Interaction of organic ions with proteins

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.

Bulk phase behaviour vs interface adsorption: Effects of anions and isotopes on β-lactoglobulin (BLG) interactions

HYPOTHESIS

Protein adsorption is highly relevant in numerous applications ranging from food processing to medical implants. In this context, it is important to gain a deeper understanding of protein-protein and protein-surface interactions. Thus, the focus of this investigation is on the interplay of bulk properties and surface properties on protein adsorption. It was hypothesised that the type of solvent and ions in solution should significantly influence the protein's bulk and interface behaviour, which has been observed in literature and previous work for other net negatively charged, globular proteins such as bovine serum albumin (BSA).

EXPERIMENTS

The phase behaviour of β-lactoglobulin (BLG) with lanthanum chloride (LaCl₃) and iodide (LaI₃) in normal water H₂O(l) and heavy water (D₂O(l)) was established via optical microscopy and ultraviolet-visible spectroscopy. The formation of an adsorption layer and its properties such as thickness, density, structure, and hydration was investigated via neutron reflectivity, quartz-crystal microbalance with dissipation, and infra-red measurements.

FINDINGS

β-lactoglobulin does not show significant anion-induced or isotope-induced effects - neither in bulk nor at the solid-liquid interface, which deviates strongly from the behaviour of bovine serum albumin. We also provide a comprehensive discussion and comparison of protein-specific bulk and interface behaviour between bovine serum albumin and β-lactoglobulin dependent on anion, cation, solvent, and substrate properties. These findings pave the way for understanding the transition from adsorption to crystallisation.

Promising insights into the kosmotropic effect of magnetic nanoparticles on proteins: The pivotal role of protein corona formation

Increasing concerns about biosafety of nanoparticles (NPs) has raised the need for detailed knowledge of NP interactions with biological molecules especially proteins. Herein, the concentration-dependent effect of magnetic NPs (MNPs) on bovine serum albumin and hen egg white lysozyme was explored. The X-ray diffraction patterns, zeta potential, and dynamic light scattering measurements together with scanning electron microscopy images were employed to characterize MNPs synthesized through coprecipitation method. Then, we studied the behavior of two model proteins with different surface charges and structural properties on interaction with Fe₃ O₄ . A thorough investigation of protein-MNP interaction by the help of intrinsic fluorescence at different experimental conditions revealed that affinity of proteins for MNPs is strongly affected by the similarity of protein and MNP surface charges. MNPs exerted structure-making kosmotropic effect on both proteins under a concentration threshold; however, binding strength was found to determine the extent of stabilizing effect as well as magnitude of the concentration threshold. Circular dichroism spectra showed that proteins with less resistance to conformational deformations are more prone to secondary structure changes upon adsorption on MNPs. By screening thermal aggregation of proteins in the presence of Fe₃ O₄ , it was also found that like chemical stability, thermal stability is influenced to a higher extent in more strongly bound proteins. Overall, this report not only provides an integrated picture of protein-MNP interaction but also sheds light on the molecular mechanism underling this process.

Characterization of Protein-Facilitated Ion-Transfer Mechanism at a Polarized Aqueous/Organic Interface

Protein electrochemistry studies at a polarized interface between two immiscible electrolyte solutions (ITIES) indicate that the detection mechanism of a protein at the interface involves a combination of protein-anion complexation and interfacial adsorption processes. A detailed characterization of the protein-facilitated mechanism of ion transfer at the ITIES will allow the development of new label-free biomolecular detection tools. Molecular dynamics simulations were performed to describe the mechanism of transfer of the hydrophobic anion tetraphenylborate (TPB^-) from a 1,2-dichloroethane (organic) phase to an aqueous phase mediated by lysozyme as a model protein under the action of an external electric field. The anion migrated to the protein at the interface and formed multiple contacts. The side chains of positively charged Lys and Arg residues formed electrostatic interactions with the anion. Nonpolar residues like Trp, Met, and Val formed hydrophobic contacts with the anion as it moved along the protein surface. During this process, lysozyme adopted multiple, partially unfolded conformations at the interface, all involving various anion-protein complexes with small free-energy barriers between them. The general mechanism of protein-facilitated ion transfer at a polarized liquid-liquid interface thus likely involves the movement of a hydrophobic anion along the protein surface through a combination of electrostatic and hydrophobic interactions.

Molecular insight into the wetting behavior and amphiphilic character of cellulose nanocrystals

The study of nanocellulose is a field of growing interest due to its many applications and its use in the development of biocompatible and eco-friendly materials. In spite of the vast number of studies in the field, many questions about the role of the molecular structure in the properties of cellulose are still subject of debate. One of these fundamental questions is the possible amphiphilic nature of cellulose and the relative role of hydrogen bonding and hydrophobic effect on the interactions of cellulose. In this work we present an extensive molecular dynamics simulation study of this question by analyzing the wetting of cellulose with water and organic solvent, its interaction with hydrophilic and hydrophobic ions and its interaction with a protein (human epidermal growth factor, hEGF). We consider two characteristic cellulose crystal planes of Iβ cellulose with very different roughness, different hydrogen bonding capability and different exposure of cellulose hydrophobic groups (the (010) plane which has exposed -OH groups and the (100) plane with buried -OH groups). Our results show that both surfaces are simultaneously hydrophilic and lipophilic, with both surfaces having very similar contact angles. In spite of the global similarity of wetting of both surfaces, the molecular details of wetting are very different and substantial local wetting heterogeneities (which strongly depend on the surface) appear for both solvents. We also observe a weak interaction of both surfaces with hydrophobic and hydrophilic solutes. These weak interactions are attributed to the simultaneous lipophilic and hydrophilic character of both (100) and (010) cellulose surfaces. Interestingly, we found a substantial interaction of both cellulose planes with polar and apolar residues of the hEGF protein.

The Chaotropic Effect as an Assembly Motif in Chemistry

Following up on scattered reports on interactions of conventional chaotropic ions (for example, I- , SCN- , ClO4- ) with macrocyclic host molecules, biomolecules, and hydrophobic neutral surfaces in aqueous solution, the chaotropic effect has recently emerged as a generic driving force for supramolecular assembly, orthogonal to the hydrophobic effect. The chaotropic effect becomes most effective for very large ions that extend beyond the classical Hofmeister scale and that can be referred to as superchaotropic ions (for example, borate clusters and polyoxometalates). In this Minireview, we present a continuous scale of water-solute interactions that includes the solvation of kosmotropic, chaotropic, and hydrophobic solutes, as well as the creation of void space (cavitation). Recent examples for the association of chaotropic anions to hydrophobic synthetic and biological binding sites, lipid bilayers, and surfaces are discussed.

Effect of organic and inorganic ions on the lower critical solution transition and aggregation of PNIPAM

We have studied the effect of different ions belonging to the extended Hofmeister series on the thermosensitive polymer poly(N-isopropylacrylamide) (PNIPAM), by combining Differential Scanning Calorimetry (DSC) and Dynamic Light Scattering (DLS). The variations in the lower critical solution temperature (TLCS) and enthalpy change during PNIPAM phase separation evidence the importance of considering both hydration and hydrophobicity to explain the interaction of ions with interfaces. The results obtained in the presence of inorganic ions can be explained by the tendency of water molecules to preferentially hydrate the PNIPAM chains or the ions, depending on the kosmotropic (highly hydrated) or chaotropic (poorly hydrated) character of the ions. On the contrary, tetraphenyl organic ions (Ph4B- and Ph4As+) interact with the hydrophobic moieties of PNIPAM chains, inducing a significant reduction of the TLCS. DLS results show that the aggregation state of PNIPAM above the TLCS is also strongly influenced by the presence of ions. While macroscopic phase separation (formation of a polymer-rich phase insoluble in water) was apparent in the presence of inorganic ions, we observed the formation of submicron PNIPAM aggregates at temperatures above the TLCS in the presence of the hydrophobic ions. Kinetically arrested monodisperse PNIPAM nanoparticles were formed in the presence of the Ph4B- anion, while a rather polydisperse distribution of particle sizes was observed in the presence of Ph4As+. These results show that ionic specificity influences both the static (thermodynamic) and dynamic (kinetically controlled aggregation) states of PNIPAM in an aqueous environment.

Adsorption of Milk Proteins (β-Casein and β-Lactoglobulin) and BSA onto Hydrophobic Surfaces

Here, we study films of proteins over planar surfaces and protein-coated microspheres obtained from the adsorption of three different proteins ( β -casein, β -lactoglobulin and bovine serum albumin (BSA)). The investigation of protein films in planar surfaces is performed by combining quartz crystal microbalance (QCM) and atomic force microscopy (AFM) measurements with all-atomic molecular dynamics (MD) simulations. We found that BSA and β -lactoglobulin form compact monolayers, almost without interstices between the proteins. However, β -casein adsorbs forming multilayers. The study of the electrokinetic mobility of protein-coated latex microspheres shows substantial condensation of ions from the buffer over the complexes, as predicted from ion condensation theories. The electrokinetic behavior of the latex-protein complexes is dominated by the charge of the proteins and the phenomenon of ion condensation, whereas the charge of the latex colloids plays only a minor role.

Investigations of the Hofmeister series and other specific ion effects using lipid model systems

From the ion point-of-view specific ion effects (SIE) arise as an interplay of ionic size and shape and charge distribution. However in aqueous systems SIE invariably involve water, and at surfaces they involve both interacting surface groups and local fields emanating from the surface. In this review we highlight the fundamental importance of ionic size and hydration on SIE, properties which encompass all types of interacting forces and ion-pairing phenomena and make the Hofmeister or lyotropic series of ions pertinent to a broad range of systems and phenomena. On the other hand ionic hydrophobicity and complexation capacity also determine ionic behavior in a variety of contexts. Over the years we have carried out carefully designed experiments on a few selected soft matter model systems, most involving zwitterionic phospholipids, to assess the importance of fundamental ionic and interfacial properties on ion specific effects. By tuning down direct Coulomb interactions, working with different interfacial geometries, and carefully tuning ion-lipid headgroup interactions it is possible to assess the importance of different parameters contributing to ion specific behavior. We argue that the majority of specific ion effects involving relatively simple soft matter systems can be at least qualitatively understood and demystified.