Protein-surface interactions at the nanoscale: Atomistic simulations with implicit solvent models

Deposition of Human-Serum-Albumin-Functionalized Spheroidal Particles on Abiotic Surfaces: Reference Kinetic Results for Bioparticles

Human serum albumin (HSA) corona formation on polymer microparticles of a spheroidal shape was studied using dynamic light scattering and Laser Doppler Velocimetry (LDV). Physicochemical characteristics of the albumin comprising the zeta potential and the isoelectric point were determined as a function of pH for various ionic strengths. Analogous characteristics of the polymer particles were analyzed. The adsorption of albumin on the particles was in situ monitored by LDV. The stability of the HSA-functionalized particle suspensions under various pHs and their electrokinetic properties were also determined. The deposition kinetics of the particles on mica, silica and gold sensors were investigated by optical microscopy, AFM and quartz microbalance (QCM) under diffusion and flow conditions. The obtained results were interpreted in terms of the random sequential adsorption model that allowed to estimate the range of applicability of QCM for determining the deposition kinetics of viruses and bacteria at abiotic surfaces.

Mimicking Pseudo-Virion Interactions with Abiotic Surfaces: Deposition of Polymer Nanoparticles with Albumin Corona

Adsorption of human serum albumin (HSA) molecules on negatively charged polystyrene microparticles was studied using the dynamic light scattering, the electrophoretic and the solution depletion methods involving atomic force microscopy. Initially, the physicochemical characteristics of the albumin comprising the hydrodynamic diameter, the zeta potential and the isoelectric point were determined as a function of pH. Analogous characteristics of the polymer particles were acquired, including their size and zeta potential. The formation of albumin corona on the particles was investigated in situ by electrophoretic mobility measurements. The size, stability and electrokinetic properties of the particles with the corona were also determined. The particle diameter was equal to 125 nm, which coincides with the size of the SARS-CoV-2 virion. The isoelectric point of the particles appeared at a pH of 5. The deposition kinetics of the particles was determined by atomic force microscopy (AFM) under diffusion and by quartz microbalance (QCM) under flow conditions. It was shown that the deposition rate at a gold sensor abruptly vanished with pH following the decrease in the zeta potential of the particles. It is postulated that the acquired results can be used as useful reference systems mimicking virus adsorption on abiotic surfaces.

Predicting the Orientation of Adsorbed Proteins Steered with Electric Fields Using a Simple Electrostatic Model

Under the most common experimental conditions, the adsorption of proteins to solid surfaces is a spontaneous process that leads to a rather compact layer of randomly oriented molecules. However, controlling such orientation is critically important for the development of catalytic surfaces. In this regard, the use of electric fields is one of the most promising alternatives. Our work is motivated by experimental observations that show important differences in catalytic activity of a trypsin-covered surface, which depended on the applied potential during the adsorption. Even though adsorption results from the combination of several processes, we were able to determine that (under the selected conditions) mean-field electrostatics play a dominant role, determining the orientation and yielding a difference in catalytic activity. We simulated the electrostatic potential numerically, using an implicit-solvent model based on the linearized Poisson-Boltzmann equation. This was implemented in an extension of the code PyGBe that included an external electric field, and rendered the electrostatic component of the solvation free energy. Our model (extensions available at the Github repository) allowed estimating the overall affinity of the protein with the surface, and their most likely orientation as a function of the potential applied. Our results show that the active sites of trypsin are, on average, more exposed when the electric field is negative, which agrees with the experimental results of catalytic activity, and confirm the premise that electrostatic interactions can be used to control the orientation of adsorbed proteins.

Competitive protein adsorption on charge regulating silica-like surfaces: the role of protonation equilibrium

We develop a molecular thermodynamic theory to study the interaction of some proteins with a charge regulating silica-like surface under a wide range of conditions, including pH, salt concentration and protein concentration. Proteins are modeled using their three dimensional structure from crystallographic data and the average experimental pKa of amino acid residues. As model systems, we study single-protein and binary solutions of cytochrome c, green fluorescent protein, lysozyme and myoglobin. Our results show that protonation equilibrium plays a critical role in the interactions of proteins with these type of surfaces. The terminal hydroxyl groups on the surface display considerable extent of charge regulation; protein residues with titratable side chains increase protonation according to changes in the local environment and the drop in pH near the surface. This behavior defines protein-surface interactions and leads to the emergence of several phenomena: (i) a complex non-ideal surface charge behavior; (ii) a non-monotonic adsorption of proteins as a function of pH; and (iii) the presence of two spatial regions, a protein-rich and a protein-depleted layer, that occur simultaneously at different distances from the surface when pH is slightly above the isoelectric point of the protein. In binary mixtures, protein adsorption and surface-protein interactions cannot be predicted from single-protein solution considerations.

A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study

We developed a method for implicit solvent molecular dynamics simulations of proteins in solvent mixtures (model with implicit solvation thermodynamics, MIST). The MIST method introduces experimental group transfer free energies to the generalized Born formulation for generating molecular trajectories without the need for developing rigorous explicit-solvent force fields for multicomponent solutions. As a test case, we studied the urea-induced denaturation of the Trp-cage miniprotein in water. We demonstrate that our method allows efficient exploration of the conformational space of the protein in only a few hundreds of nanoseconds of all-atom unbiased simulations. Furthermore, selective implementation of the transfer free energies of specific peptide groups, backbone, and side chains enables us to decouple their specific energetic contributions to the conformational changes of the protein. The approach herein developed can readily be extended to the investigation of complex matrices as well as to the characterization of protein aggregation. The MIST method is implemented in Plumed (ver. 2.8) as a separate module called SASA.

In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold

The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.

Effect of dopamine-functionalization, charge and pH on protein corona formation around TiO2 nanoparticles

Inorganic nanoparticles (NPs) are gaining increasing attention in nanomedicine because of their stimuli responsiveness, which allows combining therapy with diagnosis. However, little information is known about their interaction with intracellular or plasma proteins when they are introduced in a biological environment. Here we present atomistic molecular dynamics (MD) simulations investigating the case study of dopamine-functionalized TiO2 nanoparticles and two proteins that are overexpressed in cancer cells, i.e. PARP1 and HSP90, since experiments proved them to be the main components of the corona in cell cultures. The mechanism and the nature of the interaction (electrostatic, van der Waals, H-bonds, etc.) is unravelled by defining the protein residues that are more frequently in contact with the NPs, the extent of contact surface area and the variations in the protein secondary structures, at different pH and ionic strength conditions of the solution where they are immersed to simulate a realistic biological environment. The effects of the NP surface functionalization and charge are also considered. Our MD results suggest that less acidic intracellular pH conditions in the presence of cytosolic ionic strength enhance PARP1 interaction with the nanoparticle, whereas the HSP90 contribution is partly weakened, providing a rational explanation to existing experimental observations.

Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces

The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multiscale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of β-glucosidase A (βGA) on bare and self-assembled monolayer (SAM)-functionalized gold surfaces. We monitored the enzyme position and orientation during the molecular dynamics (MD) trajectories and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of βGA on bare gold is more stable, but less specific, and more likely to disrupt the enzyme's function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a key point when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.

Advanced descriptors for long-range noncovalent interactions between SARS-CoV-2 spikes and polymer surfaces

The recent pandemic triggered numerous societal efforts aimed to control and limit the spread of SARS-CoV-2. One of these aspects is related on how the virion interacts with inanimate surfaces, which might be the source of secondary infection. Although recent works address the adsorption of the spike protein on surfaces, there is no information concerning the long-range interactions between spike and surfaces, experimented by the virion when is dispersed in the droplet before its possible adsorption. Some descriptors, namely the interaction potentials per single protein and global potentials, were calculated in this work. These descriptors, evaluated for the closed and open states of the spike protein, are correlated to the long-range noncovalent interactions between the SARS-CoV-2 spikes and polymeric surfaces. They are associated with the surface's affinity towards SARS-CoV-2 dispersed in respiratory droplets or water solutions. Molecular-Dynamics simulations were performed to model the surface of three synthetic polymeric materials: Polypropylene (PP), Polyethylene Terephthalate (PET), and Polylactic Acid (PLA), used in Molecular Mechanics simulations to define the above potentials. The descriptors show a similar trend for the three surfaces, highlighting a greater affinity towards the spikes of PP and PLA over PET. For closed and open structures, the long-range interactions with the surfaces decreased in the following order PP ∼ PLA > PET and PLA > PP > PET, respectively. Thus, PLA and PP interact with the virion quite distant from these surfaces to a greater extent concerning the PET surface, however, the differences among the considered surfaces were small. The global potentials show that the long-range interactions are weak compared to classic binding energy of covalent or ionic bonds. The proposed descriptors are useful most of all for a comparative study aimed at quickly preliminary screening of polymeric surfaces. The obtained results should be validated by more accurate method which will be subject of a subsequent work.

Deposition of Polymer Particles with Fibrinogen Corona at Abiotic Surfaces under Flow Conditions

The deposition kinetics of polymer particles with fibrinogen molecule coronas at bare and poly-L-lysine (PLL) modified mica was studied using the microfluid impinging-jet cell. Basic physicochemical characteristics of fibrinogen and the particles were acquired using dynamic light scattering and the electrophoretic mobility methods, whereas the zeta potential of the substrates was determined using streaming potential measurements. Subsequently, an efficient method for the preparation of the particles with coronas, characterized by a controlled fibrinogen coverage, was developed. This enabled us to carry out measurements, which confirmed that the deposition kinetics of the particles at mica vanished at pH above 5. In contrast, the particle deposition of PLL modified mica was at maximum for pH above 5. It was shown that the deposition kinetics could be adequately analyzed in terms of the mean-field approach, analogously to the ordinary colloid particle behavior. This contrasts the fibrinogen molecule behavior, which efficiently adsorbs at negatively charged substrates for the entire range pHs up to 9.7. These results have practical significance for conducting label-free immunoassays governed by the specific antigen/antibody interactions.

Recent Force Field Strategies for Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) are widely distributed across eukaryotic cells, playing important roles in molecular recognition, molecular assembly, post-translational modification, and other biological processes. IDPs are also associated with many diseases such as cancers, cardiovascular diseases, and neurodegenerative diseases. Due to their structural flexibility, conventional experimental methods cannot reliably capture their heterogeneous structures. Molecular dynamics simulation becomes an important complementary tool to quantify IDP structures. This review covers recent force field strategies proposed for more accurate molecular dynamics simulations of IDPs. The strategies include adjusting dihedral parameters, adding grid-based energy correction map (CMAP) parameters, refining protein-water interactions, and others. Different force fields were found to perform well on specific observables of specific IDPs but also are limited in reproducing all available experimental observables consistently for all tested IDPs. We conclude the review with perspective areas for improvements for future force fields for IDPs.

Computer simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces

A prominent feature of coronaviruses is the presence of a large glycoprotein spike protruding from a lipidic membrane. This glycoprotein spike determines the interaction of coronaviruses with the environment and the host. In this paper, we perform all atomic molecular dynamics simulations of the interaction between the SARS-CoV-2 trimeric glycoprotein spike and surfaces of materials. We considered a material with high hydrogen bonding capacity (cellulose) and a material capable of strong hydrophobic interactions (graphite). Initially, the spike adsorbs to both surfaces through essentially the same residues belonging to the receptor binding subunit of its three monomers. Adsorption onto cellulose stabilizes in this configuration, with the help of a large number of hydrogen bonds developed between cellulose and the three receptor-binding domains of the glycoprotein spike. In the case of adsorption onto graphite, the initial adsorption configuration is not stable and the surface induces a substantial deformation of the glycoprotein spike with a large number of adsorbed residues not pertaining to the binding subunits of the spike monomers.

Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation

Surface immobilized enzymes play a key role in numerous biotechnological applications such as biosensors, biofuel cells, or biocatalytic synthesis. As a consequence, the impact of adsorption on the enzyme structure, dynamics, and function needs to be understood on the molecular level as it is critical for the improvement of these technologies. With this perspective in mind, we used a theoretical approach for investigating local protein flexibility on the residue scale that couples a simplified protein representation with an elastic network and Brownian dynamics simulations. The impact of protein adsorption on a solid surface is implicitly modeled via additional external constraints between the residues in contact with the surface. We first performed calculations on a redox enzyme, bilirubin oxidase (BOD) from M. verrucaria, to study the impact of adsorption on its mechanical properties. The resulting rigidity profiles show that, in agreement with the available experimental data, the mechanical variations observed in the adsorbed BOD will depend on its orientation and its anchor residues (i.e., residues that are in contact with the functionalized surface). Additional calculations on ribonuclease A and nitroreductase shed light on how seemingly stable adsorbed enzymes can nonetheless display an important decrease in their catalytic activity resulting from a perturbation of their mechanics and internal dynamics.

Engineering at the nano-bio interface: harnessing the protein corona towards nanoparticle design and function

Unpredictable and uncontrollable protein adsorption on nanoparticles remains a considerable challenge to achieving effective application of nanotechnologies within biological environments. Nevertheless, engineered nanoparticles offer unprecedented functionality and control in probing and altering biological systems. In this review, we highlight recent advances in harnessing the "protein corona" formed on nanoparticles as a handle to tune functional properties of the protein-nanoparticle complex. Towards this end, we first review nanoparticle properties that influence protein adsorption and design strategies to facilitate selective corona formation, with the corresponding characterization techniques. We next focus on literature detailing corona-mediated functionalities, including stealth to avoid recognition and sequestration while in circulation, targeting of predetermined in vivo locations, and controlled activation once localized to the intended biological compartment. We conclude with a discussion of biocompatibility outcomes for these protein-nanoparticle complexes applied in vivo. While formation of the nanoparticle-corona complex may impede our control over its use for the projected nanobiotechnology application, it concurrently presents an opportunity to create improved protein-nanoparticle architectures by exploiting natural or guiding selective protein adsorption to the nanoparticle surface.

Mechanism of fibrinogen /microparticle complex deposition on solid substrates: Role of pH

Deposition kinetics of fibrinogen/polystyrene particle complexes on mica and the silicon/silica substrates was studied using the direct optical and atomic force microscopy. Initially, basic physicochemical characteristics of fibrinogen and the microparticles were acquired using the dynamic light scattering and the electrophoretic mobility methods, whereas the zeta potential of the substrates was determined using the streaming potential measurements. Subsequently an efficient method for the preparation of fibrinogen/polymer microparticle complexes characterized by controlled coverage and molecule orientation was developed. It was demonstrated that for a lower suspension concentration the complexes are stable for pH range 3-9 and for a large concentration for pH below 4.5 and above 5.5. This enabled to carry out thorough pH cycling experiments where their isoelectric point was determined to appear at pH 5. Kinetic measurements showed that the deposition rate of the complexes vanished at pH above 5, whereas the kinetics of the positively charged amidine particles, used as control, remained at maximum for pH up to 9. These results were theoretically interpreted using the hybrid random sequential adsorption model. It was confirmed that the deposition kinetics of the complexes can be adequately analyzed in terms of the mean-field approach, analogously to the ordinary colloid particle behavior. This is in contrast to the fibrinogen molecule behavior, which efficiently adsorb on negatively charged substrates for the entire range pHs up to 9.7. These results have practical significance for conducting efficient immunoassays governed by the specific antigen/antibody interactions.