Multiscale Molecular Dynamics Simulations Research Articles

Proton movement and coupling in the POT family of peptide transporters

POT transporters represent an evolutionarily well-conserved family of proton-coupled transport systems in biology. An unusual feature of the family is their ability to couple the transport of chemically diverse ligands to an inwardly directed proton electrochemical gradient. For example, in mammals, fungi, and bacteria they are predominantly peptide transporters, whereas in plants the family has diverged to recognize nitrate, plant defense compounds, and hormones. Although recent structural and biochemical studies have identified conserved sites of proton binding, the mechanism through which transport is coupled to proton movement remains enigmatic. Here we show that different POT transporters operate through distinct proton-coupled mechanisms through changes in the extracellular gate. A high-resolution crystal structure reveals the presence of ordered water molecules within the peptide binding site. Multiscale molecular dynamics simulations confirm proton transport occurs through these waters via Grotthuss shuttling and reveal that proton binding to the extracellular side of the transporter facilitates a reorientation from an inward- to outward-facing state. Together these results demonstrate that within the POT family multiple mechanisms of proton coupling have likely evolved in conjunction with variation of the extracellular gate.

Dynamics of OmpF Trimer Formation in the Bacterial Outer Membrane of Escherichia coli.

The self-assembly of outer membrane protein F (OmpF) in the outer membrane of Escherichia coli Gram-negative bacteria was studied using multiscale molecular dynamics simulations. To accommodate the long time scale required for protein assembly, coarse-grained parametrization of E. coli outer membrane lipids was first developed. The OmpF monomers formed stable dimers at specific protein-protein interactions sites irrespective of the lipid membrane environment. The dimer intermediate was asymmetric but provided a template to form a symmetric trimer. Superposition analysis of the self-assembled trimer with the X-ray crystal structure of the trimer available in the protein data bank showed excellent agreement with global root-mean-square deviation of less than 2.2 Å. The free energy change associated with dimer formation was -26 ± 1 kcal mol-1, and for a dimer to bind to a monomer and to form a trimer yielded -56 ± 4 kcal mol-1. Based on thermodynamic data, an alternate path to trimer formation via interaction of two dimers is also presented.

Hybrid molecular dynamics–finite element simulations of the elastic behavior of polycrystalline graphene

In this paper, we develop an efficient multiscale molecular dynamics (MD)–finite element (FE) modeling scheme capable of determining the elastic and fracture properties of polycrystalline graphene. The local elastic properties of a grain boundary (GB) connecting two adjacent graphene grains, with different lattice orientations, were first determined using MD simulations. In a two-dimensional medium, randomly distributed grains connected with GBs were then created using the Voronoi tessellation method. The constructed Voronoi diagrams were used to create FE models of the polycrystalline graphene, where the GBs were represented by interphase regions with their local properties determined using MD. The grains were modeled as pristine graphene and the accuracy of the polycrystalline FE model was validated with MD simulations of a geometrically identical polycrystalline graphene. The results reveal good agreement between MD and FE simulations. They further show that the elastic and fracture properties of polycrystalline graphene are greatly influenced by the grain size and the misorientation angle. They also indicate that the predicted elastic properties are in agreement with earlier reported experimental and MD results. We believe that this newly proposed multiscale scheme could be easily integrated into current design software to model graphene based nano- and micro-devices.

Strong attractions and repulsions mediated by monovalent salts

Controlling interactions between proteins and nanoparticles in electrolyte solutions is crucial for advancing biological sciences and biotechnology. The assembly of charged nanoparticles (NPs) and proteins in aqueous solutions can be directed by modifying the salt concentration. High concentrations of monovalent salt can induce the solubilization or crystallization of NPs and proteins. By using a multiscale coarse-grained molecular dynamics approach, we show that, due to ionic correlations in the electrolyte, NPs pairs at high monovalent salt concentrations interact via remarkably strong long-range attractions or repulsions, which can be split into three regimes depending on the surface charge densities of the NPs. NPs with zero-to-low surface charge densities interact via a long-range attraction that is stronger and has a similar range to the depletion attraction induced by polymers with radius of gyrations comparable to the NP diameter. On the other hand, moderately charged NPs with smooth surfaces as well as DNA-functionalized NPs with no possibility of hybridization between them interact via a strong repulsion of range and strength larger than the repulsion predicted by models that neglect ionic correlations, including the Derjaguin-Landau-Vervey-Overbeek (DLVO) model. Interactions between strongly charged NPs (>2 e/nm2), both types smooth and DNA-functionalized NPs, show an attractive potential well at intermediate-to-high salt concentrations, which demonstrates that electrolytes can induce aggregation of strongly charged NPs. Our work provides an improved understanding of the role of ionic correlations in NP assembly and design rules to utilize the salting-out process to crystallize NPs.

A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4

Like all members of the Toll-like receptor (TLR) family, TLR4 comprises of a large ectodomain (ECD) involved in ligand recognition at the cell-surface, and a cytosolic Toll/interleukin-1 receptor (TIR) signalling domain, linked by a lipid membrane-anchored transmembrane (TM) domain (TMD). Binding of immunostimulatory pathogen-associated molecular patterns (PAMPs) such as bacterial lipopolysaccharide (LPS) to myeloid differentiation factor 2 (MD-2) coreceptor-complexed TLR4 leads to its dimerization, resulting in productive juxtaposition of TIR domains and the initiation of pro-inflammatory innate immune responses. Whilst the process of PAMP recognition is relatively well understood, thanks to numerous high-resolution crystallographic structures of ECDs, the mechanism by which such recognition is translated into TMD dimerization and activating conformational changes is less clear. Based on available biophysical and biochemical experimental data, ab initio modelling, and multiscale molecular dynamics (MD) simulations entailing a total of >13μs and >200μs of atomistic and coarse-grained sampling, respectively, we investigate the structural basis for TLR4 TMD dimerization within a biologically relevant lipid membrane environment. A key polar-xx-polar (637SxxS640) motif is shown to drive association of the TLR4 TMDs, and to maintain a flexible interface, which may be disrupted by selected point mutations. Furthermore, MD simulations of various TMD+ECD constructs have been used to investigate the coupling between domains, revealing that flexible linkers abrogate dimerization via aggregation of ECDs at the membrane surface, explaining previous biochemical observations. These results improve our understanding of the assembly and signalling mechanisms of TLR4, and pave the way for rational structure-based development of membrane-associated immunomodulatory molecules.

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase

Cytochrome c oxidase (CcO) catalyzes the reduction of oxygen to water and uses the released free energy to pump protons against the transmembrane proton gradient. To better understand the proton-pumping mechanism of the wild-type (WT) CcO, much attention has been given to the mutation of amino acid residues along the proton translocating D-channel that impair, and sometimes decouple, proton pumping from the chemical catalysis. Although their influence has been clearly demonstrated experimentally, the underlying molecular mechanisms of these mutants remain unknown. In this work, we report multiscale reactive molecular dynamics simulations that characterize the free-energy profiles of explicit proton transport through several important D-channel mutants. Our results elucidate the mechanisms by which proton pumping is impaired, thus revealing key kinetic gating features in CcO. In the N139T and N139C mutants, proton back leakage through the D-channel is kinetically favored over proton pumping due to the loss of a kinetic gate in the N139 region. In the N139L mutant, the bulky L139 side chain inhibits timely reprotonation of E286 through the D-channel, which impairs both proton pumping and the chemical reaction. In the S200V/S201V double mutant, the proton affinity of E286 is increased, which slows down both proton pumping and the chemical catalysis. This work thus not only provides insight into the decoupling mechanisms of CcO mutants, but also explains how kinetic gating in the D-channel is imperative to achieving high proton-pumping efficiency in the WT CcO.

Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes.

Bacteria are protected by complex molecular architectures known as the cell envelope. The cell envelope is composed of regions with distinct chemical compositions and physical properties, namely, membranes and a cell wall. To develop novel antibiotics to combat pathogenic bacteria, molecular level knowledge of the structure, dynamics, and interplay between the chemical components of the cell envelope that surrounds bacterial cells is imperative. In addition, conserved molecular patterns associated with the bacterial envelope are recognized by receptors as part of the mammalian defensive response to infection, and an improved understanding of bacteria-host interactions would facilitate the search for novel immunotherapeutics. This Perspective introduces an emerging area of computational biology: multiscale molecular dynamics simulations of chemically complex models of bacterial lipids and membranes. We discuss progress to date, and identify areas for future development that will enable the study of aspects of the membrane components that are as yet unexplored by computational methods.

The effects of wall roughness on the methane flow in nano-channels using non-equilibrium multiscale molecular dynamics simulation

This paper presents a non-equilibrium multiscale molecular dynamics simulation method to investigate the effects of periodic wall surface roughness on the structure and mass transfer of methane fluid through the silicon nano-channels. In order to accurately capture the trajectories and microstructure of methane nano-fluidics, the present modification of OPLS fully atomic model is employed. Meanwhile, we introduce the corresponding coarse-grained model to solve the problem of wall–fluid interaction for methane Poiseuille flow within silicon atomic walls using the classical Lorentz–Berthelot mixing rules. The geometries of the upper wall roughness are modeled by rectangular waves with different amplitudes and wavelengths. The three-dimensional number densities of C (H) atom and kinetic energy distribution plots give a clear observation of the impacts of surface roughness on the localization micro-information of methane fluid. Moreover, the slip length of fluid over rough surface decreases with the increase in amplitude. The diffusion coefficients appear anisotropic, and the radial distribution functions decrease with the increase in the amplitude. These properties should be taken into account in the design of energy-saving emission reduction nano-fluidic devices. All numerical results also indicate that the presented method not only can well solve the issue of wall–fluid interactions, but also could accurately predict the micro-information and dynamic properties of methane Poiseuille flow.

Water Confined in Mesoporous TiO2 Aerosols: Insights from NMR Experiments and Molecular Dynamics Simulations

The adsorption of water vapor in mesoporous TiO2 was studied by nuclear magnetic resonance (NMR) and multiscale molecular dynamics simulations. Three different water environments were distinguished and quantified: a first layer, where strongly bound water molecules exist at the inner surfaces; a second less structured layer but still with restricted mobility; and a bulk-like fraction of mobile water. The obtained NMR results can be explained in the framework of molecular dynamics simulations that give insight on the filling mechanisms in TiO2 nanoporous materials. For these highly hydrophilic materials, it is shown that adsorption isotherms may render a smaller effective pore size due to the presence of a layer of highly bound water. The synergistic combination of experimental NMR data and MD simulations renders a detailed analysis of the water dynamics inside the titania pore space.

Stability and dynamics of membrane-spanning DNA nanopores

Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

Transport properties and structure of dense methane fluid in the rough nano-channels using non-equilibrium multiscale molecular dynamics simulation

In this paper, non-equilibrium multiscale molecular dynamics simulation is applied to investigate the transport properties (shear viscosity, diffusion coefficient and thermal conductivity) and structural properties of dense methane for Poiseuille flow within rough silicon nano-channel. In this simulation, the recently modified OPLS model is used to capture the micro-information of dense methane nanofluidics, as well as its coarse-grained model to solve the problem of wall-fluid interactions via the classical Lorentz-Berthelot mixing rule. In order to calculate the local shear viscosity in fluid layers accurately, the fitted local velocity profile method is introduced to determine the viscosity value by fitting the local velocity profile based on the Navier-Stokes equations. Additionally, the Green-Kubo formula is employed to compute the diffusion coefficient and thermal conductivity of methane nanofluidics. From the simulation, we conclude that atom number density, transport and structural properties of methane nanofluidics present significant variations near the rough nano-channel walls, and the obtained data in the central part of the nano-channel is close to experiment value of bulk system. Moreover, the streamlines are distorted near rough nano-channel walls. The results above are significant in understanding of the nanoscale hydrodynamics, and should be taken into account in fluid dynamics theory and the design of nanofluidic devices.

Molecular Origin of Donor- and Acceptor-Rich Domain Formation in Bulk-Heterojunction Solar Cells with an Enhanced Charge Transport Efficiency

Understanding the origin of different morphologies in bulk-heterojunction solar cells can provide effective guidelines to rational control of the morphologies in the active layer. Here, we have uncovered the importance of molecular interactions on the morphologies for not only donor materials but also for fullerene acceptors in organic solar cells through the multiscale coarse-graining molecular dynamic simulations at the real device level (∼83 nm × 83 nm × 83 nm). It is found that oligothiophene donors with polar end groups could not only facilitate the formation of continuous donor network but also promote the aggregation and connection of fullerenes toward efficient hole and electron transport. On the contrary, fullerenes are well dispersed at the molecule levels in the less polar oligothiophene matrix and thus contribute to the poor electron transport mobility and device performance, which is consistent with the observed differences in both morphology and charge transport properties of these two systems. These results would provide effective guidelines for the rational molecule design and morphology control to further enhance the device performance of organic solar cells.

Rotation Mechanism of Molecular Motor V1-ATPase Studied by Multiscale Molecular Dynamics Simulation

Enterococcus hirae V1-ATPase is a molecular motor composed of the A3B3 hexamer ring and the central stalk. In association with ATP hydrolysis, three catalytic AB pairs in the A3B3 ring undergo conformational changes, which lead to a 120° rotation of the central stalk. To understand how the conformational changes of three catalytic pairs induce the 120° rotation of the central stalk, we performed multiscale molecular dynamics (MD) simulations in which coarse-grained and all-atom MD simulations were combined using a fluctuation matching methodology. During the rotation, a catalytic AB pair spontaneously adopted an intermediate conformation, which was not included in the initial inputs of the simulations and was essentially close to the “bindable-like” structure observed in a recently solved crystal structure. Furthermore, the creation of a space between the bindable-like and tight pairs was required for the central stalk to rotate without steric hindrance. These cooperative rearrangements of the three catalytic pairs are crucial for the rotation of the central stalk.

Direct Determination of Metal Complexes' Interaction with DNA by Atomic Telemetry and Multiscale Molecular Dynamics.

The lack of molecular mechanistic understanding of the interaction between metal complexes and biomolecules hampers their potential medical use. Herein we present a robust procedure combining resonant X-ray emission spectroscopy and multiscale molecular dynamics simulations, which allows for straightforward elucidation of the precise interaction mechanism at the atomic level. The report unveils an unforeseen hydrolysis process and DNA binding of [Pt{N(p-HC6F4)CH2}2py2] (Pt103), which showed potential cytotoxic activity in the past. Pt103 preferentially coordinates to adjacent adenine sites, instead of guanine sites as in cisplatin, because of its hydrogen bond ability. Comparison with previous research on cisplatin suggests that selective binding to guanine or adenine may be achieved by controlling the acidity of the compound.

Multiscale Dynamics of Flavivirus Fusion Peptides - Membrane Interactions via Simulation and Experiments

A primary causative agent of infectious disease is the positive single-stranded RNA flavivirus genus. Members of this family include Dengue (DENV), tick-borne encephalitis, west nile virus (WNV), japanese encephalitis, yellow fever and zika virus (ZIKV). During receptor-mediated endocytosis and exposure to lowered pH, the envelope (E) proteins undergo major structural changes and a dimeric-to-trimeric transition. This structural rearrangement leads to exposure of the hydrophobic tips - fusion peptides (FPs) which interact with the endosomal bilayer, subsequently initiating fusion of the viral and host membranes. The FP sequence is highly conserved among all known flaviviruses. Here, a multiscale molecular dynamics (MD) simulation approach has been employed to investigate the interaction of all FP sequences with lipid membranes, the results of which were compared with biophysical experiments. Following extensive validation using all-atom simulations with a range of sampling methods and force fields, coarse-grained models of the FP were derived in order to follow the long-timescale process of FP/lipid bilayer assembly. Atomic-resolution free energy profiles were calculated as a function of insertion depth within lipid bilayers composed of a physiologically realistic endosomal membrane model. These profiles were correlated with peptide structural and lipid-interaction data, and validated by comparison with fluorescence spectroscopy and NMR data. A mutant (W101A) previously shown to abolish flavivirus membrane fusion was found to possess twice as low affinity towards host lipid bilayers in comparison with the wild-type FP. The binding affinity was similarly reduced for wild-type FP interaction with pure zwitterionic membranes in comparison with realistic endosomal membrane models containing anionic lipids. Novel insights into the structural and thermodynamic basis for flavivirus virus infection process obtained here should prove useful in future rational antiviral therapeutic development.

Molecular Dynamics Simulations of G-Protein Coupled Receptor Lipid Interactions

Lipid molecules can bind selectively to specific sites on integral membrane proteins, modulating their structure, stability, and function. We have undertaken multiscale molecular dynamics simulations to investigate two distinct modes of lipid interaction with G-protein coupled receptors (GPCRs). Native mass spectrometry measurements suggest the presence of specific lipid binding sites on Neurotensin Receptor 1 (NTS1), in particular for phosphatidyl inositol phosphate (PIP) species. Coarse-grained molecular dynamics simulations of NTS1 embedded in a lipid bilayer indicate strong and specific interactions of PIP molecules with defined regions on the intracellular portion of NTS1. The predominant mode of PIP binding is via interaction with basic residues located within intracellular loop regions, inaccessible to other anionic lipid species such as phosphatidyl serine. In silico mutagenesis of key residues within these regions abrogates lipid binding. These simulation based predictions provide guidance for experimental mutagenesis of NTS1, toward structurally rationalising the proposed PIP binding sites. Molecular simulations have also been used to explore interactions of cholesterol with the extracellular domain of Smoothened (SMO), a Class F GPCR. The recent near full-length x-ray structure of SMO revealed the presence of a cholesterol molecule within a hydrophobic sterol binding groove on the extracellular cysteine rich domain (CRD). Atomistic simulations of SMO in a lipid bilayer suggest the cholesterol molecule exerts a marked effect on the structural stability of the CRD, as well as the potential for a degree of flexibility of extracellular domains of SMO relative to 7TM domain. Together these studies suggest how molecular simulations may be used in conjunction with experiment to guide the identification of lipid binding sites, and characterise the effects of lipid binding on GPCR structure and function.

Computational and theoretical approaches for studies of a lipid recognition protein on biological membranes.

Many cellular functions, including cell signaling and related events, are regulated by the association of peripheral membrane proteins (PMPs) with biological membranes containing anionic lipids, e.g., phosphatidylinositol phosphate (PIP). This association is often mediated by lipid recognition modules present in many PMPs. Here, I summarize computational and theoretical approaches to investigate the molecular details of the interactions and dynamics of a lipid recognition module, the pleckstrin homology (PH) domain, on biological membranes. Multiscale molecular dynamics simulations using combinations of atomistic and coarse-grained models yielded results comparable to those of actual experiments and could be used to elucidate the molecular mechanisms of the formation of protein/lipid complexes on membrane surfaces, which are often difficult to obtain using experimental techniques. Simulations revealed some modes of membrane localization and interactions of PH domains with membranes in addition to the canonical binding mode. In the last part of this review, I address the dynamics of PH domains on the membrane surface. Local PIP clusters formed around the proteins exhibit anomalous fluctuations. This dynamic change in protein-lipid interactions cause temporally fluctuating diffusivity of proteins, i.e., the short-term diffusivity of the bound protein changes substantially with time, and may in turn contribute to the formation/dissolution of protein complexes in membranes.

Interfacial activation of M37 lipase: A multi-scale simulation study

Lipases are enzymes of biotechnological importance that function at the interface formed between hydrophobic and aqueous environments. Hydrophobic interfaces can induce structural transitions in lipases that result in an increase in enzyme activity, although the detailed mechanism of this process is currently not well understood for many lipases. Here, we present a multi-scale molecular dynamics simulation study of how different interfaces affect the conformational dynamics of the psychrophilic lipase M37. Our simulations show that M37 lipase is able to interact both with anionic lipid bilayers and with triglyceride surfaces. Interfacial interactions with triglyceride surfaces promote large-scale motions of the lid region of M37, spanning residues 235–283, revealing an entry pathway to the catalytic site for substrates. Importantly, these results suggest a potential activation mechanism for M37 that deviates from other related enzymes, such as Thermomyces lanuginosus lipase. We also investigated substrate binding in M37 by using steered MD simulations, confirming the open state of this lipase. The exposure of hydrophobic residues within lid and active site flap regions (residues 94–110) during the activation process provides insights into the functional effect of hydrophobic surfaces on lipase activation.

Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation.

NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.