations reveal the hydrated lubrication layer's crucial role in mitigating shear stress, dispersing heat dissipation, and maintaining lubrication stability.

RNA plays a crucial role in gene expression, regulation, protein synthesis, and other cellular functions. The diversity that exists between different RNAs makes information beyond their expression level necessary for understanding more about their complex functions in a cell. Conventional ensemble approaches to RNA quantification have been used extensively to measure the quantity of RNA but lack cellular-level spatial information. This review highlights important contributions that high resolution microscopy has made to RNA quantification and cellular biophysics. Using advanced microscopy for precise localization, real-time tracking, and quantitative measurements of RNA increases our understanding of different disease states, cell- and tissue-specific gene regulation, and cellular architecture.

Gap junction channels, formed by the docking of two hemichannels from adjacent cells, are essential for intercellular communication. Connexin-43 (Cx43), the most widely expressed connexin, is critically involved in numerous physiological processes. Phosphorylation of Cx43 is a key regulatory mechanism that influences all aspects of its function, including trafficking, channel gating, and permeability. Here, we report a full-length computational model of the dodecameric Cx43 gap junction channel in double bilayers, including its intracellular loops and cytoplasmic regulatory C-terminal domains (CTDs). Furthermore, we performed all-atom molecular dynamics simulations of four systems representing different phosphorylation states. Our results demonstrate that increased phosphorylation of serine residues in the CTD induces more extended and flexible CTD conformations with greater solvent exposure, meanwhile narrowing the channel pore. Distinct gating states are closely associated with hydrophobic interactions between the N-terminal helices (NTHs) and transmembrane domain 2 (TM2). Unfolding of the NTHs disrupts the interactions, leading to pore distortion and a transition from the initial closed state to a more open conformation. These findings provide novel insights into the structural dynamics and regulatory mechanisms of the Cx43 gap junction channels.

Studying physical mechanisms and common geometric principles underlying known spherical packings is crucial for the rational design of synthetic nanocontainers. Here we model the growth of small spherical shells containing n ≤ 72 identical particles that have their own curvature and interact with each other via the Lennard-Jones potential. The shell assembly is assumed to be nonequilibrium and sequential: at each step, a new particle is attached to the most energetically favorable position, after which the system relaxes. Along with well-known structures of the smallest icosahedral viral protein shells, the proposed mechanism generates a wide range of shells exhibiting square-triangular surface order. Most of such shells are the models of synthetic or natural protein complexes that have octahedral or tetrahedral symmetries and perform various functions. We compare the obtained structures with those resulting from the equilibrium assembly and corresponding to global energy minima. Also, we consider the temperature-dependent stochastic assembly and use the double-minimum Lennard-Jones-Gauss potential to mimic anisotropic particle interactions.

Classical density functional theory (cDFT) has been established as an efficient and robust framework for predicting adsorption isotherms. Moreover, the mathematical form of cDFT─an optimization instead of the more widely used molecular simulations─opens up additional opportunities based on calculating noise-free derivatives of interfacial properties. One of these opportunities is the rapid, consistent calculation of thermodynamic properties, such as the enthalpy of adsorption. This work showcases cDFT as a thermodynamically fully consistent model for fluids that describes all homogeneous and adsorbed phases with a single model, providing access to phase equilibria, density profiles, enthalpies, and more. Because the enthalpy of adsorption of a mixture is difficult to measure experimentally and is rarely discussed in modeling approaches, we first revisit its definition from an energy balance perspective and in the context of the Clausius-Clapeyron relation, independent of specific model assumptions. We follow this up by deriving expressions for the enthalpy of adsorption suitable for cDFT. The resulting framework is demonstrated using the PC-SAFT Helmholtz energy model for the adsorption of real gases in a model slit pore for a pure fluid, a binary mixture, and a multicomponent system.

Accurate prediction of peptide self-assembly remains challenging due to the strong dependence of coarse-grained molecular dynamics (CGMD) simulations on parameter settings. Here, we establish a systematic computational-experimental framework for evaluating and optimizing Martini-based simulations of dipeptide self-assembly. Using 40 chemically diverse dipeptides, we quantitatively analyzed the effects of simulation time, peptide concentration, system size, backbone bead type assignment (H/E/C in martinize), and terminal charges on aggregation propensity (AP). We found that secondary structure and terminal charge are critical determinants of aggregation behavior by altering coarse-grained particle types and Lennard-Jones interactions, while their influence diminishes with increasing peptide length. Experimental validation by transmission electron microscopy confirmed that simulations with uncharged termini and β-sheet secondary structure assignment, which specifies the corresponding backbone bead types in the coarse-grained model, achieved the highest predictive accuracy. Applying these optimized parameters, we performed a comprehensive screening of all dipeptides and identified multiple new self-assembling candidates. This work provides mechanistic insight into parameter-dependent variability in Martini simulations and offers practical guidelines for reliable modeling of short-peptide self-assembly.

Gold nanoparticles are proving to be highly successful for delivering drugs to specific targets, exploiting carefully designed functionalizations. This work creates and optimizes the synthesis of gold nanorods (AuNRs), subsequently functionalized with a peptide, TAT, appropriately modified to allow attachment to the rods and guide their entry into the cell nucleus and nuclear growth. Various chemical and physical characterizations were performed to verify and optimize the AuNRs-TAT system. DLS, Z-potential, UV-vis, and FT-IR spectroscopies confirmed the nanosize, monodispersity, colloidal stability, and successful functionalization. Furthermore, structural characterizations conducted using synchrotron radiation were crucial for understanding the actual interaction between the gold surface and the modified TAT peptide. The study highlighted how this material is indeed a good drug delivery system, stable over time, and promising for reaching the cell nucleus.

Electrolyte solutions at high concentration are indispensable and yet poorly understood. In particular, the extent of speciation─the formation of complexes composed of multiple species─in concentrated ionic solutions is very challenging to obtain theoretically and experimentally, but can have a strong effect on solution properties. The literature is rife with contradictory estimates of speciation from experiments. We find that speciation affects transport properties and is therefore a prerequisite to accurately model concentrated solutions. We turn this to our advantage by showing that the viscosity can be used to determine the extent of complexation in concentrated aqueous solutions. Results of simulations as well as experimental measurements are presented. The atomistic Madrid-2019 force field is extended to model FeCl₂. Solutions of FeCl₂ and MgCl₂ are compared, and the observed difference in viscosity is explained by more complexation in the former, a conclusion supported by recently reported X-ray absorption and neutron scattering experiments.