Full-atom Molecular Dynamics Simulations Research Articles

Atomistic mechanism of coupling between cytosolic sensor domain and selectivity filter in TREK K2P channels

The two-pore domain potassium (K2P) channels TREK-1 and TREK-2 link neuronal excitability to a variety of stimuli including mechanical force, lipids, temperature and phosphorylation. This regulation involves the C-terminus as a polymodal stimulus sensor and the selectivity filter (SF) as channel gate. Using crystallographic up- and down-state structures of TREK-2 as a template for full atomistic molecular dynamics (MD) simulations, we reveal that the SF in down-state undergoes inactivation via conformational changes, while the up-state structure maintains a stable and conductive SF. This suggests an atomistic mechanism for the low channel activity previously assigned to the down state, but not evident from the crystal structure. Furthermore, experimentally by using (de-)phosphorylation mimics and chemically attaching lipid tethers to the proximal C-terminus (pCt), we confirm the hypothesis that moving the pCt towards the membrane induces the up-state. Based on MD simulations, we propose two gating pathways by which movement of the pCt controls the stability (i.e., conductivity) of the filter gate. Together, these findings provide atomistic insights into the SF gating mechanism and the physiological regulation of TREK channels by phosphorylation.

Two-Stage Dynamic Transformation from δ- to α-CsPbI3.

The phase transformation from δ- to α-CsPbI3has garnered extensive research interest. However, detailed understanding of this structural transformation at atomistic scale remains elusive. Here, we reported the full atomistic molecular dynamics simulation of this important phase transformation using an enhanced sampling method, Metadynamics (MetaD). Particularly, two-stage of dynamic transformation related to [PbI3]- chains' motions was observed, namely, the intrachain rearrangement followed by interchain connection. Moreover, the dynamic motion of Cs+ cations plays an important role in facilitating the interchain connection kinetically. The insights reported in this work will provide valuable guidance for further advancing the understanding of phase transformation of CsPbI3.

Computational evidences of a misfolding event in an aggregation-prone light chain preceding the formation of the non-native pathogenic dimer.

Antibody light chain amyloidosis is a disorder in which protein aggregates, mainly composed of immunoglobulin light chains, deposit in diverse tissues impairing the correct functioning of organs. Interestingly, due to the high susceptibility of antibodies to mutations, AL amyloidosis appears to be strongly patient-specific. Indeed, every patient will display their own mutations that will make the proteins involved prone to aggregation thus hindering the study of this disease on a wide scale. In this framework, determining the molecular mechanisms that drive the aggregation could pave the way to the development of patient-specific therapeutics. Here, we focus on a particular patient-derived light chain, which has been experimentally characterized. We investigated the early phases of the aggregation pathway through extensive full-atom molecular dynamics simulations, highlighting a structural rearrangement and the exposure of two hydrophobic regions in the aggregation-prone species. Next, we moved to consider the pathological dimerization process through docking and molecular dynamics simulations, proposing a dimeric structure as a candidate pathological first assembly. Overall, our results shed light on the first phases of the aggregation pathway for a light chain at an atomic level detail, offering new structural insights into the corresponding aggregation process.

Integration of Lipid-Functionalized Epigallocatechin-3-gallate into PLGA Matrix as a Novel Polyphenol-Based Nanoantioxidant.

The search for polyphenol-based materials with antioxidant activity is a growing research area in the biomedical field. To obtain an efficient and stable nanoantioxidant, a novel biosystem was designed by integrating a lipophilic derivative of epigallocatechin-3-gallate (named EGCG-C18) on the surface of poly(lactic-co-glycolic acid) (PLGA). Poly(vinyl alcohol) (PVA) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-poly(ethylene glycol) (DSPE-PEG2000) were selected as polymeric and lipidic stabilizers, respectively, and their influence on both physical properties and the antioxidant activity of nanoantioxidant was investigated by a combined in silico and experimental approach. Full-atom molecular dynamics (MD) simulations were carried out to describe the different self-assembly processes of all components and the interactions that guided the EGCG-C18 insertion inside the PLGA matrix. Together with infrared spectroscopy results, the formation of an antioxidant lipid shell on the PLGA surface was clear. Dynamic light scattering and transmission electron microscopy showed that in the presence of DSPE-PEG2000, NPs were smaller than those treated with PVA. In addition, the different stabilizers used strongly influenced the ROS-scavenging ability of nanomaterials and this effect was strictly related to the molecular organization of EGCG-C18. MD showed that the apolar interaction between the alkyl chains of DSPE-PEG2000 and EGCG-C18 oriented the phenolic groups of the polyphenol toward the solvent, providing an ability of NP to scavenge hydroxyl radicals over to free EGCG-C18 and PLGA/PVA NPs. Finally, the ability of nanoantioxidants to protect human dermal fibroblasts from cell death induced by oxidative stress has been tested, revealing the high potential of these novel NPs as polyphenol-based materials.

Construction of full-atomistic polymer amorphous structures using reverse-mapping from Kremer-Grest models.

We propose a method to build full-atomistic (FA) amorphous polymer structures using reverse-mapping from coarse-grained (CG) models. In this method, three models with different resolutions are utilized, namely the CG1, CG2, and FA models. It is assumed that the CG1 model is more abstract than the CG2 model. The CG1 is utilized to equilibrate the system, and then sequential reverse-mapping procedures from the CG1 to the CG2 models and from the CG2 to the FA models are conducted. A mapping relation between the CG1 and the FA models is necessary to generate a polymer structure with a given density and radius of chains. Actually, we have used the Kremer-Grest (KG) model as the CG1 and the monomer-level CG model as the CG2 model. Utilizing the mapping relation, we have developed a scheme that constructs an FA polymer model from the KG model. In the scheme, the KG model, the monomer level CG model, and the FA model are successively constructed. The scheme is applied to polyethylene (PE), cis 1,4-polybutadiene (PB), and poly(methyl methacrylate) (PMMA). As a validation, the structures of PE and PB constructed by the scheme were carefully checked through comparison with those obtained using long-time FA molecular dynamics (MD) simulations. We found that both short- and long-range chain structures constructed by the scheme reproduced those obtained by the FA MD simulations. Then, as an interesting application, the scheme is applied to generate an entangled PMMA structure. The results showed that the scheme provides an efficient and easy way to construct amorphous structures of FA polymers.

Molecular dynamics simulation of poly-m-phenylene isophthalamide polymer membrane modified by UiO-66 (NH2) MOF for separation of toluene/methanol mixture

Pervaporation is the purification technology which utilizes the transport properties of polymer membranes and has several important properties: energy efficiency, environmental friendliness, and a high degree of purification. To improve the transport properties, polymer membranes are modified with special nanoparticles. In this work we study the translational mobility of methanol and toluene molecules inside a poly-m-phenylene isophthalamide membrane with and without the nanoparticle of UiO-66 (NH2) metal-organic framework (UiO-66 (NH2) MOF) using full atomistic molecular dynamics simulation with microsecond trajectories. It was found that methanol has a high translational mobility inside the polymer matrix. Moreover, this mobility is significantly increased by addition of UiO-66 (NH2) MOF. Toluene molecules are practically immobile inside the polymer matrix and tend to form clusters with each other. Due to the inclusion of a nanoparticle, toluene molecules “get stuck” inside UiO-66 (NH2) MOF and its surface. We believe that the obtained results will contribute to the purposeful development and study of polymer matrices for the pervaporation process.

Atomistic simulations suggest dietary flavonoids from Beta vulgaris (beet) as promising inhibitors of human angiotensin-converting enzyme and 2-alpha-adrenergic receptors in hypertension.

Beta vulgaris (beet) is extensively reported for its antihypertensive activity. However, the mechanismunderpinning its antihypertensive activity is not well understood. In this study, we evaluated the in silico interactionsof 70 compounds derived from beta vulgaris against the active sites of angiotensin-converting enzyme (ACE) and alpha-adrenergic receptor (AR). Structure-based virtual screening against angiotensin-converting enzyme revealed that, Cochliophilin A (-9.0Kcal/mol), Miraxanthin (-8.3Kcal/mol), and quercimeritrin (-9.7Kcal/mol) had lower docking scores than the reference lisinopril (-7.9Kcal/mol). These compounds exhibited dual binding tendency as they also ranked top compounds upon screening against adrenergic receptor. The thermodynamic parameters computed from the resulting trajectories obtained from the 100 ns full atomistic molecular dynamics simulation revealed structural stability and conformational flexibility of the ligand-receptor complexes as indicated by the RMSD, RMSF, RoG, SASA, and H-bond calculations. The molecular mechanics with generalized Born and surface area solvation binding energy calculations revealed that the proteins exhibit considerable binding energy with the phytochemicals in a dynamic environment. Furthermore, the hit compounds possess good physicochemical properties and drug-likeness. Overall, cochliophilin and quercimeritrin are promising dual-target directed flavonoids from Beta vulgaris; and are suggested for further experimental and preclinical evaluation. All data was provided in the manuscript.

Electro-detachment of kinesin motor domain from microtubule in silico

Kinesin is a motor protein essential in cellular functions, such as intracellular transport and cell-division, as well as for enabling nanoscopic transport in bio-nanotechnology. Therefore, for effective control of function for nanotechnological applications, it is important to be able to modify the function of kinesin. To circumvent the limitations of chemical modifications, here we identify another potential approach for kinesin control: the use of electric forces. Using full-atom molecular dynamics simulations (247,358 atoms, total time ∼ 4.4 μs), we demonstrate, for the first time, that the kinesin-1 motor domain can be detached from a microtubule by an intense electric field within the nanosecond timescale. We show that this effect is field-direction dependent and field-strength dependent. A detailed analysis of the electric forces and the work carried out by electric field acting on the microtubule–kinesin system shows that it is the combined action of the electric field pulling on the β-tubulin C-terminus and the electric-field-induced torque on the kinesin dipole moment that causes kinesin detachment from the microtubule. It is shown, for the first time in a mechanistic manner, that an electric field can dramatically affect molecular interactions in a heterologous functional protein assembly. Our results contribute to understanding of electromagnetic field–biomatter interactions on a molecular level, with potential biomedical and bio-nanotechnological applications for harnessing control of protein nanomotors.

Antioxidant and Neuroprotective Effects of the First Tryptophyllin Found in Snake Venom (Bothrops moojeni)

In this study, we report the isolation, characterization, and synthesis of the peptide BmT-2 belonging to the tryptophyllins family, isolated from the venom of the snake Bothrops moojeni. This is the first time a tryptophyllin is identified in snake venom. We tested whether BmT-2 had cytotoxic effects and antioxidant activity in a set of experiments that included both in vitro and cell-based assays. BmT-2 presented a radical scavenging activity toward ABTS• and AAPH-derived radicals. BmT-2 protected fluorescein, DNA molecules, and human red blood cells (RBCs) from free radicals generated by the thermal decomposition of AAPH. The novel tryptophyllin was not toxic in cell viability tests, where it (up to 0.4 mg/mL) did not cause hemolysis of human RBCs and did not cause significant loss of cell viability, showing a CC50 > 1.5 mM for cytotoxic effects against SK-N-BE(2) neuroblastoma cells. BmT-2 prevented the arsenite-induced upregulation of Nrf2 in Neuro-2a neuroblasts and the phorbol myristate acetate-induced overgeneration of reactive oxygen species and reactive nitrogen species in SK-N-BE(2) neuroblastoma cells. Electronic structure calculations and full atomistic reactive molecular dynamics simulations revealed the relevant contribution of aromatic residues in BmT-2 to its antioxidant properties. Our study presents a novel peptide classified into the family of the tryptophyllins, which has been reported exclusively in amphibians. Despite the promising results on its antioxidant activity and low cytotoxicity, the mechanisms of action of BmT-2 still need to be further elucidated.

Suspended water nanodroplets evaporation and its deviation from continuum estimations

Although droplets evaporation is fundamental to many applications and phenomena, accurate prediction of their evaporation trajectory is still a technological gap today. This is even more so for nanodroplets when compared to the macro-sized droplets. Since it is technically challenging to observe real nanodroplets evaporation today, this contribution uses full atomistic molecular dynamics simulations to observe and quantify suspended water nanodroplets evaporation. There are two main findings to this contribution. First, it is shown in detail that continuum analysis significantly over predicts the evaporation rate of nanodroplets. This makes continuum analysis unsuitable to predict water nanodroplets’ behavior. Secondly, this contribution illustrates the use of data-driven approach that can be used for nanodroplets evaporation behavior prediction, instead of running full atomistic molecular dynamics simulations for every different condition, which can be prohibitively expensive. The paper hopes to encourage scientists working in similar field to share their MD results for nanodroplets evaporation to build a data-driven model that could be used to predict nanodroplets evaporation trajectory at a fraction of the cost of full-scale MD simulations.

Structure and stability of polydiacetylene membrane systems: Molecular dynamics simulation studies

We have performed full atomistic molecular dynamics (MD) simulations to investigate structure and stability of bilayer membrane systems consisting of monomeric or polymeric 10,12-pentacosadiynoic acid (PCDA) units connected with lysine groups by amide bonds. The PCDA monomer molecules show a twisted three-rod-domain structure with two kinks but upon polymerization, they possess more elongated conformation. The resulting polydiacetylene (PDA) membrane systems have stable membrane structures at room temperature, which is similar to biological lipid bilayer membranes and maintain their gel-like membrane integrity even up to as high as 370 K. Structural properties such as area per monomer, membrane thickness, density profile, 2D pair distribution function, and orientational correlation function are also calculated to understand the membrane structure and check its stability upon thermal fluctuation with atomistic resolution. This study is expected to provide the understanding about PDA membrane systems in atomistic details as well as significant insights into designing new novel PDA sensors.

Evaluation of Microscopic Damage of PEEK Polymers under Cyclic Loadings Using Molecular Dynamics Simulations.

Full-atomic molecular dynamics simulations were conducted to investigate the time evolution of microscopic damage in polyetheretherketone (PEEK) polymers under cyclic loading conditions. Three characteristics were used to quantify microscopic damage: entropy, distribution of the end-to-end distance of polymers, and the volume fraction of voids. Our results show that the degree of disentanglement of polymers and the volume fraction of voids increase with cyclic loading, which may lead to entropy generation. Uniaxial tensile strength simulations of the polymer system before and after cyclic loading were performed. The tensile strength after cyclic loading was lower than that before loading. Furthermore, two systems with the same entropy and different loading histories showed almost the same strength. These results imply that entropy generation is expressed as the total microscopic damage and can potentially be employed for effective evaluation of the degradation of material characteristics.

Insights into Hepatitis C Virus E2core Interactions with Human Cellular Receptor CD81 at Different pHs from Molecular Simulations.

Hepatitis C virus (HCV) is the second viral agent that causes the majority of chronic hepatic infections worldwide, following Hepatitis B virus (HBV) infection. HCV infection comprises several steps, from the attachment to the receptors to the delivery of the viral genetic material and replication inside the cells. Tetraspanin CD81 is a key entry factor for HCV as it accompanies the virus during attachment and internalization through clathrin-mediated endocytosis. HCV-CD81 binding takes place through the viral glycoprotein E2. We performed full-atom molecular dynamics simulations reproducing the pH conditions that occur during the viral attachment to the hepatocytes (pH 7.4) and internalization (pH 6.2-4.6). We observed that changing the pH from 7.4 to 6.2 triggers a large conformational change in the binding orientation between E2core (E2core corresponds to residues 412-645 of the viral glycoprotein E2) and CD81LEL (CD81LEL corresponds to residues 112-204 of CD81) that occurs even more rapidly at low pH 4.6. This pH-induced switching mechanism has never been observed before and could allow the virus particles to sense the right moment during the maturation of the endosome to start fusion.

Phase Transition between Crystalline Variants of Ordinary Ice.

Water is one of the most abundant molecules on Earth. However, this common and "simple" material has more than 18 different phases, which poses a great challenge to theoretically study the nature of water and ice. We designed two reaction coordinates that can distinguish between water and various ice states and used them to efficiently sample all possible states of the system in all-atom molecular dynamics simulation at ambient temperature and pressure. Various structural and thermodynamics properties, including the water-ice phase diagrams, can thus be calculated. We also present a simple model that successfully explains the thermodynamic stability of different ice states. Our work provides effective methods and data for theoretical studies of different phases of water and ice.

Molecular basis of the anchoring and stabilization of human islet amyloid polypeptide in lipid hydroperoxidized bilayers

The molecular structure of membrane lipids is formed by mono- or polyunsaturations on their aliphatic tails that make them susceptible to oxidation, facilitating the incorporation of hydroperoxide (R-OOH) functional groups. Such groups promote changes in both composition and complexity of the membrane significantly modifying its physicochemical properties. Human Langerhans islets amyloid polypeptide (hIAPP) is the main component of amyloid deposits found in the pancreas of patients with type-2 diabetes (T2D). hIAPP in the presence of membranes with oxidized lipid species accelerates the formation of amyloid fibrils or the formation of intermediate oligomeric structures. However, the molecular bases at the initial stage of the anchoring and stabilization of the hIAPP in a hydroperoxidized membrane are not yet well understood. To shed some light on this matter, in this contribution, three bilayer models were modeled: neutral (POPC), anionic (POPS), and oxidized (POPCOOH), and full atom Molecular Dynamics (MD) simulations were performed. Our results show that the POPCOOH bilayer increases the helicity in hIAPP when compared to POPC or POPS bilayer. The modification in the secondary structure covers the residues of the so-called amyloidogenic core of the hIAPP. Overall, the hydroperoxidation of the neutral lipids modifies both the anchoring and the stabilization of the peptide hIAPP by reducing the random conformations of the peptide and increasing of hydrogen bond population with the hydroperoxidized lipids.

Modified Poisson-Boltzmann theory for polyelectrolytes in monovalent salt solutions with finite-size ions.

We present a soft-potential-enhanced Poisson-Boltzmann (SPB) theory to efficiently capture ion distributions and electrostatic potential around rodlike charged macromolecules. The SPB model is calibrated with a coarse-grained particle-based model for polyelectrolytes (PEs) in monovalent salt solutions as well as compared to a full atomistic molecular dynamics simulation with the explicit solvent. We demonstrate that our modification enables the SPB theory to accurately predict monovalent ion distributions around a rodlike PE in a wide range of ion and charge distribution conditions in the weak-coupling regime. These include excess salt concentrations up to 1M and ion sizes ranging from small ions, such as Na+ or Cl-, to softer and larger ions with a size comparable to the PE diameter. The work provides a simple way to implement an enhancement that effectively captures the influence of ion size and species into the PB theory in the context of PEs in aqueous salt solutions.

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.

Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive full atomic molecular dynamics (MD) simulations with the goal of rapidly sampling large and cooperative conformational changes at full atomic resolution. We present here a systematic comparison of the utility and limits of four such hybrid methods that have been introduced in recent years: MD with excited normal modes (MDeNM), collective modes-driven MD (CoMD), and elastic network model (ENM)-based generation, clustering, and relaxation of conformations (ClustENM) as well as its updated version integrated with MD simulations (ClustENMD). We analyzed the predicted conformational spaces using each of these four hybrid methods, applied to four well-studied proteins, triosephosphate isomerase (TIM), 3-phosphoglycerate kinase (PGK), HIV-1 protease (PR) and HIV-1 reverse transcriptase (RT), which provide extensive ensembles of experimental structures for benchmarking and comparing the methods. We show that a rigorous multi-faceted comparison and multiple metrics are necessary to properly assess the differences between conformational ensembles and provide an optimal protocol for achieving good agreement with experimental data. While all four hybrid methods perform well in general, being especially useful as computationally efficient methods that retain atomic resolution, the systematic analysis of the same systems by these four hybrid methods highlights the strengths and limitations of the methods and provides guidance for parameters and protocols to be adopted in future studies.

Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon: A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study.

Intrinsically disordered proteins (IDPs) are proteins that, in comparison with globular/structured proteins, lack a distinct tertiary structure. Here, we use the model IDP, Histatin 5, for studying its dynamical properties under self-crowding conditions with quasi-elastic neutron scattering in combination with full atomistic molecular dynamics (MD) simulations. The aim is to determine the effects of crowding on the center-of-mass diffusion as well as the internal diffusive behavior. The diffusion was found to decrease significantly, which we hypothesize can be attributed to some degree of aggregation at higher protein concentrations, (≥100 mg/mL), as indicated by recent small-angle X-ray scattering studies. Temperature effects are also considered and found to, largely, follow Stokes–Einstein behavior. Simple geometric considerations fail to accurately predict the rates of diffusion, while simulations show semiquantitative agreement with experiments, dependent on assumptions of the ratio between translational and rotational diffusion. A scaling law that previously was found to successfully describe the behavior of globular proteins was found to be inadequate for the IDP, Histatin 5. Analysis of the MD simulations show that the width of the distribution with respect to diffusion is not a simplistic mirroring of the distribution of radius of gyration, hence, displaying the particular features of IDPs that need to be accounted for.

Mesoporous silica@chitosan@gold nanoparticles as “on/off” optical biosensor and pH-sensitive theranostic platform against cancer

A cancer nanotheranostic system was fabricated based on mesoporous silica@chitosan@gold (MCM@CS@Au) nanosystem targeted by aptamer toward the MUC-1 positive tumor cells. Subsequently, curcumin as an efficient herbal anticancer drug was first encapsulated into chitosan-triphosphate nanoparticles and then the resulted nanoparticle was loaded into the nanosystem (MCM@CS@Au-Apt). The nanosystem successful fabrication was approved at each synthesis step through FTIR, XRD, BET, DLS, FE-SEM, HRTEM, and fluorescence spectroscopy. Besides, the interaction between aptamer and curcumin was evaluated using full atomistic molecular dynamics simulations. The mechanism of curcumin release was likewise investigated through different kinetic models. Afterwards, the potential of the designed nanosystem in targeted imaging, and drug delivery was evaluated using fluorescence microscopy and flow cytometry. It was found that the energy transfer between the base pairs in the hairpin of double strands of DNA aptamer acts as a quencher for MCM@CS@Au fluorescence culminating in an “on/off” optical biosensor. On the other hand, the presence of pH-sensitive chitosan nanoparticles creates smart nanosystem to deliver more curcumin into the desired cells. Indeed, when the aptamer specifically binds to the MUC-1 receptor, its double strands separate under the low pH condition, leading to the drug release and the recovery of the fluorescence (“On” state). Based on the toxicity results, this nanosystem had more toxicity toward the MUC-1-positive tumor cells than MUC-1-negative cells, representing its selective targeting. Therefore, this nanosystem could be introduced as a smart anticancer nanotheranostic system for tracing particular biomarkers (MUC-1), non-invasive fluorescence imaging, and targeted curcumin delivery.

Kinetics of the interfacial curing reaction for an epoxy-amine mixture.

A better understanding of the chemical reaction between epoxy and amine compounds at a solid interface is crucial for the design and fabrication of materials with appropriate adhesive strength. Here, we examined the curing reaction kinetics of epoxy phenol novolac and 4,4'-diaminodiphenyl sulfone at the outermost interface using sum-frequency generation spectroscopy, and X-ray and neutron reflectivity in conjunction with a full atomistic molecular dynamics simulation. The reaction rate constant was much larger at the quartz interface than in the bulk. While the apparent activation energy at the quartz interface obtained from an Arrhenius plot was almost identical to the bulk value, the frequency factor at the quartz interface was greater than that in the bulk. These results could be explained in terms of the densification and orientation of reactants at the interface, facilitating the encounter of the reactants present.