All-atom Molecular Dynamics Simulation Study Research Articles

Molecular insights into the structure destabilization effects of ECG and EC on the Aβ protofilament: An all-atom molecular dynamics simulation study

The formation of Aβ into amyloid fibrils was closely connected to AD, therefore, the Aβ aggregates were the primary therapeutic targets against AD. Previous studies demonstrated that epicatechin-3-gallate (ECG), which possessed a gallate moiety, exhibited a greater ability to disrupt the preformed Aβ amyloid fibrils than epicatechin (EC), indicating that the gallate moiety was crucial. In the present study, the molecular mechanisms were investigated. Our results demonstrated that ECG had more potent disruptive impacts on the β-sheet structure and K28-A42 salt bridges than EC. We found that ECG significantly interfered the interactions between Peptide-4 and Peptide-5. However, EC could not. The disruption of K28-A42 salt bridges by ECG was mainly due to the interactions between ECG and the hydrophobic residues located at C-terminus. Interestingly, EC disrupted the K28-A42 salt bridges by the interactions with C-terminal hydrophobic residues and the cation-π interactions with K28. Moreover, our results indicated that hydrophobic interactions, H-bonds, π-π interactions and cation-π interactions between ECG and the bend of L-shaped region caused the disaggregation of interactions between Peptide-4 and Peptide-5. Significantly, gallate moiety in ECG had contributed tremendously to the disaggregation. We believed that our findings could be useful for designing prospective drug candidates targeting AD.

Effects of solvents on Li+ distribution and dynamics in PVDF/LiFSI solid polymer electrolytes: An all-atom molecular dynamics simulation study

Large-scale all-atom molecular dynamics simulations are used to investigate the structure and dynamics of a solid polymer electrolytes (SPE) model made up of polyvinylidene fluoride (PVDF) as the polymer matrix, lithium bis(fluorosulfonyl)imide salt (LiFSI), and six distinct solvent types in varying quantities. The influence of solvents on the physicochemical parameters of SPEs relevant to the Li-Battery sector is analysed. We prove that the presence of solvents containing oxygens atoms has different abilities to dissociate the LiFSI ions, form confined channels in the SPEs, and decrease the PVDF crystallinity. Besides, some solvents having a high affinity to the cations reduce the Li+ transport assembling in nano-domains, separated from the PVDF chains, when they present with a high amount, dramatically decreasing the Li+ transference number (tLi+). On the contrary, the ionic conductivity boosts preserving a good tLi+ for high dynamics solvents that form small Li+-solvent clusters. Our nanoscale investigations edify approaches for improving the ionic conductivity and controlling the arrangement of the ions in the SPE needed for proper battery operation by choosing a suitable solvent with a regulated amount.

Temperature dependence of DNA elasticity: An all-atom molecular dynamics simulation study.

We used all-atom molecular dynamics simulation to investigate the elastic properties of double-stranded DNA (dsDNA). We focused on the influences of temperature on the stretch, bend, and twist elasticities, as well as the twist-stretch coupling, of the dsDNA over a wide range of temperature. The results showed that the bending and twist persistence lengths, together with the stretch and twist moduli, decrease linearly with temperature. However, the twist-stretch coupling behaves in a positive correction and enhances as the temperature increases. The potential mechanisms of how temperature affects dsDNA elasticity and coupling were investigated by using the trajectories from atomistic simulation, in which thermal fluctuations in structural parameters were analyzed in detail. We analyzed the simulation results by comparing them with previous simulation and experimental data, which are in good agreement. The prediction about the temperature dependence of dsDNA elastic properties provides a deeper understanding of DNA elasticities in biological environments and potentially helps in the further development of DNA nanotechnology.

Targeting inhibition of microtubule affinity regulating kinase 4 by Harmaline: Strategy to combat Alzheimer's disease

Microtubule-affinity regulating kinase 4 (MARK4) is linked with the development of cancer, diabetes and neurodegenerative diseases. Due to its direct role in the hyperphosphorylation of tau protein, MARK4 is considered as an attractive target to fight Alzheimer's disease (AD) and neuroinflammation. In the present study, we have selected Harmaline (HAR), an alkaloid of Paganum harmala, to investigate its MARK4 inhibitory potential and its binding mechanism. Molecular docking and fluorescence binding studies were carried out to estimate the binding affinity of the HAR with the MARK4. We observed an excellent binding affinity of HAR to the MARK4 (K = 107 M−1), further complemented by isothermal titration calorimetric measurements. In addition, HAR significantly inhibits the kinase activity of MARK4 (IC50 value of 4.46 μM). Structural investigations suggested that HAR binds to the active site pocket and forms several non-covalent interactions with biologically important residues of MARK4. All-atom molecular dynamics simulation studies further advocated that the MARK4-HAR complex is stabilized throughout the trajectory of 200 ns and causes a little conformational change. All these findings suggest that HAR is a potential MARK4 inhibitor that can be implicated in managing MARK4-associated diseases, including AD.

Specific recognition between YTHDF3 and m6 A-modified RNA: An all-atom molecular dynamics simulation study.

The YTH domain of YTHDF3 belongs to a class of protein "readers" recognizing the N6-methyladenosine (m6 A) modification in mRNA. Although static crystal structure reveals m6 A recognition by a conserved aromatic cage, the dynamic process in recognition and importance of aromatic cage residues are not completely clear. Here, molecular dynamics (MD) simulations are performed to explore the issues and negative selectivity of YTHDF3 toward unmethylated substrate. Our results reveal that there exist conformation selectivity and induced-fit in YTHDF3 binding with m6 A-modified RNA, where recognition loop and loop6 play important roles in the specific recognition. m6 A modification enhances the stability of YTHDF3 in complex with RNA. The methyl group of m6 A, like a warhead, enters into the aromatic cage of YTHDF3, where Trp492 anchors the methyl group and constraints m6 A, making m6 A further stabilized by π-π stacking interactions from Trp438 and Trp497. In addition, the methylation enhances the hydrophobicity of adenosine, facilitating water molecules excluded out of the aromatic cage, which is another reason for the specific recognition and stronger intermolecular interaction. Finally, the comparative analyses of hydrogen bonds and binding free energy between the methylated and unmethylated complexes reveal the physical basis for the preferred recognition of m6 A-modified RNA by YTHDF3. This study sheds light on the mechanism by which YTHDF3 specifically recognizes m6 A-modified RNA and can provide important information for structure-based drug design.

Inhibition of Aβ16-22 Peptide Aggregation by Small Molecules and Their Permeation through POPC Lipid Bilayer: Insight from Molecular Dynamics Simulation Study.

Alzheimer's Disease is a rapidly progressing irreversible neurodegenerative disorder characterized by neuronal cell deterioration that endangers human health. With its proper therapeutic treatment being unavailable, several research groups throughout the world are involved in designing efficient drug molecules. However, the elusive mechanism of action of the drugs as well as their debilitating side effects pose major challenges in this regard. In the present article, we investigated the inhibitory effect of an indanone-carbamate-based molecule on Aβ16-22 peptide aggregation by employing a series of all-atom molecular dynamics simulation study. To gain explicit insights, we studied the role of inhibitor molecules on the disruption of highly arranged β-sheet of peptides by various types of analyses such as structural analysis, Cα-Cα-atom distance, residue-wise contact map, and solvent accessible surface area. The results obtained from various analyses revealed that the inhibitor molecules interacted with Aβ16-22 peptides to destabilize its arranged β-sheet conformer via hydrophobic interaction. To further comprehend the effect of inhibitors on amyloid aggregation, we also determined interaction energy, hydration number, radial distribution function, hydrogen bonding, and potential of mean forces. In addition, the permeability of the inhibitors through model POPC lipid bilayer via passive diffusion was also analyzed. Our study is noteworthy in that it elucidates the strong interaction between inhibitors and the central hydrophobic core of peptides comprising aromatic phenylalanine residues, as well as the passive translocation of inhibitors across POPC lipid bilayers.

Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes.

We present a comparative all-atom molecular dynamics simulation study of 18 biomembrane systems with lipid compositions corresponding to eukaryotic, bacterial, and archaebacterial membranes together with three single-component lipid bilayers. A total of 105 lipid types used in this study include diverse sterols and glycerol-based lipids with acyl chains of various lengths, unsaturation degrees, and branched or cyclic moieties. Our comparative analysis provides deeper insight into the influences of sterols and lipid unsaturation on the structural and mechanical properties of these biomembranes, including water permeation into the membrane hydrocarbon core. For sterol-containing membranes, sterol fraction is correlated with the membrane thickness, the area compressibility modulus, and lipid order but anticorrelated with the area per lipid and sterol tilt angles. Similarly, for all 18 biomembranes, lipid order is correlated with the membrane thickness and area compressibility modulus. Sterols and lipid unsaturation produce opposite effects on membrane thickness, but only sterols influence water permeation into the membrane. All membrane systems are accessible for public use in CHARMM-GUI Archive. They can be used as templates to expedite future modeling of realistic cell membranes with transmembrane and peripheral membrane proteins to study their structure, dynamics, molecular interactions, and function in a nativelike membrane environment.

The phase behaviour of cetyltrimethylammonium chloride surfactant aqueous solutions at high concentrations: an all-atom molecular dynamics simulation study.

We explore the phase behaviour of aqueous solutions of the cetyltrimethyl ammonium chloride (CTAC) surfactant and in particular the transition from the micellar phase (L1) to the hexagonal columnar phase (H1) by employing all-atom (AA) molecular dynamics (MD) simulations for six CTAC concentrations in the range of 34.1 wt% to 70.5 wt%, at the temperature of 318 K and pressure of 1 atm. For the concentrations considered, we examine the spontaneous occurrence of the H1 phase by testing a number of plausible values for the linear density (molecules per unit length) along the cylindrical columns. Using large simulation cells and starting from random initial configurations, the MD simulations demonstrate that the micellar phase occurs for concentrations up to 50.0 wt%, with CTAC molecules self-assembling into a mixture of spherical and rod-like micelles. At even higher concentrations, the system self-organizes into the H1 phase in accordance with the available experimental data. For the analysis of the MD trajectories, we devise a clustering algorithm based on Voronoi tesselation which enables (a) the thorough characterization of the shape and structure of both molecules and assemblies, and (b) the investigation of the positional and orientational order in the system that are further scrutinised using radial pair correlation functions and X-ray diffraction patterns. Our work paves the way for the investigation of the phase behaviour at high concentrations of other surfactants.

Structure and dynamics of spin label side chains in KvAP voltage-sensor domain: an all-atom MD simulation study

Site-directed spin labeling (SDSL) combined with continuous-wave electron paramagnetic resonance (CW-EPR) spectroscopy has become a useful approach to investigate the structural and dynamical properties of biomolecules, especially membrane protein. In this method, spin label side chains due to their motion highly depending on the local environment were employed as external molecules to probe the structure and dynamics of the membrane protein. The close relationships between the dynamics of the spin label side chain and protein structure have been studied for T4 lysozyme. Besides, molecular dynamics (MD) simulations were widely applied as a powerful tool to study the microscopic behavior of the proteins, completing experimental approaches. Here, we presented an all-atom MD simulation study of the nitroxide spin label (MTSSL) in the X-ray structure of a potassium channel voltage-sensor domain (VSD) from Aeropyrum Pernix (KvAP).

A Highly Stretchable, Real-Time Self-Healable Hydrogel Adhesive Matrix for Tissue Patches and Flexible Electronics.

The development of biocompatible self-healable hydrogel adhesives for skin or wet, stretchable surfaces in air or under water is highly desirable for various biomedical applications ranging from skin patches to bioelectronics. However, it has been proven to be very challenging because most existing hydrogel adhesives are cytotoxic, or poorly adhere to dynamic or stretchable surfaces in wet environments. In this study, multifunctional hydrogel adhesives derived from silk fibroin (SF) and tannic acid (TA) are effectively constructed with high extensibility (i.e., up to 32 000%), real-time self-healing capability, underwater adhesivity, water-sealing ability, biocompatibility, and antibiotic properties. According to all-atom molecular dynamics simulation studies, the properties of the hydrogel adhesives, especially high extensibility, are mainly attributed to the hydrogen bonds between TA and the SF chains in water, and water and TA molecules can result in loose assemblies with fewer β-sheets, and more random coils in the SF. Conductivity can also be easily introduced to the adhesive matrix and adjusted when the strain of the adhesives occurs. Considering that it has multiple functions and can be efficiently prepared, the proposed hydrogel adhesives have the potential for future medical applications, such as tissue adhesives and integrated bioelectronics.

Complexation of single stranded RNA with an ionizable lipid: an all-atom molecular dynamics simulation study

Complexation of a lipid-based ionizable cationic molecule (referred to as DML: see main text) with RNA in an aqueous medium was examined in detail by means of fully atomistic molecular dynamics simulations. The different stages of the DML-RNA association process were explored, while the structural characteristics of the final complex were described. The self-assembly process of the DML molecules was examined in the absence and in the presence of nucleotide sequences of different lengths. The formed DML clusters were described in detail in terms of their size and composition and were found to share common features in all the examined systems. Different timescales related to their self-assembly and their association with RNA were identified. It was found that beyond a time period of a few tens of ns, a conformationally stable DML-RNA complex was formed, characterized by DML clusters covering the entire contour of RNA. In a system with a 642-nucleotide sequence, the average size of the complex in the longest dimension was found to be close to 40 nm. The DML clusters were characterized by a rather low surface charge, while a propensity for the formation of larger size clusters close to RNA was noted. Apart from hydrophobic and electrostatic interactions, hydrogen bonding was found to play a key-role in the DML-DML and in the DML-RNA association. The information obtained regarding the structural features of the final complex, the timescales and the driving forces associated with the complexation and the self-assembly processes provide new insight towards a rational design of optimized lipid-based ionizable cationic gene delivery vectors.

Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study.

The major applications of carbon dots (CDs) (e.g. bio-imaging and targeted drug delivery) necessitate the latter to permeate across the lipid bilayer membrane. Unfortunately, the mechanism of permeation is poorly understood. Between the two possible routes for permeation of a nanoparticle like CDs-an endocytic pathway and direct passive permeation-the endocytic path is known to be more common, despite the fact that the passive permeation is preferred over the endocytosis for targeted drug delivery. Here, we have focused on the direct permeation of a hydroxyl functionalized CD across the POPC lipid bilayer membrane using all-atom MD simulations. We have estimated the free energy profile for the translocation of the CD across the lipid bilayer, with a barrier height of ∼170 kJ mol-1 situated at the lipid bilayer center (z = 0 nm). Using the free energy profile, we have calculated a negligible permeability coefficient value, which strongly suggests that it is almost impossible for a CD to penetrate directly across the lipid bilayer. The possible impact on the lipid bilayer structure by the CD is also investigated. Although the CD does not affect the bilayer structure up to a certain degree of penetration, the impact increases substantially when entered into the bilayer interior.

Azadirachtin inhibits amyloid formation, disaggregates pre-formed fibrils and protects pancreatic β-cells from human islet amyloid polypeptide/amylin-induced cytotoxicity.

The human islet amyloid polypeptide (hIAPP) or amylin is the major constituent of amyloidogenic aggregates found in pancreatic islets of type 2 diabetic patients that have been associated with β-cell dysfunction and/or death associated with type 2 diabetes mellitus (T2DM). Therefore, developing and/or identifying inhibitors of hIAPP aggregation pathway and/or compound that can mediate disaggregation of preformed aggregates holds promise as a medical intervention for T2DM management. In the current study, the anti-amyloidogenic potential of Azadirachtin (AZD)-a secondary metabolite isolated from traditional medicinal plant Neem (Azadirachta indica)-was investigated by using a combination of biophysical and cellular assays. Our results indicate that AZD supplementation not only inhibits hIAPP aggregation but also disaggregates pre-existing hIAPP fibrils by forming amorphous aggregates that are non-toxic to pancreatic β-cells. Furthermore, AZD supplementation in pancreatic β-cells (INS-1E) resulted in inhibition of oxidative stress; along with restoration of the DNA damage, lipid peroxidation and the associated membrane damage, endoplasmic reticulum stress and mitochondrial membrane potential. AZD treatment also restored glucose-stimulated insulin secretion from pancreatic islets exposed to hIAPP. All-atom molecular dynamics simulation studies on full-length hIAPP pentamer with AZD suggested that AZD interacted with four possible binding sites in the amyloidogenic region of hIAPP. In summary, our results suggest AZD to be a promising candidate for combating T2DM and related amyloidogenic disorders.

Influence of Hydration on the Structure of Reline Deep Eutectic Solvent: A Molecular Dynamics Study.

In this article, we have performed an all-atom molecular dynamics simulation study to investigate the influence of water on the molecular level arrangement of reline deep eutectic solvent for different hydration levels ranging from 3.4 to 58.1 wt % of water and complemented the observations of recently measured neutron scattering experimental data. This study is particularly important because water is being introduced as a second hydrogen bond donor/acceptor in reline, wherein the structure is primarily governed by hydrogen bonding and electrostatic interactions. We have analyzed the simulated X-ray scattering structure functions, their partial components, and hydrogen bonding interactions to understand the effects of water on various intermolecular interactions in reline–water mixtures. It is observed that at lower hydration level, reline structure is qualitatively retained. At higher hydration level, most water molecules preferentially solvate chloride anions and ammonium group of choline cations mostly impacting choline–choline, choline–chloride, and chloride–chloride interactions. The present study reveals that at and above 41 wt % of water, the molecular arrangement of reline drastically changes and set to transition from reline to an aqueous solution of reline components with further increase in the hydration level. Hydrogen bond analysis reveals the presence of strong chloride–water H-bonding interaction, which gradually replaces choline–chloride and urea–chloride hydrogen bondings as the hydration level in the mixture increases.

Effect of Fluorination on Friction Forces between Concentrated Polymer Brushes in the Dry State: All-atom Molecular Dynamics Simulation Study

We investigated the effect of fluorination on friction forces between polymer brushes in the dry state by means of an all-atom molecular dynamics simulation. An all-fluorinated brush produced less friction force than a non-fluorinated brush. In addition, a brush in which only the six monomers at the tips of the polymers were fluorinated produced a friction force comparable with that produced by the all-fluorinated brush. Fluorination was found to reduce the friction force by reducing entanglement between the brushes.

Microscopic Structure of Solvated Poly(benzyl methacrylate) in an Imidazolium-Based Ionic Liquid: High-Energy X-ray Total Scattering and All-Atom MD Simulation Study

We report a new approach for investigating polymer structures in solution systems, including polymer–solvent interactions at the molecular level. The solvation structure of poly(benzyl methacrylate) (PBnMA) in an imidazolium-based ionic liquid (IL) has been investigated at the molecular level using high-energy X-ray total scattering (HEXTS) with the aid of all-atom molecular dynamics (MD) simulations. The X-ray radial distribution functions derived from both experimental HEXTS and theoretical MD (Gexp(r) and GMD(r), respectively) were in good agreement in the present PBnMA/IL system. The G(r) functions were successfully separated into two components for the inter- and intramolecular contributions. Here, the former corresponds to polymer solvation (or polymer–solvent interactions) and the latter to polymer structure, such as conformation and interactions between side chains (benzyl groups) in PBnMA. The intermolecular GMDinter(r) revealed that the side chains are preferentially solvated by imidazolium cati...

Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study.

Like-charge ion-pair formation in an aqueous solution of guanidinium chloride (GdmCl) has two important facets. On one hand, it describes the role of the arginine (ARG) side chain in aggregation and dimer formation in proteins, and on the other hand, it lends support for the direct mechanism of protein denaturation by GdmCl. We employ all-atom molecular dynamics simulations to investigate the effect of GdmCl concentration on the like-charge ion-pair formation of guanidinium ions (Gdm(+)). From analyses of the radial distribution function (RDF) between the carbon atoms of two guanidinium moieties, the existence of both contact pairs and solvent-separated pairs has been observed. Although the peak height corresponding to the contact-pair state decreases, the number of Gdm(+) ions in the contact-pair state actually increases with increasing GdmCl concentration. We have also investigated the effect of the concentration of Gdm(+) on the structure of water. The effect of GdmCl concentration on the radial and tetrahedral structures of water is found to be negligibly small; however, GdmCl concentration has a considerable effect on the hydrogen-bonding structure of water. It is demonstrated that the presence of chloride ions, not Gdm(+), in the first solvation shell of water causes the distortion in the hydrogen-bonding network of water. In order to establish that Gdm(+) not only stacks against another Gdm(+) but also directly attacks the ARG residue of a protein or peptide, simulation of an ARG-rich peptide in 6 M aqueous solution of GdmCl has been performed. The analyses of RDFs and orientation distributions reveal that the Gdm(+) moiety of the GdmCl attacks the same moiety in the ARG side chain with a parallel stacking orientation.

Effect of surfactant SDS on DMSO transport across water/hexane interface by molecular dynamics simulation

Solute transport behavior across liquid–liquid interfaces plays important roles in many chemical engineering processes and usually occurs in the presence of surfactants. In this work, we report a full all-atom molecular dynamics simulation study of dimethyl sulfoxide (DMSO) crossing a water/hexane interface in different concentrations of sodium dodecylsulfate (SDS). By analyzing various properties, ranging from the configuration and energetic behaviors to the dynamic characteristics, we conclude that the presence of SDS has multiple non-trivial effects: (1) the association of SDS at the interface drives the interfacial region wider and decreases the interfacial tension with an almost linear dependence on SDS concentration; (2) higher SDS concentrations result in both a lower self-diffusion coefficient for DMSO and a smaller resistance force to DMSO moving out of the interfacial region, causing the exchange of DMSO between the interface and bulk region to become more frequent; and (3) the transition of the orientation preference of DMSO molecules passing from the interface to the water-rich phase vanishes. Current simulation studies examining the molecular level provide helpful insights for understanding the influence of surfactants on solute transport.

Fast fluctuations in deep eutectic melts: Multi-probe fluorescence measurements and all-atom molecular dynamics simulation study

Larger excitation wavelength dependence of fluorescence emission of chromophores with shorter lifetime suggests fast environmental fluctuations in (CH3CONH2+LiBr/NO3) deep eutectics. Stronger fractional viscosity dependence for rotation of a short-lifetime probe has been observed and ascribed to stronger sensitivity to these fast fluctuations. All-atom molecular dynamics simulations reveal stretched exponential relaxation for the wavenumber dependent incoherent and coherent scattering functions for acetamide with dominating sub-hundred picosecond and sub-nanosecond timescales. These simulated results provide support to the experimentally observed different fractional viscosity dependence of rotation rates for probes with different lifetimes, and stronger decoupling for short-lifetime probes in these melts.

Conformational Determinants for the Recruitment of ERCC1 by XPA in the Nucleotide Excision Repair (NER) Pathway: Structure and Dynamics of the XPA Binding Motif

XPA is an essential protein in the nucleotide excision repair (NER) pathway, in charge of recruiting the ERCC1-XPF endonuclease complex to the DNA damage site. The only currently available structural insight into the binding of XPA to ERCC1 derives from the solution NMR structure of a complex between the ERCC1 central fragment and a 14-residue peptide, corresponding to the highly conserved binding motif of the XPA N-terminus, XPA67-80. The extensive all-atom molecular-dynamics simulation study of the XPA67-80 peptide both bound to the ERCC1 central fragment and free in solution presented here completes the profile of the structural determinants responsible for the ERCC1/XPA67-80 complex stability. In addition to the wild-type, this study also looks at specific XPA67-80 mutants in complex with the ERCC1 central domain and thus contributes to defining the conformational determinants for binding, as well as all of the essential structural elements necessary for the rational design of an XPA-based, ERCC1-specific inhibitor.