Differences in protein distribution, conformation, and dynamics in hard and soft coronas: dependence on protein and particle electrostatics

Molecular Dynamics Simulations of Protein Corona Formation on Membrane Surfaces: Effects of Lipid Composition and PEGylation on Selective Plasma Protein Adsorption

The adsorption of plasma proteins (human serum albumin (SA) and apolipoproteins A-I and E-III) onto various lipid bilayers is simulated. With three different binding orientations for each protein, free energy calculations from umbrella sampling simulations show stronger binding of SA to the bilayer composed of lipids with smaller headgroups and stronger binding of apolipoproteins to the bilayer composed of anionic lipids rather than cationic or zwitterionic lipids, in agreement with experiments. Anionic residues of SA form hydrogen bonds more readily with amine headgroups of lipids than with larger trimethylammonium headgroups, where the cationic nitrogen is sterically hindered. In contrast, cationic residues of apolipoproteins form hydrogen bonds predominantly with anionic phosphate groups of lipids, indicating that protein-bilayer binding is attributed to hydrogen bonds facilitated by electrostatic attraction, depending on the electrostatics and size of lipid headgroups. For lipid bilayers grafted with polyethylene glycol (PEG), the binding strength of SA decreases while that of apolipoproteins increases, consistent with experiments, due to hydrogen bonding and hydrophobic interactions between proteins and PEG. These findings help explain experimental observations regarding the abundance of specific plasma proteins adsorbed onto various liposomes and suggest manipulating lipid composition and PEGylation to attract specific proteins to liposome-based drug carriers.

Effect of PEGylation on the Adsorption and Binding Strength of Plasma Proteins to Nanoparticle Surfaces

The adsorption of plasma proteins (human serum albumin, immunoglobulin γ-1, apolipoproteins A-I and E-III) onto polystyrene surfaces grafted with polyethylene glycol (PEG) at different grafting densities is simulated using an all-atom PEG model validated by comparing the conformations of isolated PEG chains with previous simulation and theoretical values. At high PEG density, the grafted PEG chains extend like brushes, while at low density, they significantly adsorb to the surface due to electrostatic attraction between polystyrene amines and PEG oxygens, forming a PEG layer much thinner than its Flory radius. Free energy calculations show that PEGylation can either increase or decrease the binding strength between proteins and surfaces, to an extent dependent on PEG density and specific proteins involved, in agreement with experiments. In particular, grafted PEG chains not only sterically block the binding between proteins and surfaces but also strongly interact with proteins via hydrogen bonds and electrostatic and hydrophobic interactions, with apolipoproteins exhibiting stronger hydrophobic interactions with PEG than other proteins, implying that these specific protein-PEG interactions help certain proteins remain on the PEGylated surface. These simulation findings help explain experimental observations regarding the abundance of specific plasma proteins adsorbed onto nanoparticles grafted with PEG at different densities.

Hydrodynamics and Aggregation of Nanoparticles with Protein Corona: Effects of Protein Concentration and Ionic Strength

Multiple 10 nm-sized anionic nanoparticles complexed with plasma proteins (human serum albumin (SA) or immunoglobulin gamma-1 (IgG)) at different ratios are simulated using all-atom and coarse-grained models. Coarse-grained simulations show much larger hydrodynamic radii of individual particles at a low protein concentration (a protein-to-particle ratio of 1) than at high protein concentrations or without proteins, indicating particle aggregation only at such a low protein concentration, in agreement with experiments. This particle aggregation is attributed to both electrostatic and hydrophobic particle-protein interactions, to an extent dependent on different proteins. In all-atom simulations, IgG proteins induce particle aggregation with and without salt, while SA proteins promote particle aggregation only in the presence of salt that can weaken the electrostatic repulsion between anionic particles closely linked via SA that is smaller than IgG, which also agree well with experiments. Besides charge interactions, hydrophobic interactions between particles and proteins are also important especially at the high salt concentration, leading to the increased particle-protein contact area. These findings help explain experimental observations regarding that the effects of protein concentration and ionic strength on particle aggregation depend on different plasma proteins, which are interpreted by binding free energies, electrostatic, and hydrophobic interactions between particles and proteins.

Recent Advances in Simulation Studies on the Protein Corona

When flowing through the blood stream, drug carriers such as nanoparticles encounter hundreds of plasma proteins, forming a protein layer on the nanoparticle surface, known as the "protein corona". Since the protein corona influences the size, shape, and surface properties of nanoparticles, it can modulate their circulating lifetime, cytotoxicity, and targeting efficiency. Therefore, understanding the mechanism of protein corona formation at the atomic scale is crucial, which has become possible due to advances in computer power and simulation methodologies. This review covers the following topics: (1) the structure, dynamics, and composition of protein corona on nanoparticles; (2) the effects of protein concentration and ionic strength on protein corona formation; (3) the effects of particle size, morphology, and surface properties on corona formation; (4) the interactions among lipids, membranes, and nanoparticles with the protein corona. For each topic, mesoscale, coarse-grained, and all-atom molecular dynamics simulations since 2020 are discussed. These simulations not only successfully reproduce experimental observations but also provide physical insights into the protein corona formation. In particular, these simulation findings can be applied to manipulate the formation of a protein corona that can target specific cells, aiding in the rational design of nanomedicines for drug delivery applications.

Diverse Role of Buffer Mediums and Protein Concentrations to Mediate the Multimodal Interaction of Phenylalanine-Functionalized Gold Nanoparticle and Lysozyme Protein at Same Nominal pH

Recently, buffer molecules have been known to affect intermolecular protein-protein interactions at physiological pH. However, the roles of buffer molecules and different monolayer protein concentrations remain elusive in controlling the interaction of gold nanoparticles (Au NPs) with protein molecules. Herein, for the first time taking phenylalanine functionalized gold nanoparticles (Au-Phe NPs) and lysozyme (Lyz) protein as model systems, we report that buffer molecules of different charges (at a particular pH) play diverse roles in protein-Au NPs interaction, particularly in protein induced Au NPs aggregation. Among different buffers, negatively charged buffer (citrate and phosphate) induces aggregation of both Au-Phe NPs and Lyz protein, whereas zwitterionic and positive buffer (HEPES, MOPS, and Tris) only cause the Au NPs aggregation. Taking the diverse role of buffer into account, we propose multimodal models for stability and protein induced aggregation mechanism of NPs at different monolayer (sub-, near-, and excess) concentrations of Lyz in different medium.

Impact of Protein Coronas on Lipid Nanoparticle Uptake and Endocytic Pathways in Cells

Lipid nanoparticles (LNPs), widely used in disease diagnosis and drug delivery, face the challenge of being surrounded by biological macromolecules such as proteins upon entering the human body. These molecules compete for binding sites on the nanoparticle surfaces, forming a protein corona. The impact of different types of protein coronas on LNP delivery remains unclear. In this study, we employed a newly developed, highly sensitive LNP labeling platform and analyzed the endocytosis of HeLa cells under different nutritional conditions using proteomics to address this critical issue. Our research found that under conditions of complete medium and amino acid starvation, most DNA-FITC vesicles in HeLa cells were located in the perinuclear region 4 h after transfection. In contrast, under serum starvation conditions, only a small portion of DNA-FITC vesicles were in the perinuclear region. On the other hand, through proteomics, we discovered that cells that were enriched in amino acids and complete medium contained more proteins, whereas those under serum starvation had relatively fewer enriched proteins. Through KEGG pathway enrichment analysis, we identified the phagosome and endocytosis pathways as particularly important. Lastly, differential analysis of proteins in these pathways revealed that proteins such as F-actin, Coronin, vATPase, TUBA, TUBB, MHCII, and TSP may have significant impacts on cellular endocytosis. Our research findings indicate that it is necessary to regulate cellular endocytosis based on different protein coronas to achieve optimal cytoplasmic release.

Separation of protein corona from nanoparticles under intracellular acidic conditions: effect of protonation on nanoparticle-protein and protein-protein interactions

Protein coronas separate from nanoparticles under intracellular acidic conditions however, competitive adsorption of multiple proteins and their protein network formation under different pH conditions have not yet been systematically studied at the atomic scale. Herein, we report all-atom molecular dynamics simulations of plasma proteins (human serum albumin and immunoglobulin gamma-1 chain C) adsorbed to 10 nm-sized carboxyl-terminated polystyrene (PS) nanoparticles at different protonation states that mimic extracellular and intracellular pH conditions of 7, 6-5, and 4.5. Binding free energies are calculated from umbrella sampling simulations, showing the significantly weakened binding between PS particles and proteins at the protonation state at pH 4.5, in agreement with experiments showing the separation of protein corona from nanoparticles at pH 4.5. Mixtures of multiple proteins and PS particles are also simulated, showing much less protein adsorption and protein cluster formation at the protonation state at pH 4.5 than that at higher pH values, which are further confirmed by calculating the diffusivities and hydrodynamic radii of individual proteins. In particular, electrostatic particle-protein and protein-protein interactions are significantly weakened by a combination of particle and protein protonation rather than by particle protonation alone, to an extent dependent on different proteins. These findings help explain the experimental observations regarding separation of protein corona from nanoparticles under intracellular acidic conditions at pH 4.5 but not at higher pH, supporting that acidification cannot be the only reason for this separation during the process of endosome maturation.