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Multidimensional Protein Corona Analysis Toward Predictive Nano-Bio Interface Design.

Nanoparticles entering biological fluids are rapidly coated by proteins and other biomolecules, converting their synthetic surfaces into biologically active nano-bio interfaces. These coronas regulate colloidal stability, immune recognition, cellular uptake, biodistribution, pharmacokinetics, cargo delivery, and toxicity. Yet a protein list obtained by mass spectrometry captures only part of this interface. Corona identity and function are also shaped by protein organization, binding stability, exchange dynamics, conformational changes, and molecular accessibility. Here, we discuss recent progress in protein corona isolation and analysis from a question-oriented analytical perspective, with emphasis on how centrifugation, magnetic recovery, affinity- or chemistry-enabled capture, chromatography, filtration, and field-flow fractionation (FFF) influence the fidelity, integrity, and comparability of recovered coronas. We then examine how proteomic profiling can be integrated with binding measurements, interfacial structural analysis and functional validation to distinguish descriptive corona signatures from biologically meaningful mechanisms. We further consider how biofluid composition, disease state, tissue interfaces and cellular environments remodel corona identity, presentation, and bioactivity. Finally, we argue that standardized reporting, computational modeling, and AI-enabled approaches are essential for converting protein corona datasets into reproducible and predictive knowledge that can guide the design of drug delivery systems and precision nanomedicines.

Protein Corona

Interfacial structure and lipase action. Characterization of taurodeoxycholate-didecanoylglycerol monolayers by physical and kinetic methods.

Surface pressure-area isotherms for 1,3-didecanoyl-glycerol (dicaprin) were determined as a function of the concentration of taurodeoxycholate in the subphase. Analysis of these curves indicates that, from 0.05 to 0.80 mM bile salt, surface structure is dependent only on the surface concentration of the diglyceride. The limiting areas for dicaprin in the presence and absence of bile salt were about 38 A2/molecule. Subjecting the monolayers to hydrolysis by pancreatic lipase yielded kinetic data which, together with the physical studies, support a model for monolayer glyceride molecules undergoing discrete changes of state. In the absence of bile salt, the relatively expanded state exhibits an area of 75 A2/diglyceride molecule and is not a substrate for pancreatic lipase B. The more condensed state exhibits an area of 38 A2/diglyceride molecule and is hydrolyzed at a rate proportional to its concentration in the monolayer. Taurodeoxybholate at 0.05 to 0.60 mM shifts the apparent area of the expanded state to 360 A2/diglyceride molecule.

Animals

The interaction of macromolecular solutions with macromolecular monolayers adsorbed on a hydrophobic surface.

In order to elucidate the general patterns of intermacromolecular surface interactions that may be involved in hemocompatibility phenomena, monolayers of representative macromolecules on an octadecylsilylated glass surface were exposed to solutions of other macromolecules, and the changes in interfacial composition were characterized by zeta potential-pH titration curves, as measured by alternating flow streaming current analysis and, in some cases, by radiotracer labeling. Experiments with poly(vinylpyrrolidone) (PVP), a blood-compatible linear polymer; bovine serum albumin (BSA), a representative serum protein; whole human serum (HS), a complex mixture of proteins; and erythrocyte surface glycoprotein (GP), an extended-chain macromolecular amphiphile, showed the following: 1) Penetration of the original monolayer occurred within 24 hr in 9 of the 12 possible cases; it did not occur for BSA or HS monolayers exposed to PVP, and probably not for PVP exposed to GP. 2) In all cases, penetration was accompanied by no more than partial displacement of the original monolayer, thereby generating a mixed monolayer. Each of the six possible binary mixed monolayers could be obtained by at least one of the two possible mixing sequences. 3) In the three binary systems containing BSA, the formation of the mixed monolayer could be related to increased adsorption in the two-component system. 4) The two components of the mixed monolayers were not equally distributed across their thicknesses: thus, the outer surfaces of the PVP-BSA and (at neutral pH) the PVP-HS mixed monolayers contained only PVP; that of the BSA-HS mixtures only HS. In the PVP-HS, and probably the GP-BSA and GP-HS mixed monolayers, the composition of the outer surface appeared pH-dependent. The resultant zeta potential versus pH profiles in the latter two cases resembled those of intact blood cells. The results suggest that neither the compact monolayers of globular proteins nor the diffuse monolayers of randomly coiled water-soluble polymers can, by their prior adsorption on a synthetic surface, prevent the subsequent adsorption of other globular macromolecules. It is possible that the randomly coiled polymers may impede the adhesion of platelets to the substrate since the results indicate that the adsorption of such polymers causes a displacement of the shear plane.

Adsorption

The effect of cholesterol on the viscosity of protein-lipid monolayers.

The addition of cholesterol to a layer of lipids in a membrane structure is generally believed to result in an increase in the viscosity of the layer. We have shown that cholesterol and two other monolayer-forming lipids markedly decrease the viscosity of a serum albumin monolayer at the decane-water interface, a model membrane system. However, when the protein monolayer already has a surface active lipid component present, the effect of added cholesterol depends upon the other substance. When the albumin monolayer contains tristearin, added cholesterol increases the viscosity. When the lipid is octadecanol, cholesterol decreases the viscosity. The dependence of the change in interfacial viscosity due to cholesterol upon the original composition of the interfacial layer may be useful for characterizing the composition of layers of unknown composition, e.g. some natural membranes.

Cholesterol

Temperature dependence of the interfacial behavior of uracil derivatives.

The effect of temperature on the interfacial behavior of uracil, thymine and 1,5-dimethyluracil has been used to characterize the thermodynamics of adsorption of these compounds at a mercury electrode-aqueous electrolyte interface. Between 4.5 degrees C and 40 degrees C all three compounds exhibit two adsorption regions. The first, a dilute layer where the molecules adsorb in a flat orientation on the electrode surface. The second, a compact layer where the molecules adsorb in a perpendicular orientation. The thermodynamic constants characterizing formation of these surface layers have been deduced.

Adsorption

Application of enantiomeric 2-sn-phosphatidylcholines in interfacial enzyme kinetics of lipolysis.

Two enantiomeric 2-sn-phosphatidylcholines containing hexanoyl and dodecanoyl acyl chains have been synthesized, enabling the study of the action of phospholipase A2 (EC 3.1.1.4) at lipid-water interfaces characterized by identical physico-chemical properties. Monolayer kinetics and bulk kinetics in the presence of Triton X-100 micelles were studied but the interpretation of the results is impeded by the fact that interfacial saturation conditions cannot be reached. In contrast, the use of the substrate analog n-tetradecylphosphorylcholine allows the determination of the interfacial kinetic parameters kcat and K*m. Dodecanoic acid is released from the most susceptible isomer about 13 times more rapidly than hexanoic acid from the stereoisomer in spite of the higher K*m of the former. The results are discussed in terms of the particular active site architecture and the possible influence of the "quality of the interface" on the kinetic parameters.

Binding Sites

Identification and characterization of a wet adhesive protein extracted from Dreissena bugensis, the freshwater quagga mussel.

Mechanisms of wet adhesion have evolved in several aquatic organisms over millions of years. Yet, the repertoire of synthetic biocompatible wet adhesive materials is still limited. The byssus is a well-studied proteinaceous bioadhesive structure utilized by several bivalves to support sessile lifestyles in turbulent conditions. The quagga mussel (Dreissena bugensis) is a freshwater byssate and a notorious invasive species in the Great Lakes region. To identify adhesive proteins in the quagga mussel byssus, we utilized quantitative proteomics and found several proteins enriched at the byssus-substrate interface. Among the identified proteins was the Dbfp7 protein family. Dbfp7 is a small, polymorphic, and mostly disordered protein that lacks significant amounts of 3,4-dihydroxyphenylalanine (DOPA), a modified amino acid found in several marine mussel byssal proteins. Atomic force microscopy nanomechanical mapping of Dbfp7 films demonstrates that this protein exhibits adhesive ability in aqueous conditions. While DOPA is critical for marine mussel adhesion, interfacial electrochemistry of freshwater adhesive plaques suggests that freshwater byssates circumvent catechol-based adhesion. The functional characterization of Dbfp7 as a freshwater mussel adhesive protein advances the understanding of fundamental requirements for biocompatible wet adhesion, a crucial step for the development of bioinspired wet adhesive materials, such as improved medical adhesives.

Animals

Membrane fluidity gradient model of cell transport.

A new model of cellular transport is presented, characterized by selective fluxes due to membrane fluidity gradient. This mechanism is treated in terms of the interfacial tensions at the membrane/cytoplasm and membrane/medium surfaces. A higher interior fluidity (lower interfacial tension) is maintained by cytoplasm adenosine triphosphate, which adsorbs and increases lipoprotein fluidity while it also chelates calcium and keeps it from inner membrane sites. The high medium calcium causes a stiffer membrane (higher interfacial tension) on the medium side. These two different free energy barriers at inner and outer channel mouths filter all molecules, whether ionized or nonelectrolytic. Molecules with excess of hydrophobic groups, which makes negative the free energy of transfer from the medium into the membrane, have highest influx. Intermolecular salt linkages and hydrogen-bonding are vital in making negative the free energy of transfer of amino acids and sugars. The much lower energy barrier at the cytoplasmic interface favors net efflux from the cell of the more polar ions and amphipaths. Intramembrane particles are proposed as the channel sites.

Adenosine Triphosphate

Effects of polymer surface molecular structure and force-field characteristics on blood interfacial phenomena.

To quantify the effects of major surface structural factors influencing interfacial reactions induced by polymers in native blood, model surfaces of solvent-cast films of two analogous poly(ether urethanes) and three homologous polyamides (nylon 4, 6/6, and 12) were exposed ex vivo to canine blood under the well-defined hemodynamic conditions of the Stagnation Point Flow Experiment. The selected surfaces allow for incremental changes in properties and were characterized by their "Composite Surface Free ENergy Function," gamma'S, which describes the surface force field as the sum of the mean dispersion (gammaSd) and polar (gammaSp) contributions and is computed from wettability spectra obtained with ultrapure diagnostic liquids. Blood interfacial effects were measured by the shear-limited diameter of the white cell circle formed around the stagnation point, the flow parameter at which symmetric aggregation occurred, and the surface-number density of platelets, [P s], remaining adherent under fixed conditions. At identical flows, within each group of polymers, both the WBC-circle diameter and [P s] scale with gamma Sp/gamma'S, implying that 1) only the magnitude but not the interaction mechanism varies as a function of incremental structural and surface changes, 2) the primary determinant of surface-induced effects is the polar force contribution, and 3) the magnitude of gamma'S is secondary if gammaSd/gamma'S is sufficiently great.

Adsorption

Retrieval analyses of a blade implant after 231 months of clinical function.

A blade implant that was retrieved in 1990 after 231 months of clinical function (since 1971) was analyzed with respect to clinical, histological, and biomechanical characteristics. The implant clinical records demonstrated no abnormalities or pathological lesions over the tenure of treatment. The bone to implant interface showed a mixture of interfacial tissue components and conditions with adequate direct bone contact (46.4 to 82.3 percent) for classification as osseointegrated. The abutment fracture leading to removal was characterized as a cyclic fatigue mechanism and the distribution of tissue components along the interface could not be correlated with specific biomechanical loading directions. This report considers the clinical and biomechanical records as they relate to the detailed histological investigation.

Blade Implantation

Hydroxypropyl cellulose/poly(ethylene glycol)-co-poly(propylene glycol) aqueous two-phase systems: system characterization and partition of cells and proteins.

Novel aqueous polymeric two-phase systems are described. These systems are formed by mixing hydroxypropyl cellulose (molecular mass 100,000, trade name Klucel L) with poly(ethylene glycol)-co-poly(propylene glycol) copolymer [molecular mass 6,500, poly(propylene glycol) content 50% w/w, trade name Pluronic P105], in a saline buffer. The phase diagram was measured and the interfacial tensions, phase separation times, and lower phase viscosities of three phase systems having constant Pluronic P105 concentration but varying in Klucel L concentration were determined. The partition behavior of a representative cell, bacterium, and protein and the affinity ligand-mediated alteration in the partition behavior of a protein from a yeast extract protein mixture were also characterized. The results suggest that Klucel L/Pluronic P105 phase systems may be cost-effective substitutes for, or complements to, existing aqueous polymeric phase systems. The physical characterization and representative partition data reported here should facilitate application of these new systems.

Cell Separation

Interfacial conformation of dipalmitoylglycerol and dipalmitoylphosphatidylcholine in phospholipid bilayers.

Diacylglycerols are minor constituents of membrane lipids, yet are essential in the activation and membrane association of protein kinase C. Solid-state 13C NMR experiments have been used to characterize the orientation of the glycerol backbone of dipalmitoylglycerol (DPG) and dipalmitoylphosphatidylcholine (DPPC) in egg phosphatidylcholine (PC) bilayers. The 13C NMR spectra of both DPG and DPPC specifically 13C-labeled at the sn-2 chain carbonyl exhibit a single narrow resonance (approximately 2 ppm) in liquid-crystalline egg PC bilayers. In contrast, specific 13C-labeling of both the sn-1 and sn-2 chain carbonyls results in an additional broad component (24-32 ppm) with an axially symmetric line shape. These data reveal that DPG has a distinct motionally-averaged structure in PC bilayers that is similar to that of DPPC and is not significantly affected by the absence of the large polar PC headgroup. The NMR line shapes are roughly consistent with the results of previous FTIR and NMR studies that indicate the sn-1 chain extends from the C1 carbon of the glycerol backbone into the hydrophobic interior of the bilayer, while the sn-2 chain first extends parallel to the bilayer surface and incorporates a bend at the ester linkage in order to keep the sn-1 and sn-2 chains parallel. However, the data suggest that the time-averaged orientation of the glycerol backbone is tilted from the bilayer normal, in contrast to the nearly parallel orientation observed in the crystal structures of phosphatidylcholines and phosphatidylethanolamines or the perpendicular orientation observed in the crystal structures of diacylglycerols.

1,2-Dipalmitoylphosphatidylcholine

The characterization of intima development in left ventricular assist device (LVAD) and total artificial heart (TAH).

1. The study of PNI development provides useful information in the design and improvement of the prosthetic devices. 2. Improved gelatin aldehyde impregnation on the dacron covered diaphragm of cardiac prostheses resulted in a reduced PNI thickness and minimized interfacial degeneration of PNI. 3. The PNI on the diaphragm's surface started with a platelet rich interface and ended with a striated fibrin and platelet matrix at the blood interface. 4. The PNI in the TAH's had a higher involvement of polymorphonuclear leukocytic cells at the PNI-housing or diaphragm interface than the LVAD's. 5. The aldehyde treated pericardial surface of cardiac prostheses generated a thin PNI that was fibrin-rich, a viable cell infiltration, no interfacial degeneration, and endothelial-like cells on its surface.

Aldehydes

Formation of a new stable phase of phosphatidylglycerols.

Dilauroyl and dimyristoylphosphatidylglycerol (DMPG) form a more stable gel state when aqueous suspensions are incubated several days at low temperature (0-2 degrees C), pH 7.4 with 0.15 M NaCl. This gel state is characterized by a higher transition temperature and a higher transition enthalpy. The geometry of this gel state is distinguishable from the metastable gel state that forms rapidly upon hydration on the basis of its x-ray diffraction pattern. Infrared spectra in the CH2 scissoring region indicate that the stable gel phase of DMPG is also characterized by reduced reorientational fluctuations of acyl chains and increased interchain interactions. Analysis of vibrational bands due to ester carbonyl groups of DMPG suggests that the transition to a new gel phase is initiated by changes in the interfacial and/or headgroup region of the bilayer, most likely via formation of interlipid hydrogen bonds. The melting of the stable gel phase of DMPG is accompanied by a gross morphological change resulting in vesiculation.

Calorimetry, Differential Scanning

Analysis of polarization dynamics by singularity decomposition method.

The driving point immittance (impedance or admittance) function is commonly used in electrical characterization of polarized materials and interfaces. The immittance function typically attenuates following a power function dependence on frequency. This fact has been recognized as a macroscopic dynamical property manifested by strongly interacting dielectric, viscoelastic and magnetic materials and interfaces between different conducting substances. Linear interfacial polarization processes which occur at metal electrode-electrolyte interfaces have been represented by the Fractional Power Pole [FPP] function in single or multiple stages. The FPP function is referred to as the Davidson-Cole function in the dielectrics literature. A related function widely used in mathematical modeling of dielectric and viscoelastic polarization dynamics is the Cole-Cole function. The fractional power factor which parametrizes the FPP or the Davidson-Cole function has been shown earlier to equal the logarithmic ratio of the locations of the pole-zero singularities. In this paper we first review a modified form of the singularity decomposition of the FPP function accomplished within a prescribed error range. The distribution spectrum and the corresponding simulation by a cascade R-C network, as opposed to the synthesis by a ladder R-C network, are readily obtained as the next step in the simulation. The method is then applied to decompose the Cole-Cole function; the pole-zero placement of the singularity function is determined and the equivalent cascade R-C network is synthesized.

Electric Conductivity

The mechanism of the solute-induced chain interdigitation in phosphatidylcholine vesicles and characterization of the isothermal phase transitions by means of dynamic light scattering.

A new method is introduced for the detection of chain interdigitation in phospholipid bilayers. The same method is used to measure the hydrocarbon tilt in the dipalmitoylphosphatidylcholine membranes as a function of the bulk concentration of the interdigitation-inducing solutes, such as ethanol. The hydrocarbon tilt in the phosphatidylcholine bilayers is demonstrated to be limited to angles below approx. 51 degrees. The need for higher tilt values leads to bilayer interdigitation. Solute-induced chain interdigitation is shown to be a cooperative process provoked by the excessively large lateral repulsion in the interfacial region and the concomitant excessive chain tilt. Ethanol-induced phosphatidylcholine interdigitation, for example, proceeds via interdigitated domains formation and finally gives rise to the bilayers with fully intercalated chains tilted by at least 30 degrees (and sometimes as much as 50 degrees) with respect to the membrane normal.

Ethanol

Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins.

Shell matrix proteins (SMPs) are key organic components of molluscan biominerals, yet previous nacre proteomics have remained largely qualitative, limiting evaluation of the abundance and fraction association of individual SMPs. Here, we established a quantitative proteomic approach for the nacreous layer of the pearl oyster Pinctada fucata by integrating optimized shell preservation, stepwise fractionation, and data-independent acquisition (DIA) proteomics. SMPs were separated into an ethylenediaminetetraacetic acid (EDTA)-soluble matrix (ESM), an EDTA-insoluble but sodium dodecyl sulfate/dithiothreitol (SDS/DTT)-soluble matrix (SSM), and an SDS/DTT-insoluble matrix (ISM). DIA outperformed data-dependent acquisition in proteome coverage and enabled quantification of 327 SMPs across a broad dynamic range. Fraction-resolved abundance profiling showed that each fraction was characterized by distinct SMP compositions. To summarize these distributions, we introduced a solubility-based type classification that grouped SMPs into four types according to their quantitative partitioning among fractions. Well-known SMPs, including nacrein, Pif 80, and MSI60, were assigned to intuitively consistent types, whereas proteases, protease inhibitors, and tyrosinases also showed biased type distributions. These results support a three-compartment model of the nacreous layer consisting of (i) an insoluble interlamellar membrane core, (ii) a relatively extractable interfacial layer, and (iii) a soluble matrix fraction enriched in proteins potentially involved in ionic regulation and protein maturation. This study provides a quantitative framework for understanding coordinated SMP functions during nacre formation and for comparative analyses of molluscan shell proteomes.

Animals

Operando X-ray Spectroscopy Unveils Light-Driven Redox Selectivity for Photo-Assisted Li-S Batteries.

Photo-assisted lithium-sulfur batteries (PALSBs) can accelerate the sluggish redox kinetics of sulfur cathodes. However, the introduced light field inevitably complicates interfacial reactions, necessitating in situ evidence under realistic operating conditions. Here, we construct a TiO2/FePS3 (TF) p-n junction bifunctional photoelectrode and employ a multiphysics-coupled in situ x-ray spectroscopic technique to elucidate light-regulated catalysis from the interface into the bulk. Operando low-energy XPS identifies potential interfacial catalytic sites. High-energy operando XAFS is, for the first time, applied in PALSBs to track the K-edge position of catalytic centers throughout cycling. The results show that the reversible dynamic valence evolution synchronizes with the stepwise sulfur redox process, revealing that photogenerated carriers and electrocatalytic electrons act cooperatively to promote polysulfide conversion. DFT calculations corroborate, from thermodynamic and kinetic perspectives, that illumination strengthens polysulfide anchoring and lowers the energy barriers of key conversion steps, consistent with the operando spectroscopic observations. Benefiting from this photoelectrochemical co-regulation, the TF-based PALSB maintains excellent reversible capacity and cycling stability under high sulfur loading and low electrolyte content. This work establishes a characterization paradigm for the rational design of high-performance photo-assisted Li-S cathodes.

operando x‐ray spectroscopy