Energy Landscape of Negatively Charged BSA Adsorbed on a Negatively Charged Silica Surface

Estimating Binding Energies of π-Stacked Aromatic Dimers Using Force Field-Driven Molecular Dynamics

π-π stacking are omnipresent interactions, crucial in many areas of chemistry, and often studied using quantum chemical methods. Here, we report a simple and computationally efficient method of estimating the binding energies of stacked polycyclic aromatic hydrocarbons based on steered molecular dynamics. This method leverages the force field parameters for accurate calculation. The presented results show good agreement with those obtained through DFT at the ωB97X-D3/cc-pVQZ level of theory. It is demonstrated that this force field-driven SMD method can be applied to other aromatic molecules, allowing insight into the complexity of the stacking interactions and, more importantly, reporting π-π stacking energy values with reasonable precision.

Impact of the Crystal Structure of Silica Nanoparticles on Rhodamine 6G Adsorption: A Molecular Dynamics Study

Understanding the mechanism of adsorption of Rhodamine 6G (R6G) to various crystal structures of silica nanoparticles (SNPs) is important to elucidate the impact of dye size when measuring the size of the dye-SNP complex via the time-resolved fluorescence anisotropy method. In this work, molecular dynamics (MD) simulations were used to get an insight into the R6G adsorption process, which cannot be observed using experimental methods. It was found that at low pH, α-Cristobalite structured SNPs have a strong affinity to R6G; however, at high pH, more surface silanol groups undergo ionization when compared with α-Quartz, preventing the adsorption. Therefore, α-Quartz structured SNPs are more suitable for R6G adsorption at high pH than the α-Cristobalite ones. Furthermore, it was found that stable adsorption can occur only when the R6G xanthene core is oriented flat with respect to the SNP surface, indicating that the dye size does not contribute significantly to the measured size of the dye-SNP complex. The requirement of correct dipole moment orientation indicates that only one R6G molecule can adsorb on any sized SNP, and the R6G layer formation on SNP is not possible. Moreover, the dimerization process of R6G and its competition with the adsorption has been explored. It has been shown that the highest stable R6G aggregate is a dimer, and in this form, R6G does not adsorb to SNPs. Finally, using steered molecular dynamics (SMD) with constant-velocity pulling, the binding energies of R6G dimers and R6G complexes with both α-Quartz and α-Cristobalite SNPs of 40 Å diameter were estimated. These confirm that R6G adsorption is most stable on 40 Å α-Quartz at pH 7, although dimerization is equally possible.

α-Helix-Mediated Protein Adhesion

Proteins have been adopted by natural living organisms to create robust bioadhesive materials, such as biofilms and amyloid plaques formed in microbes and barnacles. In these cases, β-sheet stacking is recognized as a key feature that is closely related to the interfacial adhesion of proteins. Herein, we challenge this well-known recognition by proposing an α-helix-mediated interfacial adhesion model for proteins. By using bovine serum albumin (BSA) as a model protein, it was discovered that the reduction of disulfide bonds in BSA results in random coils from unfolded BSA dragging α-helices to gather at the solid/liquid interface (SLI). The hydrophobic residues in the α-helix then expose and break through the hydration layer of the SLI, followed by the random deposition of hydrophilic and hydrophobic residues to achieve interfacial adhesion. As a result, the first assembled layer is enriched in the α-helix secondary structure, which is then strengthened by intermolecular disulfide bonds and further initiates stepwise layering protein assembly. In this process, β-sheet stacking is transformed from the α-helix in a gradually evolving manner. This finding thus indicates a valuable clue that β-sheet-featuring amyloid may form after the interfacial adhesion of proteins. Furthermore, the finding of the α-helix-mediated interfacial adhesion model of proteins affords a unique strategy to prepare protein nanofilms with a well-defined layer number, presenting robust and modulable adhesion on various substrates and exhibiting good resistance to acid, alkali, organic solvent, ultrasonic, and adhesive tape peeling.

Chitin and Chitosan Binding to the α-Chitin Crystal: A Molecular Dynamics Study

Understanding the binding of chitosan oligomers to the surface of a chitin nanocrystal is important for improving the enzymatic deacetylation of chitin and for the design of chitin/chitosan composite films. Here, we study the binding of several chito-oligomers to the (100) surface of an α-chitin crystal using molecular dynamics (MD), steered MD, and umbrella sampling. The convergence of the free energy was carefully considered and yielded a binding energies of -12.5 and -2 kcal mol^-1 for 6-monomer-long chitin and uncharged chitosan oligomers, respectively. We also found that the results for the umbrella sampling were consistent with the force profile from the steered MD and with classical MD simulations of the adsorption process. Our results give insight into the molecular-scale interactions, which can be helpful for the design of new chitin composite films. Furthermore, the free energy curves we present can be used to validate coarse-grained models for chitin and chitosan, which are necessary to study the self-assembly of chitin crystals due to the long time scale of the process.

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.

Adsorption properties of albumin and fibrinogen on hydrophilic/hydrophobic TiO2 surfaces: A molecular dynamics study

In serval experimental researches, UV-induced hydrophilicity enabled better hemocompatibility in the TiO₂ surface, which was considered to be caused by the removal of the carboxylic acid contamination from the surface. In this paper, we altered the surface wetting property by applying the formate contamination on the rutile (110) surface, and systematically investigated the adsorption properties of albumin and fibrinogen on hydrophilic/hydrophobic TiO₂ surface. Unique contacts were found between the charged residues and the hydrophilic surface, anchoring the protein on the surface. The small size and the heart shape of albumin make it easy to cross the stable water layers near the surface. Besides, albumin has a higher proportion of charged residues, so it can form more unique contacts on the hydrophilic surface. Therefore, the albumin tends to adsorb on the hydrophilic surface. For the hydrophobic surface, the water layers near the surface are weakened, which helps the fibrinogen diffusing to the surface and adjusting its orientation. Although the hydrophobic surface cannot form the unique contacts, the larger size of fibrinogen can provide more residues to form enough ordinary contacts after adjusting, and then achieves stable adsorption. Therefore, fibrinogen tends to adsorb on the hydrophobic surface.

Simulating Peptide Monolayer Formation: GnRH-I on Silica

Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for both sexes. It was previously shown that inoculation with silica nanoparticles (SiNPs) coated with GnRH-I makes an effective anti-fertility vaccine due to how the peptide adsorbs to the nanoparticle and is presented to the immune system. In this paper, we develop and employ a protocol to simulate the development of a GnRH-I peptide adlayer by allowing peptides to diffuse and adsorb in a staged series of trajectories. The peptides start the simulation in an immobile state in solution above the model silica surface, and are then released sequentially. This facile approach allows the adlayer to develop in a natural manner and appears to be quite versatile. We find that the GnRH-I adlayer tends to be sparse, with electrostatics dominating the interactions. The peptides are collapsed to the surface and are seemingly free to interact with additional solutes, supporting the interpretations of the GNRH-I/SiNP vaccine system.

Impact of Silane Monolayers on the Adsorption of Streptavidin on Silica and Its Subsequent Interactions with Biotin: Molecular Dynamics and Steered Molecular Dynamics Simulations

Protein adsorption on surfaces is used in analytical tools as an immobilization mean to trap the analyte to be detected. However, protein adsorption can lead to a conformational change in the protein structure, resulting in a loss of bioactivity. Here, we study adsorption of a streptavidin-biotin complex on amorphous SiO₂ surfaces functionalized with five different silane self-assembled monolayers by all-atom molecular dynamics simulations. We find that the streptavidin global conformational change, as well as the nature of residues with high mobility, depends on the alkyl chain length and head-group charge of silane molecules. Effects on interactions with biotin are further investigated by steered molecular dynamics (SMD) simulations, which mimics atomic force microscopy (AFM) with the biotin attached on the tip. We show the combined effects of adsorption-induced global conformational changes and of the position of residues with high mobility on the streptavidin-biotin rupture force. By comparing our results to experimental and SMD rupture forces obtained in water, without any surface, we conclude that silane with uncharged and short alkyl chains allows streptavidin immobilization, while keeping biotin interactions better than silanes with long alkyl chains or charged head groups.

A novel approach to calculate protein adsorption isotherms by molecular dynamics simulations

Protein adsorption plays a role in many fields, where in some it is desirable to maximize the amount adsorbed, in others it is important to avoid protein adsorption altogether. Therefore, theoretical methods are needed for a better understanding of the underlying processes and for the prediction of adsorption quantities. In this study, we present a proof-of-concept that the calculation of protein adsorption isotherms by molecular dynamics (MD) simulations is possible using the steric mass action (SMA) theory. Here we are investigating the adsorption of bovine/human serum albumin (BSA/HSA) and hemoglobin (bHb) on Q Sepharose FF. Protein adsorption isotherms were experimentally determined and modeled. Free energy profiles of protein adsorption were calculated by MD simulations to determine the Henry isotherms as a first step. Although each simulation contained only one protein, notably the calculated isotherms are in reasonably good agreement with the experimental isotherms. Hence, we could show that MD data can lead to protein adsorption data in good agreement with experimental data. The results were critically discussed and requirements for future applications are identified.

Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase

The conformational lock was a bio-thermodynamic theory to explain the characteristics of interfaces in oligomeric enzymes and their effects on catalytic activity. The previous studies on superoxide dismutases (Cu, Zn-SODs) showed that the dimeric structure contributed to the high catalytic efficiency and the stability. In this study, steered molecular dynamics simulations were used firstly to study the main interactions between two subunits of Cu, Zn-SODs. The decomposition process study showed that there were not only four pairs of hydrogen bonds but also twenty-five residue pairs participating hydrophobic interactions between A and B chains of SOD, and van der Waals interactions occupied a dominant position among these residue pairs. Moreover, the residue pairs of hydrogen bonds played a major role in maintaining the protein conformation. The analysis of the energy and conformational changes in the SMD simulation showed that there were two groups (two conformational locks) between A and B chains of SOD. The first group consisted of one hydrogen-bond residues pair and seven hydrophobic interactions residues pairs with a total average energy of −30.10 KJ/mol, and the second group of three hydrogen-bond residues pair and eighteen hydrophobic interactions residues pairs formed with a total average energy of −115.23 KJ/mol.

Orientation effects on the nanoscale adsorption behavior of bone morphogenetic protein-2 on hydrophilic silicon dioxide

Bone Morphogenetic Protein-2 (BMP-2) is a growth factor associated with different developmental functions in regenerative medicine and tissue engineering. Because of its favorable properties for the development of bone and cartilage tissue, BMP-2 promotes the biocompatibility of medical implants. In this research, molecular dynamics simulations were implemented to simulate the interaction of BMP-2 with a flat hydrophilic silicon dioxide substrate, an important biomaterial for medical applications. We considered the influence of four orthogonal protein orientations on the adsorption behavior. Results showed that arginine and lysine were the main residues to interact with the silicon dioxide substrate, directly adsorbing onto the surface and overcoming water layers. However, between these charged residues, we observed a preference for arginine to adsorb. Orientations with the α-helix loop closer to the surface at the beginning of the simulations had greater loss of secondary structure as compared to the other configurations. Among all the orientations, the end-on B configuration had favorable adsorption characteristics with a binding energy of 14 000 kJ mol⁻¹ and retention of 21.7% β-sheets as confirmed by the Ramachandran plots. This research provides new insights into the nanoscale interaction of BMP-2 and silicon dioxide substrate with applications in orthopedic implants and regenerative medicine.

Preferential binding of charged residues with hydrophilic silicon dioxide substrate during adsorption of BMP-2 in end-on B configuration.

Polyallylamine hydrochloride coating enhances the fluorescence emission of Human Serum Albumin encapsulated gold nanoclusters

Protein encapsulated gold nanoclusters have received much attention due to the possibility of using them as a non-toxic fluorescent probe or marker for biomedical applications, however one major disadvantage currently is their low brightness and quantum yield in comparison to currently used fluorescent markers. A method of increasing the fluorescence emission of Human Serum Albumin (HSA) encapsulated gold nanoclusters (AuNCs) via a Polyallylamide hydrochloride (PAH) coating is described. PAH molecules with a molecular weight of ~17,500 Da were found to enhance the fluorescence emission of HSA-AuNCs by 3-fold when the protein/polymer concentration ratio is 2:1 in solution. Interestingly, the fluorescence lifetime of the AuNCs was found to decrease while the native tryptophan (TRP) fluorescence lifetime also decreased during the fluorescence emission intensity enhancement caused by the PAH binding. Coinciding with the decrease in fluorescence lifetime, the zeta potential of the system was observed to be zero during maximum fluorescence intensity enhancement, causing the formation of large aggregates. These results suggest that PAH binds to the HSA-AuNCs acting as a linker; causing aggregation and rigidification, which results in a decrease in separation between native TRP of HSA and AuNCs; improving Förster Resonance Energy Transfer (FRET) and increasing the fluorescence emission intensity. These findings are critical to the development of brighter protein encapsulated AuNCs.

Sudlow site II of human serum albumin remains functional after gold nanocluster encapsulation: a fluorescence-based drug binding study of L-Dopa

Fluorescent protein-encapsulated gold nanoclusters (AuNCs) offer a non-toxic means of sensing and imaging biological phenomena on the nanoscale. However, the biofunctionality of proteins encapsulating AuNCs has not been fully elucidated to date. Here we studied the biofunctionality of the second major drug binding site (Sudlow II) of Human Serum Albumin (HSA) encapsulated AuNCs after AuNC synthesis. L-Dopa, a fluorescent drug molecule associated with the clinical treatment of Parkinson's disease, which commonly binds to the Sudlow II site, was used to study the availability of the site before and after AuNC synthesis through changes to its fluorescence characteristics. L-Dopa was observed using its intrinsic fluorescence to readily bind to HSA-AuNCs complexes. Interestingly, the fluorescence emission intensity of AuNCs linearly increased with L-Dopa concentration while exciting the AuNC directly at 470 nm, Using a 400 nM HSA-AuNC solution, L-Dopa was rapidly detected at a limit of 300 pM, indicating that HSA-AuNCs fluorescence is extremely sensitive to molecular binding at the Sudlow II binding site. Future research may be able to utilize this sensitivity to improve the fluorescence characteristics of AuNCs within HSA-AuNCs for imaging and sensing including drug binding studies.