Influence of Single-Stranded DNA Coatings on the Interaction between Graphene Nanoflakes and Lipid Bilayers

Recent advances of graphene-biomacromolecule nanocomposites in medical applications

In recent years, graphene-based composites have received increasing attention due to their high biocompatibility, large specific surface area, high electrical conductivity and unique mechanical properties. The combination of biomacromolecules and graphene provides a promising route for the preparation of novel graphene-based nanocomposites. Novel graphene-based nanocomposites with unique functions could be applied to medicine, biology, biosensors, environmental science, energy storage and other fields. Graphene-biomacromolecule nanocomposites have excellent biocompatibility, outstanding biofunctionality and low cytotoxicity, and have more advantages and development prospects than other traditional graphene-based materials in biological and biomedical fields. In this work, we summarize the research on the covalent and non-covalent interactions between different biomacromolecules (peptides, DNA/RNA, proteins and enzymes) and graphene, as well as the synthesis methods of novel functionalized graphene-biomacromolecule composites in recent years. We mainly introduce the recent advances (last 5 years) of graphene-biomacromolecule nanocomposites in medical applications, such as medical detection and disease treatment. We hope that this review will help readers to understand the methods and mechanisms of biomolecules modifying the surface of graphene, as well as the synthesis and application of graphene-based nanocomposites, which will promote the future developments of graphene-biomolecule composites in biomedicine, tissue engineering, materials engineering, and so on.

The aggregation of multiple miR-29a cancer biomarkers induced by graphene quantum dots: Molecular dynamics simulations

MicroRNAs (miRNAs) are small non-coding RNAs that play a role in regulating gene expression. MiRNAs are focused on as potential cancer biomarkers due to their involvement in the cancer development. New effective techniques for extracting miRNA from a biological matrix is important. Recently, graphene quantum dots (GQDs) have been used to detect DNA/RNA in many sensor platforms, but the application in miRNA extraction remains limited. To extract miRNAs, the miRNA adsorption and desorption on GQD are the key. Thus, in this work, the adsorption mechanism of excess miRNA on GQD in solution is revealed using Molecular dynamics simulations. The miRNA assemblies on one and two GQDs were studied to explore the possibility of using GQD for miRNA extraction. The folded miR-29a molecule, one of key cancer biomarkers, is used as an miRNA model. Three systems with one (6miR) and two GQDs (with parallel (6miR_2GP) and sandwich (6miR_2GS) organisations) in six-miR-29a solution were set. The data show excess miR-29a can reduce the miR-29a-GQD binding efficiency. The opening of intrabase pairing of GQD-absorbed miR-29a facilitates the interbase coupling resulting in the self-aggregation of miR-29a. The GQD organisation also affects the miR-29a adsorption ability. The additional GQDs result in the tighter miR-29a adsorption which can retard the miR-29a desorption. The proper GQD concentration is thus important to successfully collect all miR-29a and accommodate the easy miR-29a dissociation. Our results can be useful for a design of DNA probe and choosing decent nanosized GRA concentration for experimental setups.

Molecular insights into the resistance of phospholipid heads to the membrane penetration of graphene nanosheets

The interaction between nanomaterials and phospholipid membranes underlies many emerging biological applications. To what extent hydrophilic phospholipid heads shield the bilayer from the integration of hydrophobic nanomaterials remains unclear, and this open question contains important insights for understanding biological membrane physics. Here, we present molecular dynamics (MD) simulations to clarify the resistance of phospholipid heads to the membrane penetration of graphene nanosheets. With 130 simulation trials, we observed that ∼22% graphene nanosheets penetrate the POPC bilayer. Sharp corners of the nanosheets should have a lower energy barrier than nanosheet edges, but interestingly, the membrane penetration mainly starts from the edge-approaching orientation. We thoroughly analyzed the pentration pathway and propulsion, indicating that the membrane penetration of graphene nanosheets is dominated by the joint effects of nanosheet edges and corners. Furthermore, the molecular origin of the resistance is clarified by evaluating the bilayers of different phospholipids, which successfully correlates the penetration resistance of phospholipid heads with the correlated motions of neighboring phospholipids for the first time. These results are expected to inspire future studies on the dynamic behavior of phospholipids, bio-nano interfaces, and design of biological nanomaterials.

Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene

Spike glycoprotein of the SARS-CoV-2 virus and its structure play a crucial role in the infections of cells containing angiotensin-converting enzyme 2 (ACE2) as well as in the interactions of this virus with surfaces. Protection against viruses and often even their deactivation is one of the great varieties of graphene applications. The structural changes of the non-glycosylated monomer of the spike glycoprotein trimer (denoted as S-protein in this work) triggered by its adsorption onto graphene at the initial stage are investigated by means of atomistic molecular dynamics simulations. The adsorption of the S-protein happens readily during the first 10 ns. The shape of the S-protein becomes more prolate during the adsorption, but this trend, albeit less pronounced, is observed also for the freely relaxing S-protein in water. The receptor-binding domain (RBD) of the free and adsorbed S-protein manifests itself as the most rigid fragment of the whole S-protein. The adsorption even enhances the rigidity of the whole S-protein as well as its subunits. Only one residue of the RBD involved in the specific interactions with ACE2 during the cell infection is involved in the direct contact of the adsorbed S-protein with the graphene. The new intramolecular hydrogen bonds formed during the S-protein adsorption replace the S-protein-water hydrogen bonds; this trend, although less apparent, is observed also during the relaxation of the free S-protein in water. In the initial phase, the secondary structure of the RBD fragment specifically interacting with ACE2 receptor is not affected during the S-protein adsorption onto the graphene.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

Modeling the Adsorption of the miR-29a Cancer Biomarker on a Graphene Quantum Dot

MicroRNAs (miRNAs) are small noncoding RNA molecules associated with the regulation of gene expression in organisms. MiRNAs are focused on as potential cancer biomarkers due to their involvement in cancer development. New potential techniques for miRNA detection are rapidly developed, while there is a lack of effective extraction approaches, especially for miRNAs. Recently, graphene quantum dots (GQDs) have been involved in many disease biosensor platforms including miRNA detection, but no application in miRNA extraction is studied. To extract miRNAs, miRNA adsorption and desorption on GQDs are the key. Thus, in this work, the adsorption mechanism of miRNA on GQDs in solution is revealed using molecular dynamics simulations. The aim is to explore the possibility of using GQDs for miRNA extraction. The folded miR-29a molecule, one of the key cancer biomarkers, is used as a miRNA model. Two systems with one (1miR) and four (4miR) chains of miR-29a were set. MiR-29a molecules in all systems are simultaneously adsorbed on the GQD surface. Our finding highlights the ability of the GQD in collecting miRNAs in solution. In 1miR, the whole miR-29a chain sits on the GQD face, whereas all miR-29a molecules in 4miR show the "clamping" conformation. No "lying flat" orientation of miR-29a is observed due to the existence of the preserved hairpin region. Interestingly, the 5' end shows tighter binding than the 3' terminus. A design of complementary DNA with the recognition segment involving the sequences close to the 3' end can promote effective miR-29a desorption.

Molecular mechanisms underlying the role of the puckered surface in the biocompatibility of black phosphorus

As a newly emerging two-dimensional material, black phosphorus (BP) has received broad attention in the field of biomedical applications. Prior to its clinical application, its cytotoxicity to cells should be carefully evaluated; however, this field is still in its infancy. Motivated by this, we performed molecular dynamics (MD) simulations to systematically investigate the potential mechanisms of the cytotoxicity of BP to the lipid membrane, including lipid extraction, penetration into the membrane, and the impacts of BP on the physical properties of the membrane. Surprisingly, we observed that BP could not extract lipid molecules from the membrane. The thermodynamic analyses suggested that the puckered surface structure could weaken the interactions between BP and lipid molecules, thus inhibiting the lipid extraction. Additionally, through simulating the spontaneous interaction modes between BP and the lipid membrane, we found that the "passivated" edges of BP prohibited it from penetrating into the membrane. As a result, BP could only spontaneously lie parallel on the surface of the membrane, in which manner BP exerted little influence on the properties of the lipid membrane. To comprehensively appraise the cytotoxicity, we even artificially inserted BP into the membrane and compared the effects of BP and graphene on the properties of the membrane. Simulation results showed that the influences of the inserted BP on the lipid properties were much milder than those of graphene. Overall, the present work suggests that BP possesses distinctive biocompatibility benefiting from its puckered surface structure. This work provides a better understanding of the interactions between BP and the membrane, which may offer some useful suggestions for exploring strategies to improve the biocompatibility of nanomaterials.

Encapsulation of Graphene in the Hydrophobic Core of a Lipid Bilayer

Theoretical simulations have predicted that a lipid bilayer forms a stable superstructure when a sheet of graphene is inserted in its hydrophobic core. We experimentally produced for the first time a lipid-graphene-lipid assembly by combining the Langmuir-Blodgett and the Langmuir-Schaefer methods. Graphene is sandwiched and remains flat within the hydrophobic core of the lipid bilayer. Using infrared spectroscopy, ellipsometry, and neutron reflectometry, we characterized the superstructure at every fabrication step. The hybrid superstructure is mechanically stable and graphene does not disturb the natural lipid bilayer structure.

Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery

In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.

Entropy at Bio-Nano Interfaces

Entropy, one of the central concepts of thermodynamics, can be a predominant contribution to structural formation and transition. Although it is well-known that diverse forces and energies can significantly contribute to the structures and activities at bio-nano interfaces, the potential entropic contribution remains less well understood. Therefore, this review article seeks to provide a conceptual framework demonstrating that entropy can be exploited to shape the physicochemical properties of bio-nano interfaces and thereby regulate the structures, responses, and functions of biological systems. We introduce the typical types of entropy that matter at bio-nano interfaces. Moreover, some key characteristics featuring entropy at bio-nano interfaces, such as the difference between entropic force and energetic interaction and the associated implications for biomimetic research, are discussed. We expect that this review could stimulate further effort in the fundamental research of entropy in biology and in the biological applications of entropic effects in designer biomaterials.

Improving the Sensory Properties of Layered Phospholipid-Graphene Films Due to the Curvature of Graphene Layers

This article is devoted to the in silico study of the sensory properties of mono- and bilayer phospholipid-graphene films with planar and curved graphene sheets. The DPPC (dipalmitoylphosphatidylcholine) molecules are considered as phospholipid structures. These molecules are part of lipid bilayers, liposomes and cell membranes. To find a way to improve the sensory properties of phospholipid-graphene films, we studied the effect of the curvature of the graphene sheet on the charge transfer and electrical conductivity of the films. The distribution of the electron charge density over the film atoms was calculated using the self-consistent-charge density-functional tight-binding method (SCC-DFTB). The calculation of the current through phospholipid-graphene films was carried out within the framework of the Landauer-Buttiker formalism using the Keldysh nonequilibrium Green function technique. As a result of the calculations, the optimal configuration of the arrangement of DPPC molecules between two graphene layers was established. This configuration provides the maximum possible increase in current to 1 μA at low voltages of ~0.2 V and is achieved for curved graphene with a radius of curvature of ~2.7 nm at individual points of graphene atomic network.