An In Situ Investigation of the Protein Corona Formation Kinetics of Single Nanomedicine Carriers by Self-Regulated Electrochemiluminescence Microscopy

Protein coronas are present extensively at the bio-nano interface due to the natural adsorption of proteins onto nanomaterials in biological fluids. Aside from the robust property of nanoparticles, the dynamics of the protein corona shell largely define their chemical identity by altering interface properties. However, the soft coronas are normally complex and rapidly changing. To real-time monitor the entire formation, we report here a self-regulated electrochemiluminescence (ECL) microscopy based on the interaction of the Ru(bpy)₃³⁺ with the nanoparticle surface. Thus, the heterogeneity of the protein corona is in situ observed in single nanoparticle “cores” before and after loading drugs in nanomedicine carriers. The label-free, optical stable and dynamic ECL microscopy minimize misinterpretations caused by the variation of nanoparticle size and polydispersity. Accordingly, the synergetic actions of proteins and nanoparticles properties are uncovered by chemically engineered protein corona. After comparing the protein corona formation kinetics in different complex systems and different nanomedicine carriers, the universality and accuracy of this technique were well demonstrated via the protein corona formation kinetics curves regulated by competitive adsorption of Ru(bpy)₃³⁺ and multiple proteins on surface of various carriers. The work is of great significance for studying bio-nano interface in drug delivery and targeted cancer treatment.     

Extending the applicability of the O-ring theory to protein–DNA complexes

Many biological processes depend on protein-based interactions, which are governed by central regions with higher binding affinities, the hot-spots. The O-ring theory or the “Water Exclusion” hypothesis states that the more deeply buried central regions are surrounded by areas, the null-spots, whose role would be to shelter the hot-spots from the bulk solvent. Although this theory is well-established for protein–protein interfaces, its applicability to other protein interfaces remains unclear. Our goal was to verify its applicability to protein–DNA interfaces. We performed Molecular Dynamics simulations in explicit solvent of several protein–DNA complexes and measured a variety of solvent accessible surface area (SASA) features, as well as, radial distribution functions of hot-spots and null-spots. Our aim was to test the influence of water in their coordination sphere. Our results show that hot-spots tend to have fewer water molecules in their neighborhood when compared to null-spots, and higher values of ΔSASA, which confirms their occlusion from solvent. This study provides evidence in support of the O-ring theory with its applicability to a new type of protein-based interface: protein–DNA.     

Growth and aggregation of surfactant islands during the displacement of an adsorbed protein monolayer: a Brownian dynamics simulation study

We present Brownian dynamics simulations of the displacement of a protein monolayer by competitive adsorption. The protein film is modelled as a network of spherical bonded particles adsorbed at a fluid interface. Spherical displacer particles, which have a stronger affinity for the interface than the protein film particles, are introduced into the system through the sub-phase. At early stages, these particles diffuse to the interface and are adsorbed in the gaps in the network. Soon thereafter, however, further adsorption initiates displacement of the film particles, ultimately leading to the complete removal of the protein layer from the surface. We study the evolution of the number and size of the displacer islands formed at the interface. The introduction of a direct long-range repulsion between film and displacer particles is shown to lead to a phase-separation-type behaviour at intermediate time scales. Further comparisons with the displacement of a non-bonded monolayer are also presented.     

Modeling the interplay between geometrical and energetic effects in protein folding

A theoretical framework is constructed with the aid of a free-energy functional method that is capable of describing the interplay between geometrical and energetic effects on protein folding. In this paper, we generalize a free-energy functional model based on polymer theory to make it more appropriate for comparison with protein folding simulations and experiments. This generalization is made by introducing cooperativity into the configurational entropy and the internal energy. Modifications to configurational entropy enable the model to account for the loop-loop interactions, a contribution neglected in the original model. Modifications to the internal energy introduce many-body corrections, which are needed to establish quantitative contact to simulations as well as experimental observations. To demonstrate the efficiency of the modified analytical model, we compare our results with C(alpha) structure-based (Go) model simulations of chymotrypsin inhibitor II and the SH3 domain of src.     

Comparison of block-copolymer with soap in micelle formation

Simple equations for the micelle formation of block-copolymers are derived from the concept of Leibler-Orland-Wheeler. The size of micelle, core, and corona are expressed in terms of chain length of block-copolymers and homopolymers and the interaction parameters of the components based on the balance between the interface energy and the strain energy of the polymer chains. These equations are extended to the soap micelle by taking the electric repulsion of soap ions into consideration. Various data on the micelle size, the solubility, the critical micelle concentration, the critical solution temperature, and the salt effect can be explained quantitatively by the theory. The solubilization ability is also discussed.     

Protein‐Sized Bright Fluorogenic Nanoparticles Based on Cross‐Linked Calixarene Micelles with Cyanine Corona

The key challenge in the field of fluorescent nanoparticles (NPs) for biological applications is to achieve superior brightness for sizes equivalent to single proteins (3–7 nm). We propose a concept of shell‐cross‐linked fluorescent micelles, in which PEGylated cyanine 3 and 5 bis‐azides form a covalently attached corona on micelles of amphiphilic calixarene bearing four alkyne groups. The fluorescence quantum yield of the obtained monodisperse NPs, with a size of 7 nm, is a function of viscosity and reached up to 15 % in glycerol. In the on‐state they are circa 2‐fold brighter than quantum dots (QD‐585), which makes them the smallest PEGylated organic NPs of this high brightness. FRET between cyanine 3 and 5 cross‐linkers at the surface of NPs suggests their integrity in physiological media, organic solvents, and living cells, in which the NPs rapidly internalize, showing excellent imaging contrast. Calixarene micelles with a cyanine corona constitute a new platform for the development of protein‐sized ultrabright fluorescent NPs.     

Ion Flow Effects on Negative Direct Current Corona in Air

Numerical simulations are presented for the ion flow effects on the negative direct current corona in air. One dimensional equivalent steady corona model containing the continuity equations for electrons and ions on the basis of Townsend theory coupled with Poisson’s equation is applied. The conductor radius and the electric field intensity on conductor surface keep constant under the standard atmosphere condition in this paper. The results suggest that the space charges within the plasma region have no influence on the electric field distribution throughout the interelectrode gap, which is only governed by the ion flow. The influences of the gap distance and the corona current on the corona discharge within the plasma region have been investigated. If the voltage-current characteristics of the negative corona discharge are measured, the ion flow region and the plasma region can be investigated individually. Based on Kaptzov’s hypothesis, the plasma region can be investigated solely.     

Geometrical features of the protein folding mechanism are a robust property of the energy landscape: a detailed investigation of several reduced models

The concept of a funneled energy landscape and the principle of minimal frustration are the theoretical foundation justifying the applicability of structure-based models. In simulations, a protein is commonly reduced to a C(alpha)-bead representation. These simulations are sufficient to predict the geometrical features of the folding mechanism observed experimentally utilizing a concise formulation of the Hamiltonian with low computational costs. Toward a better understanding of the interplay between energetic and geometrical features in folding, the side chain is now explicitly included in the simulations. The simplest choice is the addition of C(beta)-beads at the center-of-mass position of the side chains. While one varies the energetic parameters of the model, the geometric aspects of the folding mechanism remain robust for a broad range of parameters. Energetic properties like folding barriers and protein stability are sensitive to the details of simulations. This robustness to geometry and sensitivity to energetic properties provide flexibility in choosing different parameters to represent changes in sequences, environments, stability or folding rate effects. Therefore, minimal frustration and the funnel concept guarantee that the geometrical features are robust properties of the folding landscape, while mutations and/or changes in the environment easily influence energy-dependent properties like folding rates or stability.     

Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation

We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.     

Hydrophilicity Regulates the Stealth Properties of Polyphosphoester‐Coated Nanocarriers

Increasing the plasma half‐life is an important goal in the development of drug carriers, and can be effectively achieved through the attachment of polymers, in particular poly(ethylene glycol) (PEG). While the increased plasma half‐life has been suggested to be a result of decreased overall protein adsorption on the hydrophilic surface in combination with the adsorption of specific proteins, the molecular reasons for the success of PEG and other hydrophilic polymers are still widely unknown. We prepared polyphosphoester‐coated nanocarriers with defined hydrophilicity to control the stealth properties of the polymer shell. We found that the log P value of the copolymer controls the composition of the protein corona and the cell interaction. Upon a significant change in hydrophilicity, the overall amount of blood proteins adsorbed on the nanocarrier remained unchanged, while the protein composition varied. This result underlines the importance of the protein type for the protein corona and cellular uptake.     

The interaction of peptides and proteins with nanostructures surfaces: a challenge for nanoscience

The impact of nanotechnologies in biomedicine and biotechnology is becoming more and more evident. It imposes practical challenges, for instance, raising specific issues on the biocompatibility of nanostructures. Nanoparticles are characterized by a high surface-to-volume ratio, which makes them reactive to foreign species. Thus, when proteins or peptides approach an inorganic nanoparticle, as well as a flat surface, they are likely to interact with the substrate to some extent. This interaction is crucial for applications in drug delivery, imaging, diagnostics, implants, and other medical devices. Specifically, gold nanoparticles are highly versatile and particularly appealing. It is widely accepted that the surfaces of nanoparticles adsorb proteins either transiently in the soft corona layer or permanently in the hard corona layer. As a consequence, the protein structure and/or function may undergo profound adjustments or remain conserved. Detailing the interaction of different inorganic substrates with proteins and peptides at the atomic level, and designing ways to control the interaction, is the key for biomedical applications of nanoparticles, both from a fundamental viewpoint and for practical implementations. In the last decade, we have addressed protein–nanoparticle interactions, focusing on interfaces of gold surfaces and nanoparticles with amyloidogenic peptides and protein models. We have developed classical force fields, performed advanced molecular dynamics simulations, and compared computational outcomes with data from nuclear magnetic resonance experiments. Protein–gold complexes with differently coated gold nanoparticles have been modeled to explore the effects of charge and size on the protein structure. Our work unravels that a complex interplay between surface properties and characteristics of the biological adsorbate determines whether peptide conformation is influenced and whether protein aggregation is accelerated or inhibited by the presence of the substrate. General guidelines to cope with amyloidogenic proteins could be inferred: these can be essentially summarized with the necessity of balancing the hydrophobic and electrostatic interactions that the amyloidogenic proteins establish with the coating moieties.     

Analytical Methods for Characterizing the Nanoparticle–Protein Corona

When nanoparticles (NPs) enter a biological environment, medium components, especially proteins, compete for binding to the NP’s surface, leading to development of a new interface, commonly referred to as the “protein corona.” This rich protein shell gives the NPs a biological identity that can be very different from their synthetic one, in terms of their chemical–physical properties. Understanding NP–protein interaction is crucial for both the bioapplications and safety of nanomaterials. The protein corona provides the primary contact to the cells and their receptors. It defines in vivo fate of the delivery systems, governing the stability, immunogenicity, circulation, clearance rates and organ biodistribution of the NPs. Given its importance, the application and the development of analytical methods to investigate the protein corona are crucial. This review gives an overview of chromatographic, electrophoretic, mass spectrometric and proteomic methods because these techniques have the advantage to be able to identify and quantify individual proteins adsorbed onto the corona. This capability opens up the possibility to exploit the protein corona for specific cell targeting.     

Analytical Methods for Characterizing the Nanoparticle–Protein Corona

When nanoparticles (NPs) enter a biological environment, medium components, especially proteins, compete for binding to the NP’s surface, leading to development of a new interface, commonly referred to as the “protein corona.” This rich protein shell gives the NPs a biological identity that can be very different from their synthetic one, in terms of their chemical–physical properties. Understanding NP–protein interaction is crucial for both the bioapplications and safety of nanomaterials. The protein corona provides the primary contact to the cells and their receptors. It defines in vivo fate of the delivery systems, governing the stability, immunogenicity, circulation, clearance rates and organ biodistribution of the NPs. Given its importance, the application and the development of analytical methods to investigate the protein corona are crucial. This review gives an overview of chromatographic, electrophoretic, mass spectrometric and proteomic methods because these techniques have the advantage to be able to identify and quantify individual proteins adsorbed onto the corona. This capability opens up the possibility to exploit the protein corona for specific cell targeting.

     

Understanding and controlling the interaction of nanomaterials with proteins in a physiological environment

Nanomaterials hold promise as multifunctional diagnostic and therapeutic agents. However, the effective application of nanomaterials is hampered by limited understanding and control over their interactions with complex biological systems. When a nanomaterial enters a physiological environment, it rapidly adsorbs proteins forming what is known as the protein 'corona'. The protein corona alters the size and interfacial composition of a nanomaterial, giving it a biological identity that is distinct from its synthetic identity. The biological identity determines the physiological response including signalling, kinetics, transport, accumulation, and toxicity. The structure and composition of the protein corona depends on the synthetic identity of the nanomaterial (size, shape, and composition), the nature of the physiological environment (blood, interstitial fluid, cell cytoplasm, etc.), and the duration of exposure. In this critical review, we discuss the formation of the protein corona, its structure and composition, and its influence on the physiological response. We also present an 'adsorbome' of 125 plasma proteins that are known to associate with nanomaterials. We further describe how the protein corona is related to the synthetic identity of a nanomaterial, and highlight efforts to control protein-nanomaterial interactions. We conclude by discussing gaps in the understanding of protein-nanomaterial interactions along with strategies to fill them (167 references).     

球形嵌段共聚物胶束的温度效应

基于标度理论建立了嵌段共聚物溶剂体系的胶束模型，通过Flory-Huggins相互作用参数间接讨论了温度对胶束平衡性质的一般性影响.分析了胶束过渡区聚合物链的状态，通过分段的过渡区密度分布函数，考察了温度对聚集数、过渡区密度分布和胶束内外半径的影响.结果显示,温度升高使过渡区链状态呈现多种分层情况，并导致胶束聚集数的显著增加.但过渡区链状态的变化对过渡区密度的总体影响不显著，胶束的总体半径变化不大，表明过渡区溶剂随温度升高而逐渐“挤出”.理论预测与实验结果较一致.     

Enabling grand‐canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy ). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte‐Carlo/molecular dynamics (MD) simulations in the grand‐canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand‐canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand‐canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand‐canonical scheme is only minimal. © 2012 Wiley Periodicals, Inc.     

Exploiting three kinds of interface propensities to identify protein binding sites

Predicting the binding sites between two interacting proteins provides important clues to the function of a protein. In this study, we present a building block of proteins called order profiles to use the evolutionary information of the protein sequence frequency profiles and apply this building block to produce a class of propensities called order profile interface propensities. For comparisons, we revisit the usage of residue interface propensities and binary profile interface propensities for protein binding site prediction. Each kind of propensities combined with sequence profiles and accessible surface areas are inputted into SVM. When tested on four types of complexes (hetero-permanent complexes, hetero-transient complexes, homo-permanent complexes and homo-transient complexes), experimental results show that the order profile interface propensities are better than residue interface propensities and binary profile interface propensities. Therefore, order profile is a suitable profile-level building block of the protein sequences and can be widely used in many tasks of computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the protein remote homology detection.     

十八烷基聚氧乙烯表面空间结构和蛋白质吸附行为研究

为探讨聚合物-水界面十八烷基聚氧乙烯链(SPEO)空间结构和白蛋白选择性吸附行为的内在联系,本文采用聚甲基丙烯酸甲酯接枝十八烷基聚氧乙烯(PMMA-g-SPEO),通过不同热处理方式获得了具有“环形链”(A)和“尾形链”(B)结构的两种模型表面.在A表面,水相接触角随水化时间的延长而迅速降低,最终亲水性的界面可同时有效阻抗白蛋白和纤维蛋白原的吸附,但不呈现对白蛋白的选择性吸附;而在B表面,水相接触角随水化时间的延长变化不大,最终疏水性的界面可在有效阻抗纤维蛋白原的吸附同时,有效诱导白蛋白的选择性吸附,具有聚氧乙烯(PEO)阻抗非特异性吸附和十八烷基选择性吸附协同作用的特点.