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Energy and angular distributions of reflections and sputtered atoms are essential inputs for feature profile evolution simulations. Molecular dynamics simulations are used to compute the three-dimensional energy and angular distributions for reflected and sputtered products when both Ar/sup +/ and Cu/sup +/ ions bombard a copper surface. We term these "spatiokinetic" distribution functions (SKDF's). We show by example that SKDF's for reflected Ar/sup +/ ions focus as the incident angle /spl theta//sub i/ (normal=0/spl deg/) is increased from 60-75/spl deg/ and broaden as the incident energy E/sub i/ is increased from 55-175 eV. We show that the SKDF's for glancing-angle reflected Cu/sup +/ ions focus when E/sub i/ is increased from 55-175 eV. We show that the SKDF's for copper atoms sputtered by 175 eV Ar/sup +/ are insensitive to /spl theta//sub i/;. We report total sputter yields for Ar/sup +/ and Cu/sup +/ ions at 55 and 175 eV for incident angles between 0/spl deg/ and 85/spl deg/, and sticking probabilities for Cu/sup +/ ions for these energies and angles. Comparison to representative experimental results (Doughty et al., 1997) is given.

One of the most important processing steps during copper metallization is the deposition of a thin yet conformal copper seed layer, often using ionized physical vapor deposition, prior to electroplating. A key need in designing this step is assuring that copper of sufficient thickness is deposited at all points within a high aspect ratio (AR) feature. In this work, we present feature evolution simulations of copper seed layer deposition, using ion reflection and neutral copper sputtering distributions calculated using molecular dynamics simulations. Independent variables in the model include neutral-ion and ion-ion flux ratios as well as substrate bias voltage. We show that trenches of AR=5 can be conformally lined with proper variation of these independent variables using a simple composition and ion energy cycling strategy. Furthermore, we show that the use of reflection and sputtering distributions obtained by molecular dynamics simulation results in qualitatively different feature shape predictions than when using isotropic (cosine) sputtering distributions with no possibility of ion reflection, with the degree of difference a function of the ion-neutral flux ratio and the ion energy.

Numerous profile evolution simulation studies strongly suggest that ions reflecting with glancing angles from etched feature sidewalls are responsible for microtrench formation at the feature bottom. Within these studies such reflections are traditionally assumed specular, where the ion retains all of its incident energy. In this study, we gauge the validity of that assumption by describing the distributions of reflected ion energies, Er, reflected ion angles (polar, θr; azimuthal, φr; and total scatter, αr), obtained via MD simulations of Ar+ bombardment of model SiO2 surfaces. We modeled the physics of the surface atom interactions using an empirical interatomic potential energy function developed by Feuston and Garofalini [J. Chem Phys. 89, 5818 (1988)]. We considered Ar+ ion energies, Ei, of 100 and 200 eV, and incident polar angles, θi, of 0°, 30°, 45°, 60°, 75°, and 85°, measured from the macroscopic surface normal. Each (Ei,θi) combination was used to generate a unique roughened model oxide surface...

We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods., Comment: Accepted for publication on Entropy

Biphasic autoxidation of tetralin has been carried out using surface-active tetramethylethylenediamine complexes of manganese, chromium, and nickel as catalysts, tetralin as the substrate and organic phase, and dodecyl sodium sulfate as emulsifier. Advantages of the biphasic reaction over the homogeneous and heterogeneous counterparts include avoidance of the use of a troublesome solvent, ease of catalyst recovery and substrate recycle, and attainment of high reactivity, selectivity, and reproducibility under mild reaction conditions (T ∼ 60 °C, P ∼ 1 atm). The main reaction products are α-tetralone and α-tetralol. The selectivity for the former decreases from 95% with the chromium complex to 90% with the nickel complex and 60% with the manganese complex, and the activity varies in a reverse order. The biphasic reaction stops at a bulk tetralin conversion of 35% due to the buildup of inhibitive, higher oxidation products. Similar product inhibition has been reported in one-liquid-phase systems. The biphas...

We investigate the fundamental aspects of cell-to-cell signaling by diffusing signaling compounds produced at nonuniform rates using an analytical model. Given a time-averaged secretion rate, we consider the effects of “pulsing” the secretion with different pulse interval lengths. The effective communication distance increases with decreasing pulse length, but this increase is theoretically limited to approximately twice the effective communication distance in the case of steady secretion. The time intervals in which signal transfer is permitted also decrease as pulse time decreases. These results illustrate important limiting cases in which the mode of the secretion of signaling compounds can have significant effects on cell-to-cell signaling.

Pathways are computed for transport of H2O and CO in myoglobin (Mb), using the single sweep and zero-temperature string methods in a fully atomistic, explicitly solvated model system. Our predictions of sites and barriers in the pathways for CO transport agree with previous studies. For H2O, we predict a binding site in the distal pocket (DP), in agreement with crystallographic observations, and another one close to Leu 29 which explains the importance of this residue in controlling the pocket's hydrophobicity, as well as disordered minima in the largely apolar xenon cavities. In particular, H2O can occupy and transition among the xenon cavities, Xe4, Xe2, and Xe3. Our results support the hypothesis that the thermodynamically most favorable entry/exit portal for H2O is the so-called histidine gate (HG), the same as for CO. This result, along with the observation of water occupation of both DP and apolar Xe cavities, suggest that water and small gas molecules like CO compete for access to the protein interior, and therefore models of gas molecule transport within proteins should also explicitly consider water transport.

Insulin regulates blood glucose levels in higher organisms by binding to and activating insulin receptor (IR), a constitutively homodimeric glycoprotein of the receptor tyrosine kinase (RTK) superfamily. Therapeutic efforts in treating diabetes have been significantly impeded by the absence of structural information on the activated form of the insulin/IR complex. Mutagenesis and photo-crosslinking experiments and structural information on insulin and apo-IR strongly suggest that the dual-chain insulin molecule, unlike the related single-chain insulin-like growth factors, binds to IR in a very different conformation than what is displayed in storage forms of the hormone. In particular, hydrophobic residues buried in the core of the folded insulin molecule engage the receptor. There is also the possibility of plasticity in the receptor structure based on these data, which may in part be due to rearrangement of the so-called CT-peptide, a tandem hormone-binding element of IR. These possibilities provide opportunity for large-scale molecular modeling to contribute to our understanding of this system. Using various atomistic simulation approaches, we have constructed all-atom structural models of hormone/receptor complexes in the presence of CT in its crystallographic position and a thermodynamically favorable displaced position. In the "displaced-CT" complex, many more insulin-receptor contacts suggested by experiments are satisfied, and our simulations also suggest that R-insulin potentially represents the receptor-bound form of hormone. The results presented in this work have further implications for the design of receptor-specific agonists/antagonists.

We discuss a method for parametric calculation of free energy functions in arbitrary collective variables using molecular simulations. The method uses a variant of temperature accelerated molecular dynamics to evolve on-the-fly the parameters of the free energy function to their optimum values by minimization of a cumulative gradient error. We illustrate how the method performs using simple examples and discuss its application in the derivation of effective pairwise potentials for multiscale molecular simulations.

The insulin receptor (IR) is a homo-dimeric, disulfide-linked, membrane-spanning tyrosine kinase. IR displays negative cooperativity in insulin binding to its two pockets, suggesting "see-sawing" between symmetry-inverted conformations. The crystal structure of the dimeric IR ectodomain, IRDeltabeta [PDB code 2DTG (McKern et al., Nature 2006 443:218-221)], provides structural bases for this speculation. Unfortunately, neither binding pocket of the crystallographic IRDeltabeta structure allows steric accommodation of insulin. During almost 70-ns of all-atom, explicit-water MD simulation ( approximately 0.5 million atoms), IRDeltabeta undergoes significant asymmetric interdomain and intersubunit conformational fluctuations that do not alter its quaternary structure. Subtle variations in intersubunit buried surface area coincide with these conformational fluctuations, resulting in one easily-accessible insulin binding pocket with the other blocked. We use a combination of Metropolis Monte-Carlo and MD simulations to dock both T- and R-state insulin into the open binding pocket. Both complexes remain stable during 30-ns of MD simulation. In these complexes, "hexamer interface" residues on insulin directly contact the "site-2" epitope on the first type-III fibronectin domain (F1) of IR. Our results support the hypothesis that intersubunit flexibility of IR, governed by alternating modulation of buried intersubunit surface area, is the physical mechanism underlying a "see-saw" model of negative cooperativity.

The type 1 insulin-like growth factor receptor (IGF1R), a trans-membrane glycoprotein, is activated by binding of its cognate growth hormones, IGF1 and IGF2. The IGF family was suggested to play a key role in cancer development and progression, thereby making it a potential target for anti-cancer therapeutic efforts. However, the molecular mechanisms underlying hormone-receptor interactions are unclear, as are the molecular bases for differing affinity of each hormone, due in part to the fact that there have been so far no detailed structural models of IGFs-bound-IGF1R to test. Constructed using a homology model of the IGF1R ectodomain, and the NMR structures of IGF1/2, with the help of an MD-assisted Monte-Carlo approach, we present the first experimentally consistent all-atom structural models of IGF1/IGF1R and IGF2/IGF1R complexes. Our models are notable because each hormone remains stably bound in independent 36-ns long explicit-solvent molecular dynamics (MD) simulations. The asymmetric structural relaxation of the apo-IGF1R homology model in a 30-ns MD equilibration facilitated the computational docking of each hormone. Our predicted complexes are significant because we observe simultaneous contacts of each hormone with the site 1 (formed by L1 and CR), and site 2 (formed by L2, and the fibronectin domains), of the receptor, suggesting cross-linking of receptor subunits. Interestingly, we observe differences in recognition of each hormone by IGF1R, because IGF1 interacts relatively strongly with L1 and CR (IGF1R), whereas IGF2 has stronger interactions with L2 and the fibronectin domains. Our simulations also provide direct evidence in favor of previously suggested electrostatic complementarity between the C-domains of IGF1/2 and the CR-domain of the receptor. Additionally, we provide detailed hormone-receptor contacts that are consistent with earlier mutagenesis studies.

The serotonin 5-HT3 receptor (5-HT3R) is a member of the Cys-loop ligand-gated ion channel family. We used a combination of site-directed mutagenesis, homology modeling, and ligand-docking simulations to analyze antagonist-receptor interactions. Mutation of E236, which is near loop C of the binding site, to aspartate prevents expression of the receptor on the cell surface, and no specific ligand binding can be detected. On the other hand, mutation to glutamine, asparagine, or alanine produces receptors that are expressed on the cell surface, but decreases receptor affinity for the competitive antagonist d-tubocurarine (dTC) 5-35-fold. The results of a double-mutant cycle analysis employing a panel of dTC analogs to identify specific points of interactions between the dTC analogs and E236 are consistent with E236 making a direct physical interaction with the 12 –OH of dTC. dTC is a rigid molecule of known three-dimensional structure. Together with previous studies linking other regions of dTC to specific residues in the binding site, these data allow us to define the relative spatial arrangement of three different residues in the ligand-binding site: R92 (loop D), N128 (loop A), and E236 (near loop C). Molecular modeling employing these distance constraints followed by molecular-dynamics simulations produced a dTC/receptor complex consistent with the experimental data. The use of the rigid ligands as molecular rulers in conjunction with double-mutant cycle analysis provides a means of mapping the relative positions of various residues in the ligand-binding site of any ligand-receptor complex, and thus is a useful tool for delineating the architecture of the binding site.

Highly cross-linked polymer (HCP) networks are becoming increasingly important as high-performance adhesives and multifunctional composite materials. Because of their cross-linked molecular architectures, HCPs can be strong but brittle. One key goal in improving the performance of an HCP is to increase toughness without sacrificing strength. Using large scale molecular-dynamics simulation, we compare and characterize the mechanical behavior of two model HCPs under tensile deformation. In the first case, bond angles among any three connected monomers are unconstrained and in the second case we impose harmonic tetrahedral bond angle constraints. We perform a detailed microstructural analysis that establishes a unique correlation between macroscopic mechanical behavior and the microscopic structure of an HCP. While, in the unconstrained system, strain-hardening behavior is observed that is attributed to the formation of microvoids, the void growth is completely arrested in the constrained system and no strain hardening is observed. Moreover, after the initial strain-hardening phase, the unconstrained system displays the same stress-strain behavior as that of a constrained network. Strain hardening makes the unconstrained system ductile while it retains the same tensile strength as the constrained system. We suggest that bond angle flexibility of cross-linkers might be a possible means to control ductility in an HCP network at a constant cross-linker density. We have also studied the effect of temperature, strain rate, and intermonomer nonbonded interaction strength on the stress-strain behavior. Interestingly at a strong intermonomer nonbonded interaction strength, no strain hardening is observed even in the unconstrained system and fracture sets in at around 1% strain, similar to what is observed in an experimental system such as epoxy and vinyl-ester based thermosets. This indicates that strong nonbonded interactions play a key role in making an HCP strong but brittle.

Mechanical properties of highly cross-linked polymer (HCP) networks, e.g., thermosets, can be significantly modified by adding linear polymer chains, e.g., thermoplastics. In this work, we study thermoset/thermoplastic polymer alloys by means of large scale molecular dynamics simulations (MD) of a coarse-grained model. We focus here on the effect of the linear chain fraction, Gammal, on the mechanical properties of HCP network for a fixed chain length. Our MD simulations show that the ductility (measured by the strain-to-fracture) of an alloy decreases with increasing Gammal up to a threshold fraction, Gammal*, beyond which it increases with Gammal. We find that for GammalGammal* the fracture is predominantly cohesive, while for GammalGammal* adhesive failure occurs. We suggest that the possible origin of this unexpected non-monotonic behavior is due to a competition between (a) growth of microvoids which stores mechanical energy and is compromised as Gammal increases, and (b) reduction of cross-linker density with increasing Gammal.

Using molecular dynamics simulations of a generic model, we observe strain hardening in highly cross-linked polymer glasses under tensile deformation. We show that formation of microvoids, without bond breaking, constitutes the microscopic origins of strain hardening. A well-defined functional form is observed for the void size distribution that is consistent with voids in dense equilibrium Lennard-Jones particle packings, independent of strain. Microvoid-based strain hardening is not observed in a separate model with tetrahedral bond angle constraints, indicating that flexible cross-linkers are the key factor in the development of strain hardening behavior.

The Escherichia coli chaperonin GroEL is a complex of identical subunit proteins (57 kDa each) arranged in a back-to-back stacking of two heptameric rings. Its hallmarks include nested positive intra-ring and negative inter-ring cooperativity in adenosine trisphosphate (ATP) binding and the ability to mediate the folding of newly transcribed and/or denatured substrate proteins. We performed unbiased molecular dynamics simulations of the GroEL subunit protein in explicit water both with and without the nucleotide KMgATP to understand better the details of the structural transitions that enable these behaviors. Placing KMgATP in the equatorial domain binding pocket of a t state subunit, which corresponds to a low ATP-affinity state, produced a short-lived (6ns) state that spontaneously transitioned to the high ATP-affinity r state. The important feature of this transition is a large-scale rotation of the intermediate domain’s helix M to close the ATP binding pocket. Pivoting of helix M is accompanied by counterclockwise rotation and slight deformation of the apical domain, important for lowering the affinity for substrate protein. Aligning simulation conformations into model heptamer rings demonstrates that the t→r transition in one subunit is not sterically hindered by t state neighbors, but requires breakage of Arg197-Glu386 intersubunit salt bridges, which are important for inter-ring positive cooperativity. Lowest-frequency quasi-harmonic modes of vibration computed pre- and post-transition clearly show that natural vibrations facilitate the transition. Finally, we propose a novel mechanism for inter-ring cooperativity in ATP binding inspired by the observation of spontaneous insertion of the side chain of Ala480 into the empty nucleotide pocket.

We discuss a generic computational model of eukariotic chemotaxis in 2D random porous domains. The model couples the fully time-dependent finite-difference solution of a reaction–diffusion equation for the concentration field of a chemoattractant to biased random walks representing individual chemotactic cells. We focus in particular on the influence of consumption of chemoattractant by the boundaries of obstacles with irregular shapes which are distributed randomly in the domain on the chemotactic response of the cells. Cells are stimulated to traverse a field of obstacles by a line source of chemoattractant. We find that the reactivity of the obstacle boundaries with respect to the chemoattractant strongly determines the transit time of cells through two primary mechanisms. The channeling effect arises because cells are effectively repelled from surfaces which consume chemoattractant, and opposing surfaces therefore act to keep cells in the middle of channels. This reduces traversal times relative to the case with unreactive boundaries, provided that the appropriate Peclet number relating the strength of reactivity to diffusion in governing chemoattractant transport is neither too low nor too high. The dead-zone effect arises due to a realistic threshold on the chemotactic response, which at steady state results in portions of the domain having no detectable gradient. Of these two, the channeling effect is responsible for 90% of the sensitivity of transit times to boundary reactivity. Based on these results, we speculate that it may be possible to tune the rates of cellular penetration into porous domains by engineering the reactivity of the internal surfaces to cytokines.

An overriding goal in cell motion modeling and simulations is to understand relevant underlying variables which modulate cell motility. Mathematical modeling of cell movement has traditionally focused on migration of population of cells in response to various chemoattractants (e.g., cytokines) with steady state concentration fields. In this paper, we discuss a generic model from an engineering perspective intending to aid in grasping an improved understanding of how the transient affects the mechanism of individual cell locomotion behavior. The cell migration simulations were implemented for a 2D homogenous domain with a stationary point source. Results indicate that transience has an important influence on regulating cell migration behavior. While diffusivity does not influence how fast cells reach the chemoattractant source in case of continuous production, in the case of production in "bursts" of random strength and separated by random time intervals, it becomes a determining factor.

Rational design and selection of candidate porous biomaterials to serve as tissue engineering constructs rests on our ability to understand the influence of the porous microarchitecture on the transport of chemical species (e.g., nutrients and signaling compounds), fluid flow, and cellular locomotion and growth. We have begun to study the behavior of chemotactically mobile cells in response to unsteady signaling molecule concentration fields using a computational simulation-based model. The model couples fully time-dependent finite-difference solution of a reaction-diffusion equation for the concentration field of a generic chemoattractant to biased random walks representing individual moving cells. This model is a first step in building a quantitative, pore-level model of mass and cellular transport in porous tissue-engineered constructs. In these proceedings, we focus on our recent findings regarding the influence of flux-reactive boundary conditions in heterogeneous 2D domains on the chemotactic response of otherwise randomly moving cells. In particular, we find that, when cells are forced to “crawl” around obstacles in order to approach a point source of chemoattractant, the reactivity of the obstacle surface with respect to the chemoattractant strongly determines the morphology of the cells' paths of locomotion. Cells crawl along non-reactive surfaces and strongly avoid reactive surfaces, due to the nature of the chemoattractant concentration gradients near the surface. We show further that tuning the reactivity of the surfaces of two obstacles defining a gap can control the passage of cells through the gap. From our work, we infer the importance of a proper treatment of boundary conditions in any future pore-level quantitatve modeling of mass transport and cellular response in porous media.

We discuss results of molecular dynamics simulations of dense liquids of BPA-PC adjacent to (111) nickel surfaces. The BPA-PC molecule is modeled using a dual-resolution coarse-grained representation, in which the chemical repeat unit is represented by four spherical beads, each roughly corresponding to a comonomeric functional group, except at the chain ends, where the terminal carbonate groups are represented atomistically. This dual resolution scheme is necessary to give access to an orientational degree of freedom upon which the polymer/surface interaction potential sensitively depends. The results expand upon those of Ref. [Abr03b], in which chains of length N = 10 repeat units were considered, by considering chains of length N = 20. We observe that the structure of the liquid near the wall is sensitively affected by the strong attraction of the chain ends to the surface for both chain lengths. The liquid forms two layers: in the innermost layer near the wall, most chains have both ends adsorbed, while in the outermost layer, most chains have a single end adsorbed. This structure leads to an interesting profile in chain orientation, where chains are flattened in the innermost layer and stretched in the outermost layer. The overlap between these two layers is more diffuse in the case of the N = 20 chains.

The adsorption of a phenol molecule on a Ni(111) surface is studied by employing an ab initio DFT approach. Adsorption energies and geometries at each surface high symmetry site are determined and compared with the analogous case of benzene. Adsorption at the bridge site, with C-C bond along the $[2\ifmmode\bar\else\textasciimacron\fi{}11]$ direction, is found to be the most energetically favorable. Application of the current results to a multiscale modeling of polycarbonates interacting with a metal surface is briefly discussed.

We present a dual-resolution coarse-graining scheme for efficient molecular dynamics simulations of bisphenol-$A$-polycarbonate $(\mathrm{BP}\ensuremath{-}A\ensuremath{-}\mathrm{PC})$ liquids in contact with a (111) nickel surface. The essential feature of this model is the strong adsorption of phenoxy chain ends, and the absence of adsorption by other parts of the chains. Details of how phenoxy chain ends interact with the nickel surface were extracted from Car-Parrinello molecular dynamics calculations of adsorption of phenol on nickel. These calculations show that phenol adsorption on nickel is short ranged $(l3\mathrm{\AA{}})$ and strongly dependent on the ${\mathrm{C}}_{1}\ensuremath{-}{\mathrm{C}}_{4}$ orientation of the ring. The structure of $\mathrm{BP}\ensuremath{-}A\ensuremath{-}\mathrm{PC}$ prevents internal phenylene groups from interacting with the surface, due to steric hindrances from the noninteracting isopropylidenes. These dependencies are incorporated in the coarse-grained model of the $\mathrm{BP}\ensuremath{-}A\ensuremath{-}\mathrm{PC}$ chain by resolving chain-terminating carbonate groups with atomistic detail, while the rest of the chain is represented by coarsened ``beads.'' This allows specification of the ${\mathrm{C}}_{1}\ensuremath{-}{\mathrm{C}}_{4}$ orientation of the terminal phenoxy groups, while overall allowing for system equilibration with reasonable computer time. We simulate liquids of up to 240 chains of ten chemical repeat units, confined in a slit pore formed by two frozen (111) planes of atoms with the lattice spacing of nickel. We find that the strong adsorption of chain ends has a large effect on the liquid structure through a distance of more than two bulk radii of gyration from the surface. These effects are explained by a competition among single- and double-end adsorption, and dense packing. The structure of the interface less than $10\mathrm{\AA{}}$ from the wall is greatly sensitive to the orientational dependence of the phenoxy adsorption.

Upon aging, a collapsed long chain evolves from a crumpled state to a self-entangled globule which can be thought of as a large knot. Swelling of an equilibrium globule in good solvent is a two-step process: (i) fast swelling into an arrested stretched structure with conserved entanglement topology followed by (ii) slow disentanglement. Using computer simulation, we found both mass-mass (m-m) and entanglement-entanglement (e-e) power law correlations inside the swollen globule. The m-m correlations are characterized by a set of two exponents in agreement with a Flory-type argument. The e-e correlations are also characterized by two exponents, both of them larger (by $\ensuremath{\sim}0.3$) than the related m-m exponents. We interpret this difference as evidence of distance-dependent repulsion $E=\ensuremath{-}0.3\mathrm{ln} (\ensuremath{\rho}){k}_{B}T$ between entanglements sliding along the polymer chain.

We review some recent approaches to simulate polymer melts on different levels of description. The methods aim at a link between these approaches, in order to faithfully simulate specific materials and eventually predict material properties. In the present contribution this is explained in some detail for different coarse grained bead spring models and different micro-meso mapping schemes for bulk properties. In the case of polycarbonate near surfaces a combined approach of mesoscale model simulations and QM-DFT calculations is presented.

We study the properties of a polycarbonate melt near a nickel surface as a model system for the interaction of polymers with metal surfaces by employing a multiscale modeling approach. For bulk properties a suitably coarse grained bead spring model is simulated by molecular dynamics (MD) methods with model parameters directly derived from quantum chemical calculations. The surface interactions are parameterized and incorporated by extensive quantum mechanical density functional calculations using the Car-Parrinello method. We find strong chemisorption of chain ends, resulting in significant modifications of the melt composition when compared to an inert wall., Comment: 8 pages, 3 figures (2 color), 1 table

Human immunodeficiency virus (HIV) is the primary etiologic agent responsible for the AIDS pandemic. In this work, we used a chimeric recombinant protein strategy to test the possibility of irreversibly destroying the HIV-1 virion using an agent that simultaneously binds the Env protein and viral membrane. We constructed a fusion of the lectin cyanovirin-N (CVN) and the gp41 membrane-proximal external region (MPER) peptide with a variable-length (Gly 4 Ser) x linker (where x is 4 or 8) between the C terminus of the former and N terminus of the latter. The His-tagged recombinant proteins, expressed in BL21(DE3)pLysS cells and purified by immobilized metal affinity chromatography followed by gel filtration, were found to display a nanomolar efficacy in blocking BaL-pseudotyped HIV-1 infection of HOS.T4.R5 cells. This antiviral activity was HIV-1 specific, since it did not inhibit cell infection by vesicular stomatitis virus (VSV) or amphotropic-murine leukemia virus. Importantly, the chimeric proteins were found to release intraviral p24 protein from both BaL-pseudotyped HIV-1 and fully infectious BaL HIV-1 in a dose-dependent manner in the absence of host cells. The addition of either MPER or CVN was found to outcompete this virolytic effect, indicating that both components of the chimera are required for virolysis. The finding that engaging the Env protein spike and membrane using a chimeric ligand can destabilize the virus and lead to inactivation opens up a means to investigate virus particle metastability and to evaluate this approach for inactivation at the earliest stages of exposure to virus and before host cell encounter.

The membrane spanning domain (MSD) of HIV-1 gp41 has been shown experimentally to anchor envelope protein gp41 in the viral membrane and to play a role in fusion/infection. One conserved structural motif of the MSD is a midspan arginine, probably charged, located in the hydrophobic lipid bilayer core. It has therefore been postulated that the positively-charged guanidino sidegroup of the midspan arginine (R694) snorkels to negatively-charged headgroups in the membrane. The configurational differences between the wild-type (WT) MSD and a fusion-impaired mutant (R694L) MSD are studied here using molecular dynamics (MD). The conformational distribution and PMF of the R694L MSD peptide were compared with that of the WT MSD peptide using the technique of metadynamics. The mutant and WT peptides both have stable, alpha-helical conformations. Equilibrium properties of these stable, alpha-helical conformations were studied by long (300ns) MD. The presence of greater water around the C-terminal and the greater tilt of the WT MSD indicates that perhaps a role of the charged midspan arginine is partial solvation of the C-terminal, which may function to hold the viral membrane in a metastable prefusion state.

Using large-scale molecular-dynamics simulation of a generic model, we study the mechanical behavior of thermoset/thermoplastic polymer alloys under shear. We investigate the effect of thermoplastic mass fraction Γl and the thermoplastic chain length Nl. Our results show two different fracture peaks in the stress-strain behavior. The first peak occurs at around 60% strain followed by a stress plateau, and the system fails at around 90% strain. This "slip-stick" fracture is independent of shear rate and only occurs when Γl is less than the threshold concentration Γ* at which thermoplastic chains start to overlap. A micro-structural analysis suggests that the escape of thermoplastic chains from cavities near the fractured interfaces gives rise to slip-stick behavior. Slip-stick behavior has a strong chain length dependence and is only observed when Nl is greater than critical chain length Nlc=40. Slip-stick fracture makes an alloy of Γl=4.7% more than 40% tougher than a neat thermoset.

We describe the salient characteristics and analyze the entropic origins of the spontaneous crystal nucleation and growth as observed in extensive Monte Carlo simulations of dense packings of athermal polymers of freely-jointed chains of tangent hard spheres of uniform size (N. Karayiannis, K. Foteinopoulou and M. Laso, Phys. Rev. Lett., 2009 (103), 045703). Self-assembly of well-defined nano-patterns, in the form of randomly alternating layers of hexagonal close packing (hcp) or face centered cubic (fcc) character with a single stacking direction, is realized spontaneously at volume fractions (packing densities) of 0.58 and above independently of the average chain length and the shape of the applied molecular weight distribution. Finally, the entropic origins of the crystallization are revealed: throughout the ordering transition, while the free volume around each monomer site remains unaltered in size, its shape becomes more spherical and more symmetric. In turn, spheres along the chains are able to explore more efficiently their accessible volume in the ordered (crystalline) state increasing the translational entropy of the system.

Using large-scale molecular-dynamics simulations, we investigate the mechanical behavior of thermoset/thermoplastic polymer alloys. We focus here on the effect of linear-chain mass fraction Γl, for different chain lengths Nl, and strain rates . Our results show that tensile strain (i.e., strain to break) decreases with increasing Γl up to a threshold value Γ*l, beyond which it increases with Γl. This non-monotonic behavior, which we call "anomalous ductility", is qualitatively independent of and Nl, so long as fracture occurs in bulk. However, for larger strain rates (i.e., ) adhesive fracture occurs and no anomalous ductility is observed. Γ*l decreases with increasing Nl and we observe microscopic evidence that Γ*l signifies the onset of interchain interactions. A simple scaling argument suggests that Γ*l is related to the overlap concentration c* of the thermoplastic homopolymer in the cured thermoset matrix.

Insulin, a protein hormone, regulates glucose homeostasis and carbohydrate metabolism in higher organisms. Therapeutic formulations of hormone are preserved against degradation and denaturation by antimicrobial preservatives such as phenols, cooperative binding of which stabilizes hexameric complexes of insulin. Dissociation of hexameric species (on minutes to days time scale) into biologically active monomers is facilitated by rapid unbinding of phenols (on milliseconds time scale). However, a clear understanding of dissolution kinetics and determinants of the rates of ligand unbinding remains obscure, chiefly due to unresolved ambiguities in NMR results. We have used random acceleration molecular dynamics (RAMD) to identify and characterize a variety of potential ligand dissociation mechanisms. We observe three distinct exit routes for the ligand and resolve potentials of mean force (PMFs) along them by performing free energy calculations. Free energy profiles for each mechanism are computed with the help of second order cumulant expansion of Jarzynski's equality and non-equilibrium work statistics gathered from multiple independent steered molecular dynamics (SMD) simulations. Based on energetic barriers and structural properties, we suggest a plausible preferred mechanism for the ligand exchange. The most likely pathway with the lowest free energy barrier involves a leap over the “gate” formed by HisF5 and IleA10, with simultaneous passage of the ligand through a narrow channel existing between LeuA13, LeuH17, and the “gate”. Free energy profiles also display several weakly-bound metastable states for the ligand during entry and exit from R6 insulin hexamer.

We conduct molecular simulations of liquid methane in a system where molecular resolution fluctuates between atomically explicit and spherically symmetric united atoms. An appropriate dual-resolution canonical ensemble is constructed using (a) effective united atom pair potentials and (b) resolution-control potentials that confine explicit and united atoms chiefly to different slabs in the simulation domain. A Monte Carlo simulation is developed to sample this ensemble. We show that compatibility of the united-atom potentials with the explicit potentials in a concurrent simulation can be tuned by adjusting the width of the interface between the two resolution regions and by direct modification of the united-atom pair potentials. Our results lay the groundwork for treatment of larger atomically specific molecules with similar concurrent multiresolution techniques.

The human insulin receptor (IR) is a homodimeric membrane-spanning ligand-activated tyrosine kinase. Although a detailed theory describing how binding of the hormone insulin triggers kinase activity of IR remains elusive, the recently published crystal structure of the IR ectodomain offers the unique opportunity to use physical modeling to begin to construct this theory. We present here the results of ∼100 ns of explicit-solvent all-atom molecular dynamics (MD) simulations of IR in both the apo and putative T and R-state insulin docked states. Our simulations confirm the large interdomain flexibility of IR and the stability of its dimeric interfaces. More importantly, however, our simulations demonstrate the evolution of large-scale asymmetry in IR relative to the crystal structure, a result that reflects the structural requirements of a “see-saw” mechanism that guarantees negative homeotropic allostery in insulin binding. This asymmetry also manifests itself in the opening of one of the two equivalent insulin binding pockets and closing of its partner. This result is significant because it allows for the first time computational docking of an intact molecule of insulin into its binding pocket on an intact IR ectodomain. We use a Monte-Carlo docking algorithm followed by MD equilibration to predict bound states of insulin on IR. These simulations allow us to identify unambiguously the residues on IR that form the “site-2” binding epitope which recognizes residues on insulin responsible for its hexamerization.

The envelope spike on HIV surface is a non-covalent trimer of gp120 and gp41 dimers; with gp120 responsible for binding to the CD4 receptor and the mandatory coreceptor, CCR5 or CXCR4. Blocking the gp120-CD4 or gp120-coreceptor interaction can block viral entry and infection. The HNG family of peptides (sequence RINNIXWSEAMM, X= derivatized azidoproline) is a promising class of dual-site entry inhibitors thought to allosterically inhibit the binding process and trap the flexible gp120 molecule in an inactive state. To date, there have been no reports on the structure of the peptide or the peptide/gp120 complex. Here we have used Molecular Dynamics to develop a docking model in which the peptide binds in a tripartite fashion, preventing the formation of the bridging sheet in gp120, which is necessary for coreceptor attachment and initiation of entry. The protein undergoes significant induced fit conformational changes involving movement of large loops which allows the peptide to bind tightly. Our model is consistent with experimental observations on the peptide footprint on gp120, pointing to a hydrophobic core underneath the bridging sheet and close to the F43 pocket as the putative binding site. Our results provide an explanation for why the stereochemistry of the triazole moiety on the proline is important for peptide function, in addition to explaining the inactivity of D-tryptophan in the sequence. Furthermore, saturation transfer difference (STD) NMR experiments point to the I-X-P hydrophobic center on the peptide as the central contact point in the complex, which is consistent with the peptide pose proposed in MD studies. Our model may provide a unique basis for rational design of allosteric entry inhibitors of HIV and ultimately small molecule inhibitors of viral entry.

Measuring diffusion rates of ligands plays a key role in understanding the kinetic processes inside proteins. For example, although many molecular simulation studies have reported free energy barriers to infer rates for CO diffusion in myoglobin (Mb), they typically do not include direct calculation of diffusion rates because of the long simulation times needed to infer these rates with statistical accuracy. We show in this talk how to apply Markovian milestoning along minimum free-energy pathways to calculate diffusion rates of both CO inside Mb and O2 inside monomeric sarcosine oxidase (MSOX). In Markovian milestoning, one partitions a suitable reaction coordinate space into regions and performs restrained molecular dynamics in each region to accumulate kinetic statistics that, when assembled across regions, provides an estimate of the mean first-passage time between states. We show here that the milestones can be chosen from a Voronoi tessellation defined by discrete centers taken from minimum free-energy pathways computed using the single-sweep reconstruction method. In the case of CO/Mb, we find that, although simulations predict the existence of many potential portals that connect the solvent phase with the distal pocket (DP, the site of CO attachment to the heme iron), the so-called “histidine gate” pathway is kinetically dominant for both CO entry and exit by approximately a factor of ten, in qualitative agreement with existing experimental data. Our calculations also semi-quantitatively agree with experiment, predicting a 60-ns mean exit time for CO from the DP and a mean entry time of 50 microsec under CO-saturating conditions. The Markovian milestoning approach seems from these results to be a promising way to estimate biomolecule-related transition rates, and ongoing work involves using it to time conformational changes.

International audience; Glucose-6-phosphate dehydrogenase (G6PDH) plays a housekeeping role in cell metabolism by generating reducing power (NADPH) and fueling the production of nucleotide precursors (ribose-5-phosphate). Based on its indispensability for pathogenic parasites from the genus Trypanosoma, G6PDH is considered a drug target candidate. Several steroid-like scaffolds were previously reported to target the activity of G6PDH. Epiandrosterone (EA) is an uncompetitive inhibitor of trypanosomal G6PDH for which its binding site to the enzyme remains unknown. Molecular simulation studies with the structure of Trypanosoma cruzi G6PDH revealed that EA binds in a pocket close to the G6P binding-site and protrudes into the active site blocking the interaction between substrates and hence catalysis. Site directed mutagenesis revealed the important steroid-stabilizing effect of residues (L80, K83 and K84) located on helix α-1 of T. cruzi G6PDH. The higher affinity and potency of 16α-Br EA by T. cruzi G6PDH is explained by the formation of a halogen bond with the hydrogen from the terminal amide of the NADP+-nicotinamide. At variance with the human enzyme, the inclusion of a 21-hydroxypregnane-20-one moiety to a 3β-substituted steroid is detrimental for T. cruzi G6PDH inhibition. The species-specificity of certain steroid derivatives towards the parasite G6PDH and the corresponding biochemically validated binding models disclosed in this work may prove valuable for the development of selective inhibitors against the pathogen's enzyme.