Lysozyme orientation and conformation on MoS2 surface: Insights from molecular simulations

Nanobio Interface Between Proteins and 2D Nanomaterials

Two-dimensional (2D) nanomaterials have significantly contributed to recent advances in material sciences and nanotechnology, owing to their layered structure. Despite their potential as multifunctional theranostic agents, the biomedical translation of these materials is limited due to a lack of knowledge and control over their interaction with complex biological systems. In a biological microenvironment, the high surface energy of nanomaterials leads to diverse interactions with biological moieties such as proteins, which play a crucial role in unique physiological processes. These interactions can alter the size, surface charge, shape, and interfacial composition of the nanomaterial, ultimately affecting its biological activity and identity. This review critically discusses the possible interactions between proteins and 2D nanomaterials, along with a wide spectrum of analytical techniques that can be used to study and characterize such interplay. A better understanding of these interactions would help circumvent potential risks and provide guidance toward the safer design of 2D nanomaterials as a platform technology for various biomedical applications.

Wrapping-Trapping versus Extraction Mechanism of Bactericidal Activity of MoS2 Nanosheets against Staphylococcus aureus Bacterial Membrane

The promising broad-spectrum antibacterial activity of two-dimensional molybdenum disulfide (2D MoS₂) has been widely recognized in the past decade. However, a comprehensive understanding of how the antibacterial pathways opted by the MoS₂ nanosheets varies with change in lipid compositions of different bacterial strains is imperative to harness their full antibacterial potential and remains unexplored thus far. Herein, we present an atomistic molecular dynamics (MD) study to investigate the distinct modes of antibacterial action of MoS₂ nanosheets against Staphylococcus aureus (S. aureus) under varying conditions. We observed that the freely dispersed nanosheets readily adhered to the bacterial membrane outer surface and opted for an unconventional surface directed "wrapping-trapping" mechanism at physiological temperature (i.e., 310 K). The adsorbed nanosheets mildly influenced the membrane structure by originating a compact packing of the lipid molecules present in its direct contact. Interestingly, these surface adsorbed nanosheets exhibited extensive phospholipid extraction to their surface, thereby inducing transmembrane water passage analogous to the cellular leakage, even at a slight increment of 20 K in the temperature. The strong van der Waals interactions between lipid fatty acyl tails and MoS₂ basal planes were primarily responsible for this destructive phospholipid extraction. In addition, the MoS₂ nanosheets bound to an imaginary substrate, controlling their vertical alignment, demonstrated a "nano-knives" action by spontaneously piercing inside the membrane core through their sharp corner, subsequently causing localized lipid ordering in their vicinity. The larger nanosheet produced a more profound deteriorating impact in all of the observed mechanisms. Keeping the existing knowledge about the bactericidal activity of 2D MoS₂ in view, our study concludes that their antibacterial activity is strongly governed by the lipid composition of the bacterial membrane and can be intensified either by controlling the nanosheet vertical alignment or by moderately warming up the systems.

Nano-bio interactions of 2D molybdenum disulfide

Two-dimensional (2D) molybdenum disulfide (MoS₂) is an ultrathin nanomaterial with a high degree of anisotropy, surface-to-volume ratio, chemical functionality and mechanical strength. These properties together enable MoS₂ to emerge as a potent nanomaterial for diverse biomedical applications including drug delivery, regenerative medicine, biosensing and bioelectronics. Thus, understanding the interactions of MoS₂ with its biological interface becomes indispensable. These interactions, referred to as "nano-bio" interactions, play a key role in determining the biocompatibility and the pathways through which the nanomaterial influences molecular, cellular and biological function. Herein, we provide a critical overview of the nano-bio interactions of MoS₂ and emphasize on how these interactions dictate its biomedical applications including intracellular trafficking, biodistribution and biodegradation. Also, a critical evaluation of the interactions of MoS₂ with proteins and specific cell types such as immune cells and progenitor/stem cells is illustrated which governs the short-term and long-term compatibility of MoS₂-based biomedical devices.

Interfacial Interactions within Amyloid Protein Corona Based on 2D MoS2 Nanosheets

The interfacial interaction within the amyloid protein corona based on MoS₂ nanomaterial is crucial, both for understanding the biological effects of MoS₂ nanomaterial and the evolution of amyloid diseases. The specific nano-bio interface phenomenon of human islet amyloid peptide (hIAPP) and MoS₂ nanosheet was investigated by using theoretical and experimental methods. The MoS₂ nanosheet enables the attraction of hIAPP monomer, dimer, and oligomer on its surface through van der Waals forces. Especially, the means of interaction between two hIAPP peptides might be changed by MoS₂ nanosheet. In addition, it is interesting to find that the hIAPP oligomer can stably interact with the MoS₂ nanosheet in one unique "standing" binding mode with an entire exposed β-sheet surface. All the interaction modes on the surface of MoS₂ nanosheet can be the essence of amyloid protein corona that may provide the venue to facilitate the fibrillation of hIAPP proteins. Further, it was verified experimentally that MoS₂ nanosheets could accelerate the fibrillation of hIAPP at a certain concentration mainly based on the newly formed nano-bio interface. In general, our results provide insight into the molecular interaction mechanism of the nano-bio interface within the amyloid protein corona, and shed light on the pathway of amyloid protein aggregation that is related to the evolution of amyloid diseases.

Lysozyme Adsorption on Different Functionalized MXenes: A Multiscale Simulation Study

Recently, MXenes, due to their abundant advantages, have been widely applied in energy storage, separation, catalysis, biosensing, et al. In this study, parallel tempering Monte Carlo and molecular dynamics methods were performed to investigate lysozyme adsorption on different functionalized Ti₃C₂T_x (-O, -OH, and -F). The simulation results show that lysozyme can adsorb effectively on Ti₃C₂T_x surfaces, and the order of interaction strength is Ti₃C₂O₂ > Ti₃C₂F₂ > Ti₃C₂(OH)₂. Electrostatics together with van der Waals interactions control protein adsorption. The orientation distributions of lysozyme adsorbed on the Ti₃C₂O₂ and Ti₃C₂F₂ surfaces are more concentrated than that on the Ti₃C₂(OH)₂ surface. During adsorption, the conformation of lysozyme remains stable, suggesting the good biocompatibility of Ti₃C₂T_x. Besides, the distribution of the interfacial water layer on the Ti₃C₂T_x surface has a certain impact on protein adsorption. This study provides theoretical insights for understanding the biocompatibility of 2D Ti₃C₂T_x materials and may help us evaluate the engineering of their surfaces for future biorelated applications.

Lysozyme Adsorption on Porous Organic Cages: A Molecular Simulation Study

Recently, porous organic cages (POCs) have emerged as a novel porous material with many merits and are widely utilized in many application fields. In this work, for the first time, molecular dynamics simulations were performed to investigate the mechanism of lysozyme adsorption onto the CC3 crystal, a kind of widely studied POC material. The simulation results show that lysozyme adsorbs onto the surface of CC3 with "top end-on," "back-on," or "side-on" orientations. It is found that the van der Waals interaction is the primary contribution to the binding; the conformation of the lysozyme is well preserved during the adsorption process. This provides some evidence for its biocompatibility and feasibility in biorelated applications. Arginine plays an important role in mediating the adsorption through nonpolar aliphatic chains. More importantly, the distribution and structure of the water layer on the POC surface has a significant impact on adsorption. This study provides insights into the development of POC materials with defined morphologies for the adsorption of biomolecules and may help the rational design of biorelated systems.

The molecular mechanism of robust macrophage immune responses induced by PEGylated molybdenum disulfide

Molybdenum disulfide (MoS2), a representative hexagonal transition metal dichalcogenide (TMD), has been extensively exploited in biomedical applications due to its unique physicochemical properties and biocompatibility. However, the lack of adequate data regarding how MoS2 activates immunological responses of macrophages remains a key concern for its risk assessment. Here, we employ a combined theoretical and experimental approach to investigate the interactions of MoS2 and PEGylated MoS2 (MoS2-PEG) with macrophages. We first perform molecular dynamics simulations to examine the atomic-detailed interactions of MoS2 and MoS2-PEG nanoflakes with a realistic model of the macrophage membrane. We show that a small MoS2 nanoflake (edge length of 2.86 nm) is capable of penetrating the macrophage membrane independent of its concentration. We also demonstrate that when initiated with a corner point-on configuration, the surface-bound PEG chains of MoS2-PEG hinder its membrane insertion process, leading to a prolonged passage through the membrane. Moreover, when placed in a face-on arrangement initially, the MoS2-PEG exhibits a lower binding free energy than pristine MoS2 after its adsorption on the membrane surface. The PEG chains can even insert and get buried in the outer leaflet of the membrane, providing additional contact for membrane adsorption. Our flow cytometric experiments then show that the responses of macrophages to either MoS2-PEG or MoS2 are significantly higher than that of the control (no nanomaterial stimulus), with MoS2-PEG eliciting stronger cytokine secretion than the pristine MoS2. The characteristics of slower/prolonged membrane penetration and stronger membrane adsorption of MoS2-PEG compared to pristine MoS2 explain why it triggers more sustained stimulation and higher cytokine secretion in macrophages as observed in our experiments. Our findings reveal the underlying molecular mechanism of how MoS2-PEG influences the immune responses and suggest its potential applications in nanomedicine involving immune stimulation.

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 Mechanisms of Interactions between Monolayered Transition Metal Dichalcogenides and Biological Molecules

Single layered two-dimensional (2D) materials such as transition metal dichalcogenides (TMDs) show great potential in many microelectronic or nanoelectronic applications. For example, because of extremely high sensitivity, TMD-based biosensors have become promising candidates for next-generation label-free detection. However, very few studies have been conducted on understanding the fundamental interactions between TMDs and other molecules including biological molecules, making the rational design of TMD-based sensors (including biosensors) difficult. This study focuses on the investigations of the fundamental interactions between proteins and two widely researched single-layered TMDs, MoS₂, and WS₂ using a combined study with linear vibrational spectroscopy attenuated total reflectance FTIR and nonlinear vibrational spectroscopy sum frequency generation vibrational spectroscopy, supplemented by molecular dynamics simulations. It was concluded that a large surface hydrophobic region in a relatively flat location on the protein surface is required for the protein to adsorb onto a monolayered MoS₂ or WS₂ surface with preferred orientation. No disulfide bond formation between cysteine groups on the protein and MoS₂ or WS₂ was found. The conclusions are general and can be used as guiding principles to engineer proteins to attach to TMDs. The approach adopted here is also applicable to study interactions between other 2D materials and biomolecules.

Graphene Oxide and Lysozyme Ultrathin Films with Strong Antibacterial and Enhanced Osteogenesis

There is a great demand worldwide for bone-related implant materials. The drawbacks of chronic infections and poor bone healing of current implant materials have limited their clinical applications. Functionalizing the implant surfaces with antibacterial and osteogenic films on implant materials provides new opportunities for fabricating novel implant materials. In the present study, an ultrathin (GO/Lys)₈ film of several tens of nanometers was fabricated using a layer-by-layer (LBL) technique with alternative deposition of graphene oxide (GO) and lysozyme (Lys). The deposition of the (GO/Lys) _n film exhibited a successive growth as supported by ellipsometry, UV-vis, and Fourier transform infrared data, and the physical properties (morphology, roughness, and stiffness) of this film were characterized with an atomic force microscope. The ultrathin films exhibited a great effect on bacterium sterilization of Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli and enhanced osteogenic differentiation efficiency, showing the potential application in bone implant coatings. We believe that this LBL assembling strategy will pave the way for fabricating dual-functional surfaces and guide the design of the implanted surfaces in the future.

Potential blockade of the human voltage-dependent anion channel by MoS2 nanoflakes

Despite significant interest in molybdenum disulfide (MoS2) nanomaterials, particularly in biomedicine, their biological effects have been understudied. Here, we explored the effect of MoS2 nanoflakes on the ubiquitous mitochondrial porin voltage-dependent anion channel (VDAC1), using a combined computational and functional approach. All-atomic molecular dynamics simulations suggest that MoS2 nanoflakes make specific contact interactions with human VDAC1. We show that the initial contacts between hVDAC1 and the nanoflake are hydrophobic but are subsequently enhanced by a complex interplay of van der Waals (vdW), hydrophobic and electrostatic interactions in the equilibrium state. Moreover, the MoS2 nanoflake can insert into the lumen of the hVDAC1 pore. Free-energy calculations computed by the potential of mean force (PMF) verify that the blocked configuration of the MoS2-hVDAC1 complex is more energetically favorable than the non-blocked binding mode. Consistent with these predictions, we showed that MoS2 depolarizes the mitochondrial membrane potential (Ψm) and causes a decrease in the viability of mammalian tissue culture cells. These findings might shed new light on the potential biological effect of MoS2 nanomaterials.

Interactions of Transition Metal Dichalcogenide Nanosheets With Mucin: Quartz Crystal Microbalance With Dissipation, Surface Plasmon Resonance, and Spectroscopic Probing

Ultrathin 2-dimensional transition metal dichalcogenides (TMDs) have become a class of high-potential materials in biomedicine due to their intriguing properties. They have been applied to solve biomedical challenges, such as biosensing, bioimaging, drug delivery, and cancer therapy. However, studies of the interactions between these materials and biomolecules are insufficient. Mucous tissue serves as a barrier to foreign hazardous substances and a gel layer for substance exchange. The main organic matter of mucous tissue is mucin, so it was selected as a model biomolecule to study its interactions with six different TMD nanosheets (NSs), including single-layered (SL), few-layered (FL), and small few-layered (SFL) MoS2 and WS2 NSs, using quartz crystal microbalance (QCM) with a dissipation monitor (QCM-D) and surface plasmon resonance (SPR). Additionally, UV absorption, fluorescence, and circular dichroism (CD) spectroscopy were applied to investigate the mechanism of the interactions and to study the conformational change of mucin. We found that the TMD NSs could adsorb on the mucin layer and affect its viscoelasticity. The results indicated that the SL WS2 NSs exhibited the highest initial absorption rate and the maximum absorption amount, while the SL MoS2 NSs exhibited the highest initial desorption rate. During the adsorption, the viscoelasticity variations of the mucin layer caused by the WS2 nanosheets were weaker than those caused by the MoS2 nanosheets. Furthermore, the conformational changes of mucin caused by the SL MoS2, SL WS2, and SFL MoS2 NSs were higher than those resulting from other TMD NSs. These findings provide important information on the interactions between TMD NSs and mucin and provide useful insights into the interfacial behavior of TMD NSs before they enter tissues.

Computer simulations of the adsorption of an N-terminal peptide of statherin, SN15, and its mutants on hydroxyapatite surfaces

Salt-bridge adsorption of the SN15 peptide and its mutants on the HAP(001) surface.

Ultra-High Signal Detection of Human Embryonic Stem Cells Driven by Two-Dimensional Materials

We observed a unique bioelectric signal of human embryonic stem cells using direct current-voltage measurements facilitated by few-layered 2D-MoS₂ sheets. A 1.828 mA cell signal was achieved (2 orders of magnitude higher than previous electrical-based detection methods) as well as multiple cell reading cycles demonstrating I ∼ 1.9 mA. Native stem cell proliferation, viability, and pluripotency were preserved. Molecular dynamics simulations elucidated the origin of the 2D-MoS₂ sheet-assisted increase in current flow. This paves the way for the development of a broadly applicable, fast, and damage-free stem cell detection method capable of identifying pluripotency with virtually any complementary-metal-oxide-semiconductor circuits.

Molecular interactions between single layered MoS2 and biological molecules

In this research, molecular interactions between several de novo designed alpha-helical peptides and monolayer MoS₂ have been studied.

Two-dimensional (2D) materials such as graphene, molybdenum disulfide (MoS₂), tungsten diselenide (WSe₂), and black phosphorous are being developed for sensing applications with excellent selectivity and high sensitivity. In such applications, 2D materials extensively interact with various analytes including biological molecules. Understanding the interfacial molecular interactions of 2D materials with various targets becomes increasingly important for the progression of better-performing 2D-material based sensors. In this research, molecular interactions between several de novo designed alpha-helical peptides and monolayer MoS₂ have been studied. Molecular dynamics simulations were used to validate experimental data. The results suggest that, in contrast to peptide–graphene interactions, peptide aromatic residues do not interact strongly with the MoS₂ surface. It is also found that charged amino acids are important for ensuring a standing-up pose for peptides interacting with MoS₂. By performing site-specific mutations on the peptide, we could mediate the peptide–MoS₂ interactions to control the peptide orientation on MoS₂.