Molecular Dynamics Simulations of Supramolecular Assemblies in Biology and Bionanotechnology

Molecular self-assembly is an energy driven process where randomly organized building blocks interact noncovalently to form highly organized supramolecular nanostructures. In biology, the cytoskeleton is a classic example of a dynamic self-assembly, forming long filamentous structures from monomeric protein subunits. Similarly, the self-assembly process is widely exploited in nanotechnology to build bio-functional nanostructures. In this work, we studied biological (microtubule) and synthetic (peptide drug amphiphile nanotube) self-assembled systems. We utilized long time-scale molecular dynamics simulation to investigate the structural and dynamical properties of these systems. At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT) is driven by the nucleotide state (GTP vs. GDP) in the β subunit of the tubulin dimers at the MT cap. We used large-scale molecular dynamics (MD) simulations and normal mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed by two neighboring protofilaments (PFs). We utilized recently reported high-resolution structures of dynamic MTs to simulate a GDP octamer both with and without a single GTP cap layer. We performed multiple replicas of long-time atomistic MD simulations (3 replicas, 0.3μs for each replica, 0.9 μs for each octamer system, and 1.8 μs total) of both octamers. We observed that a single GTP cap layer induces structural differences in neighboring PFs. While one PF possesses a gradual curvature, the second PF possesses a kinked conformation. This conformational difference results in either curling or splaying between these PFs. We suggest these results are caused by the asymmetric strengths of longitudinal contacts between the two PFs. Furthermore, using NMA, we calculated mechanical properties of these octamer systems and found that octamer system with a single GTP cap layer possesses a lower flexural rigidity. Peptide self-assembly has been used to design an array of nanostructures with functional biomedical applications. Experimental studies have reported nanofilament and nanotube formation from peptide-based drug amphiphiles (DAs). Each DA consists of an anticancer drug camptothecin (CPT) conjugated to a short peptide sequence via a biodegradable disulphide linker. These DAs have been shown to possess an inherently high drug loading with a tunable release mechanism. Recently, long-time atomistic MD simulations of supramolecular nanotubes composed of these DAs have been reported. Based on these all-atomistic simulations we parameterized a coarse grained (CG) model for the DA to study the self-assembly process and the structure and stability of preassembled nanotubes at longer timescales (microseconds). We investigated the self-assembly mechanism using a randomly organized system. We found aggregation between these DAs is an instantaneous process (sub-microsecond) that forms large and ordered assemblies. Additionally, we observed that the radial density distribution of peptides, CPTs, and water molecules and CPT orientation from CG models compared well with results from previously reported atomistic simulations. Furthermore, using all-atomistic MD simulations, we characterized the interaction of the DA nanotube with a model cell membrane. We performed these simulations using advanced sampling method (umbrella sampling). The reaction coordinate used to calculate potential of mean force was the distance between the center of mass of the nanotube and the center of mass of the membrane. Preliminary results indicate that the DA nanotube has a very strong repulsive interaction that can induce a huge bending fluctuation in the membrane. Taken together, these results offer important insights for the rational design of bio-functional supramolecular nanostructures

Understanding the Dynamics of the Structural States of Cannabinoid Receptors and the Role of Different Modulators

The cannabinoid receptors CB1R and CB2R are members of the G protein-coupled receptor (GPCR) family. These receptors have recently come to light as possible therapeutic targets for conditions affecting the central nervous system. However, because CB1R is known to have psychoactive side effects, its potential as a drug target is constrained. Therefore, targeting CB2R has become the primary focus of recent research. Using various molecular modeling studies, we analyzed the active, inactive, and intermediate states of both CBRs in this study. We conducted in-depth research on the binding properties of various groups of cannabinoid modulators, including agonists, antagonists, and inverse agonists, with all of the different conformational states of the CBRs. The binding effects of these modulators were studied on various CB structural features, including the movement of the transmembrane helices, the volume of the binding cavity, the internal fluids, and the important GPCR properties. Then, using in vitro experiments and computational modeling, we investigated how vitamin E functions as a lipid modulator to influence THC binding. This comparative examination of modulator binding to CBRs provides significant insight into the mechanisms of structural alterations and ligand affinity, which can directly help in the rational design of selective modulators that target either CB1R or CB2R

Potential Pro-Inflammatory Effect of Vitamin E Analogs through Mitigation of Tetrahydrocannabinol (THC) Binding to the Cannabinoid 2 Receptor

Vitamin E acetate, which is used as a diluent of tetrahydrocannabinol (THC), has been reported as the primary causative agent of e-cigarette, or vaping, product use-associated lung injury (EVALI). Here, we employ in vitro assays, docking, and molecular dynamics (MD) computer simulations to investigate the interaction of vitamin E with the membrane-bound cannabinoid 2 receptor (CB2R), and its role in modulating the binding affinity of THC to CB2R. From the MD simulations, we determined that vitamin E interacts with both CB2R and membrane phospholipids. Notably, the synchronized effect of these interactions likely facilitates vitamin E acting as a lipid modulator for the cannabinoid system. Furthermore, MD simulation and trajectory analysis show that when THC binds to CB2R in the presence of vitamin E, the binding cavity widens, facilitating the entry of water molecules into it, leading to a reduced interaction of THC with CB2R. Additionally, the interaction between THC and vitamin E in solution is stabilized by several H bonds, which can directly limit the interaction of free THCs with CB2R. Overall, both the MD simulations and the in vitro dissociation assay results indicate that THC binding to CB2R is reduced in the presence of vitamin E. Our study discusses the role of vitamin E in limiting the effect of THCs and its implications on the reported pathology of EVALI

Potential Pro-Inflammatory Effect of Vitamin E Analogs through Mitigation of Tetrahydrocannabinol (THC) Binding to the Cannabinoid 2 Receptor

Vitamin E acetate, which is used as a diluent of tetrahydrocannabinol (THC), has been reported as the primary causative agent of e-cigarette, or vaping, product use-associated lung injury (EVALI). Here, we employ in vitro assays, docking, and molecular dynamics (MD) computer simulations to investigate the interaction of vitamin E with the membrane-bound cannabinoid 2 receptor (CB2R), and its role in modulating the binding affinity of THC to CB2R. From the MD simulations, we determined that vitamin E interacts with both CB2R and membrane phospholipids. Notably, the synchronized effect of these interactions likely facilitates vitamin E acting as a lipid modulator for the cannabinoid system. Furthermore, MD simulation and trajectory analysis show that when THC binds to CB2R in the presence of vitamin E, the binding cavity widens, facilitating the entry of water molecules into it, leading to a reduced interaction of THC with CB2R. Additionally, the interaction between THC and vitamin E in solution is stabilized by several H bonds, which can directly limit the interaction of free THCs with CB2R. Overall, both the MD simulations and the in vitro dissociation assay results indicate that THC binding to CB2R is reduced in the presence of vitamin E. Our study discusses the role of vitamin E in limiting the effect of THCs and its implications on the reported pathology of EVALI

Effect of Nucleotide State on the Protofilament Conformation of Tubulin Octamers

At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT) is driven by the nucleotide state (GTP vs GDP) in the β subunit of the tubulin dimers at the MT cap. Here, we use large-scale molecular dynamics (MD) simulations and normal-mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed of two neighboring protofilaments (PFs). We utilize recently reported high-resolution structures of dynamic MTs to simulate a GDP octamer both with and without a single GTP cap layer. We perform multiple replicas of long-time atomistic MD simulations (3 replicas, 0.3 μs for each replica, 0.9 μs for each octamer system, and 1.8 μs total) of both octamers. We observe that a single GTP cap layer induces structural differences in neighboring PFs, finding that one PF possesses a gradual curvature, compared to the second PF which possesses a kinked conformation. This results in either curling or splaying between these PFs. We suggest that this is due to asymmetric strengths of longitudinal contacts between the two PFs. Furthermore, using NMA, we calculate mechanical properties of these octamer systems and find that octamer system with a single GTP cap layer possesses a lower flexural rigidity