Interaction forces measured using AFM between colloids and surfaces coated with both dextran and protein

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol-1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.

Complementary Powerful Techniques for Investigating the Interactions of Proteins with Porous TiO2 and Its Hybrid Materials: A Tutorial Review

Understanding the adsorption and interaction between porous materials and protein is of great importance in biomedical and interface sciences. Among the studied porous materials, TiO₂ and its hybrid materials, featuring distinct, well-defined pore sizes, structural stability and excellent biocompatibility, are widely used. In this review, the use of four powerful, synergetic and complementary techniques to study protein-TiO_2-based porous materials interactions at different scales is summarized, including high-performance liquid chromatography (HPLC), atomic force microscopy (AFM), surface-enhanced Raman scattering (SERS), and Molecular Dynamics (MD) simulations. We expect that this review could be helpful in optimizing the commonly used techniques to characterize the interfacial behavior of protein on porous TiO₂ materials in different applications.

Physico-chemistry from initial bacterial adhesion to surface-programmed biofilm growth

Biofilm formation is initiated by adhesion of individual bacteria to a surface. However, surface adhesion alone is not sufficient to form the complex community architecture of a biofilm. Surface-sensing creates bacterial awareness of their adhering state on the surface and is essential to initiate the phenotypic and genotypic changes that characterize the transition from initial bacterial adhesion to a biofilm. Physico-chemistry has been frequently applied to explain initial bacterial adhesion phenomena, including bacterial mass transport, role of substratum surface properties in initial adhesion and the transition from reversible to irreversible adhesion. However, also emergent biofilm properties, such as production of extracellular-polymeric-substances (EPS), can be surface-programmed. This review presents a four-step, comprehensive description of the role of physico-chemistry from initial bacterial adhesion to surface-programmed biofilm growth: (1) bacterial mass transport towards a surface, (2) reversible bacterial adhesion and (3) transition to irreversible adhesion and (4) cell wall deformation and associated emergent properties. Bacterial transport mostly occurs from sedimentation or convective-diffusion, while initial bacterial adhesion can be described by surface thermodynamic and Derjaguin-Landau-Verwey-Overbeek (DLVO)-analyses, considering bacteria as smooth, inert colloidal particles. DLVO-analyses however, require precise indication of the bacterial cell surface, which is impossible due to the presence of bacterial surface tethers, creating a multi-scale roughness that impedes proper definition of the interaction distance in DLVO-analyses. Application of surface thermodynamics is also difficult, because initial bacterial adhesion is only an equilibrium phenomenon for a short period of time, when bacteria are attached to a substratum surface through few surface tethers. Physico-chemical bond-strengthening occurs in several minutes leading to irreversible adhesion due to progressive removal of interfacial water, conformational changes in cell surface proteins, re-orientation of bacteria on a surface and the progressive involvement of more tethers in adhesion. After initial bond-strengthening, adhesion forces arising from a substratum surface cause nanoscopic deformation of the bacterial cell wall against the elasticity of the rigid peptidoglycan layer positioned in the cell wall and the intracellular pressure of the cytoplasm. Cell wall deformation not only increases the contact area with a substratum surface, presenting another physico-chemical bond-strengthening mechanism, but is also accompanied by membrane surface tension changes. Membrane-located sensor molecules subsequently react to control emergent phenotypic and genotypic properties in biofilms, most notably adhesion-associated ones like EPS production. Moreover, also bacterial efflux pump systems may be activated or mechano-sensitive channels may be opened upon adhesion-induced cell wall deformation. The physico-chemical properties of the substratum surface thus control the response of initially adhering bacteria and through excretion of autoinducer molecules extend the awareness of their adhering state to other biofilm inhabitants who subsequently respond with similar emergent properties. Herewith, physico-chemistry is not only involved in initial bacterial adhesion to surfaces but also in what we here propose to call "surface-programmed" biofilm growth. This conclusion is pivotal for the development of new strategies to control biofilm formation on substratum surfaces, that have hitherto been largely confined to the initial bacterial adhesion phenomena.

Probing molecular interaction mechanisms of organic fouling on polyamide membrane using a surface forces apparatus: Implication for wastewater treatment

Surface fouling is the dominant fouling mechanism of thin-film composite (TFC) membranes used in reverse osmosis (RO) technology. Understanding the complex interactions between foulant-membrane which drive the attachment and growth of foulants on membrane surface is of both fundamental and practical importance. This work aims to understand the molecular interaction mechanisms of organic fouling on RO-TFC membranes. A surface forces apparatus (SFA) was employed to directly measure the interaction forces and time-dependent adsorption behaviors between model organic foulants: humic acid (HA), bovine serum albumin (BSA), and lipopolysaccharides (LPS) and a polyamide (PA) thin film. PA thin film was prepared by interfacial condensation polymerization on mica substrates using m-phenylenediamine and 1,3,5-benzenetricarbonyltrichloride. The interaction forces between PA films and different foulant (HA, BSA, LPS) were directly measured under controlled solution chemistries in an asymmetric configuration (foulant-deposited PA films vs. PA films). The adsorption behaviors of these foulants on PA films were directly monitored in a symmetric configuration (PA films vs. PA films). These interactions were examined as a function of both contact time and solution chemistry (ionic strength). In asymmetrical configuration, both HA and BSA show repulsion with PA surface during approach and adhesion during separation, but LPS demonstrates repulsion only. In symmetrical configuration, all the foulants show adsorption on PA surface and the initial adsorption rate of foulant to PA surface follows the order of BSA>LPS>HA. The interaction mechanisms between PA films and foulants were discussed based on the interaction forces and interaction dynamics measurement.

Adhesion forces of the sea-water bacterium Paracoccus seriniphilus on titanium: Influence of microstructures and environmental conditions

The bacterial attachment to surfaces is the first step of biofilm formation. This attachment is governed by adhesion forces which act between the bacterium and the substrate. Such forces can be measured by single cell force spectroscopy, where a single bacterium is attached to a cantilever of a scanning force microscope, and force-distance curves are measured. For the productive sea-water bacterium Paracoccus seriniphilus, pH dependent measurements reveal the highest adhesion forces at pH 4. Adhesion forces measured at salinities between 0% and 4.5% NaCl are in general higher for higher salinity. However, there is an exception for 0.9% where a higher adhesion force was measured than expected. These results are in line with zeta potential measurements of the bacterium, which also show an exceptionally low zeta potential at 0.9% NaCl. In the absence of macromolecular interactions, the adhesion forces are thus governed by (unspecific) electrostatic interactions, which can be adjusted by pH and ionic strength. It is further shown that microstructures on the titanium surface increase the adhesion force. Growth medium reduces the interaction forces dramatically, most probably through macromolecular bridging.

Molecular Interactions of Protein with TiO2 by the AFM-Measured Adhesion Force

Understanding the interactions between porous materials and biosystems is of great important in biomedical and environmental sciences. Upon atomic force microscopy (AFM) adhesion measurement, a new experimental approach was presented here to determine the molecular interaction force between proteins and mesoporous TiO₂ of various surface roughnesses. The interaction force between each protein molecule and the pure anatase TiO₂ surface was characterized by fitting the adhesion and adsorption capacity per unit contact area, and it was found that the adhesion forces were approximately 0.86, 2.63, and 4.41 nN for lysozyme, myoglobin, and BSA, respectively. Moreover, we reported that the molecular interaction force was independent of the surface topography of the material but the protein type is a factor of the interaction. These experimental results on the molecular level provide helpful insights for stimulating model calculation and molecular simulation studies of protein interaction with surfaces.

Colloid-probe AFM studies of the interaction forces of proteins adsorbed on colloidal crystals

In recent years, colloid-probe AFM has been used to measure the direct interaction forces between colloidal particles of different size or surface functionality in aqueous media, as one can study different forces in symmerical systems (i.e., sphere-sphere geometry). The present study investigates the interaction between protein coatings on colloid probes and hydrophilic surfaces decorated with hexagonally close packed single particle layers that are either uncoated or coated with proteins. Controlled solvent evaporation from aqueous suspensions of colloidal particles (coated with or without lysozyme and albumin) produces single layers of close-packed colloidal crystals over large areas on a solid support. The measurements have been carried out in an aqueous medium at different salt concentrations and pH values. The results show changes in the interaction forces as the surface charge of the unmodified or modified particles, and ionic strength or pH of the solution is altered. At high ionic strength or pH, electrostatic interactions are screened, and a strong repulsive force at short separation below 5 nm dominates, suggesting structural changes in the absorbed protein layer on the particles. We also study the force of adhesion, which decreases with an increment in the salt concentration, and the interaction between two different proteins indicating a repulsive interaction on approach and adhesion on retraction.

ATR-FTIR spectroscopy study of the influence of pH and contact time on the adhesion of Shewanella putrefaciens bacterial cells to the surface of hematite

Attachment of live cells of Shewanella putrefaciens strain CN-32 to the surface of hematite (α-Fe(2)O(3)) was studied with in situ ATR-FTIR spectroscopy at variable pH (4.5-7.7) and contact times up to 24 h. The IR spectra indicate that phosphate based functional groups on the cell wall play an important role in mediating adhesion through formation of inner-sphere coordinative bonds to hematite surface sites. The inner-sphere attachment mode of microbial P groups varies with pH, involving either a change in protonation or in coordination to hematite surface sites as pH is modified. At all pH values, spectra collected during the early stages of adhesion show intense IR bands associated with reactive P-groups, suggestive of preferential coordination of P-moieties at the hematite surface. Spectra collected after longer sorption times show distinct frequencies from cell wall protein and carboxyl groups, indicating that bacterial adhesion occurring over longer time scales is to a lesser degree associated with preferential attachment of P-based bacterial functional groups to the hematite surface. The results of this study demonstrate that pH and reaction time influence cell-mineral interactions, implying that these parameters play an important role in determining cell mobility and biofilm formation in aqueous geochemical environments.

In situ hydrodynamic lateral force calibration of AFM colloidal probes

Lateral force microscopy (LFM) is an application of atomic force microscopy (AFM) to sense lateral forces applied to the AFM probe tip. Recent advances in tissue engineering and functional biomaterials have shown a need for the surface characterization of their material and biochemical properties under the application of lateral forces. LFM equipped with colloidal probes of well-defined tip geometries has been a natural fit to address these needs but has remained limited to provide primarily qualitative results. For quantitative measurements, LFM requires the successful determination of the lateral force or torque conversion factor of the probe. Usually, force calibration results obtained in air are used for force measurements in liquids, but refractive index differences between air and liquids induce changes in the conversion factor. Furthermore, in the case of biochemically functionalized tips, damage can occur during calibration because tip-surface contact is inevitable in most calibration methods. Therefore, a nondestructive in situ lateral force calibration is desirable for LFM applications in liquids. Here we present an in situ hydrodynamic lateral force calibration method for AFM colloidal probes. In this method, the laterally scanned substrate surface generated a creeping Couette flow, which deformed the probe under torsion. The spherical geometry of the tip enabled the calculation of tip drag forces, and the lateral torque conversion factor was calibrated from the lateral voltage change and estimated torque. Comparisons with lateral force calibrations performed in air show that the hydrodynamic lateral force calibration method enables quantitative lateral force measurements in liquid using colloidal probes.

Atomic force microscopy studies of the initial interactions between fibrinogen and surfaces

Atomic force microscopy (AFM) was used to analyze the interactions between fibrinogen and model surfaces having different levels of water wettability. In contrast to most AFM studies, proteins were coupled to the substrate while model surface colloids were attached to the end of the AFM probe, thereby ensuring that proteins undergo only a single compression/decompression cycle. Similar values of adhesion force were observed between fibrinogen and all of the highly wettable surfaces; in the same manner, fibrinogen showed similar adhesion forces against all poorly wettable surfaces, with a step-like transition observed between the two groups. Relationships between the adhesion forces and loading rates were used to analyze the energy profiles involved in protein/surface interactions. Multiple energy barriers were found in the interaction of proteins with poorly wettable surfaces; whereas a single energy barrier was found for protein interactions with highly wettable surfaces. Contact time-dependent adhesion data were fit to an exponential model and showed that the rate constants of the protein unfolding process on highly wettable surface were smaller at low loading rates, but increased rapidly to yield values similar to those on poorly wettable surfaces at high loading rates. The activation energies of protein unfolding derived from the data offer insight into the role of surface wettability in affecting adhesion, conformational changes, and ultimately, the activity of proteins at biomaterial surfaces.

Adhesion and retention of a bacterial phytopathogen Erwinia chrysanthemi in biofilm-coated porous media

The goal of this study is to investigate the impact of biofilm physical and biological properties on bacterial transport and deposition in porous media. Experiments were performed in packed columns to examine the removal of Erwinia chrysanthemi (Ech3937), a phytopathogen, from the bulk fluid due to its attachmentto glass beads coated with Pseudomonas aeruginosa biofilms. Two isogenic P. aeruginosa strains, PAO1 and PD0300, with different EPS secretion capabilities and EPS compositions, were used to culture biofilms. The Ech3937 transport and distribution in packed columns were studied in both upflow and downflow cell injection modes over a range of solution ionic strengths. The results show that the presence of biofilm strongly interferes with the deposition behavior of Ech3937 in porous media. The spatial variation of deposited Ech3937 cells contradicts the log-linear pattern predicted by the classic filtration theory, indicating that the biofilm physical structure and polymeric interactions between the biofilm EPS and Ech3937 cell surface are the main mechanisms that control bacterial deposition. When the biofilm accumulation is relatively small, bacterial adhesion onto biofilm-coated porous media is mainly inhibited by steric forces. By contrast, cell deposition is enhanced by the reduced porous media porosity when biofilm is more abundant.

Adhesion characteristics of two Burkholderia cepacia strains examined using colloid probe microscopy and gradient force analysis

Colloid probe atomic force microscopy (CP-AFM) was used to investigate two strains of Burkholderia cepacia in order to determine what molecular scale characteristics of strain Env435 make it less adhesive to surfaces than the parent strain, G4. CP-AFM approach curves analyzed using a gradient force method showed that in a high ionic strength solution (IS=100 mM, Debye length=1 nm), the colloid probe was attracted to the surface of strain G4 at a distance of approximately 30 nm, but it was repelled over a distance of 25 nm when approaching strain Env435. Adhesion forces measured under the same solution conditions during colloid retraction showed that 1.38 nN of force was required to remove the colloid placed in contact with the surface of strain G4, whereas only 0.58 nN was required using strain Env435. At IS=1mM (Debye length=10nm), the attractive force observed with G4 was no longer present, and the repulsive force seen with Env435 was extended to approximately 250 nm. The adhesion of the bacteria to the probe was much less at low IS solution (1 mM) than at high IS (100 mM). The greater adhesion characteristics of strain G4 compared to Env435 were confirmed in column tests. Strain G4 had a collision efficiency of alpha=0.68, while strain Env435 had a much lower collision efficiency of alpha=0.01 (IS=100 mM). These results suggest that the reduced adhesion of strain Env435 measured in column tests is due to the presence of high molecular weight extracellular polymeric substances that extend out from the cell surface, creating long-range steric repulsion between the cell and a surface. Adhesion is reduced as these polymers do not appear to be "sticky" when placed in contact with a surface in AFM tests.

Effects of surface wettability and contact time on protein adhesion to biomaterial surfaces

Atomic force microscopy (AFM) was used to directly measure the adhesion forces between three test proteins and low density polyethylene (LDPE) surfaces treated by glow discharge plasma to yield various levels of water wettability. The adhesion of proteins to the LDPE substrates showed a step dependence on the wettability of surfaces as measured by the water contact angle (theta). For LDPE surfaces with theta> approximately 60-65 degrees , stronger adhesion forces were observed for bovine serum albumin, fibrinogen and human FXII than for the surfaces with theta<60 degrees . Smaller adhesion forces were observed for FXII than for the other two proteins on all surfaces although trends were identical. Increasing the contact time from 0 to 50s for each protein-surface combination increased the adhesion force regardless of surface wettability. Time varying adhesion data was fit to an exponential model and free energies of protein unfolding were calculated. This data, viewed in light of previously published studies, suggests a 2-step model of protein denaturation, an early stage on the order of seconds to minutes where the outer surface of the protein interacts with the substrate and a second stage involving movement of hydrophobic amino acids from the protein core to the protein/surface interface. Impact statement: The work described in this manuscript shows a stark transition between protein adherent and protein non-adherent materials in the range of water contact angles 60-65 degrees , consistent with known changes in protein adsorption and activity. Time-dependent changes in adhesion force were used to calculate unfolding energies relating to protein-surface interactions. This analysis provides justification for a 2-step model of protein denaturation on surfaces.

Charge-transfer complex study by chemical force spectroscopy: a dynamic force spectroscopic approach

Charge-transfer interaction, as a reversible and rapid phenomenon, was evidenced by force microscopy. Pull-off forces were measured between a tip grafted with a trinitrofluorenone derivative and a surface functionalized with an electron-rich aromatic anthracene compound in a dodecane environment. The effect of the sweep time on the measured interaction forces is described, together with an extensive study of a competitive influence of free aromatic molecules in dodecane diluted solutions. These forces depend on the nature of the competitor and its concentration as well as on the velocity of tip/sample separation.

Proprietary Rel-Ease drug delivery technology: opportunity for sustained delivery of peptides, proteins and small molecules

Proprietary Rel-Ease (Praecis Pharmaceuticals) drug delivery technology uses biocompatible polymers as carriers to incorporate a drug into a polymer matrix through opposite charge interaction or complexation. The resulting low solubility complexes can be used to prepare sustained release depot injections or potentially sustained release formulations for oral administration. As a regulatory approved and commercialised drug delivery technology, Rel-Ease is used in abarelix for injectable suspension, a monthly depot injection for the treatment of patients with advanced prostate cancer. The technology offers high drug loading and minimal-to-no initial burst effect in vivo. It uses aqueous processes and is compatible for complexation with many peptide and protein therapeutics; its mechanism can also be applied to many small-molecule therapeutics and offers conventional and alternative methods for sustained release delivery via an oral route.

ATR-FTIR spectroscopy reveals bond formation during bacterial adhesion to iron oxide

The contribution of various bacterial surface functional groups to adhesion at hematite and ZnSe surfaces was examined using attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy. When live Shewanella oneidensis, Pseudomonas aeruginosa, and Bacillus subtilis cells were introduced to a horizontal hematite (alpha-Fe(2)O(3))-coated internal reflection element (IRE), FTIR peaks emerged corresponding to bacterial phosphate group binding. These IR peaks were not observed when bacteria were introduced to the uncoated ZnSe IRE. When cells were added to colloidal suspensions of alpha-Fe(2)O(3) at pH 7, spectra included peaks corresponding to P-OFe and nu(COOH), the latter being attributed to bridging of carboxylate at mineral surface OH groups. Selected model organic compounds with P-containing functionalities (phenylphosphonic acid [PPA], adenosine 5'-monophosphate [AMP], 2'-deoxyadenyl(3'-->5')-2'-deoxyadenosine [DADA], and deoxyribonucleic acid [DNA]) produce spectra with similar peaks corresponding to P-OFe when adsorbed to alpha-Fe(2)O(3). The data indicate that both terminal phosphate/phosphonate and phosphodiester groups, either exuded from the cell or present as surface biomolecules, are involved in bacterial adhesion to Fe-oxides through formation of innersphere Fe-phosphate/phosphonate complexes.