Globular structure of a human immunodeficiency virus-1 protease (1DIFA dimer) in an effective solvent medium by a Monte Carlo simulation

A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease (1DIFA dimer) consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg(41) and Arg(140) (most electrostatic and polar) are not the least mobile; despite the higher energy, the hydrophobic residues (Ile, Leu, and Val) are least mobile and form the core by pinning down the local segments for the globular structure. Variations in the gyration radius (R(g)) and energy (E(c)) of the protein show nonmonotonic dependence on the interaction strength with the smallest R(g) around the largest value of E(c). Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse.

Role of solvent selectivity in the equilibrium surface composition of monolayers formed from a solution containing mixtures of organic thiols

We have developed a simple model to quantify the effect of solvent selectivity on the surface composition of two-component self-assembled monolayers formed from solutions containing mixtures of organic thiols. The coarse-grained molecular model incorporates the relevant intermolecular interactions in the solution and monolayer to yield an expression for the free energy of monolayer formation. Minimization of the free energy results in a simple and analytically tractable expression for the monolayer composition as a function of solvent selectivity (defined as the difference in the Flory-type interaction parameters of the two organic thiols in the solution) and the degree of incompatibility between the adsorbate molecules. A comparison of our theory to experiments on the formation of two-component self-assembled monolayers from solution indicates that the coarse-grained molecular model captures the trends in the experimental data quite well.

Polarization at metal-biomolecular interfaces in solution

Metal surfaces in contact with water, surfactants and biopolymers experience attractive polarization owing to induced charges. This fundamental physical interaction complements stronger epitaxial and covalent surface interactions and remains difficult to measure experimentally. We present a first step to quantify polarization on even gold (Au) surfaces in contact with water and with aqueous solutions of peptides of different charge state (A3 and Flg-Na3) by molecular dynamics simulation in all-atomic resolution and a posteriori computation of the image potential. Attractive polarization scales with the magnitude of atomic charges and with the length of multi-poles in the aqueous phase such as the distance between cationic and anionic groups. The polarization energy per surface area is similar on aqueous Au {1 1 1} and Au {1 0 0} interfaces of approximately -50 mJ m(-2) and decreases to -70 mJ m(-2) in the presence of charged peptides. In molecular terms, the polarization energy corresponds to -2.3 and -0.1 kJ mol(-1) for water in the first and second molecular layers on the metal surface, and to between -40 and 0 kJ mol(-1) for individual amino acids in the peptides depending on the charge state, multi-pole length and proximity to the surface. The net contribution of polarization to peptide adsorption on the metal surface is determined by the balance between polarization by the peptide and loss of polarization by replaced surface-bound water. On metal surfaces with significant epitaxial attraction of peptides such as Au {1 1 1}, polarization contributes only 10-20% to total adsorption related to similar polarity of water and of amino acids. On metal surfaces with weak epitaxial attraction of peptides such as Au {1 0 0}, polarization is a major contribution to adsorption, especially for charged peptides (-80 kJ mol(-1) for peptide Flg-Na(3)). A remaining water interlayer between the metal surface and the peptide then reduces losses in polarization energy by replaced surface-bound water. Computed polarization energies are sensitive to the precise location of the image plane (within tenths of Angstroms near the jellium edge). The computational method can be extended to complex nanometre and micrometer-size surface topologies.

Bioassembled layered silicate-metal nanoparticle hybrids

Here we report on the bioenabled assembly of layered nanohybrids using peptides identified with regard to their affinity to the nanoparticle surface. A dodecamer peptide termed M1, determined from a phage peptide display library, was found to bind to the surface of a layered aluminosilicate (montmorillonite, MMT). Fusion of a metal binding domain to the M1 peptide or the M1 peptide by itself was able to direct the growth of metal nanoparticles, such as gold and cobalt-platinum, respectively, on the MMT. This method of producing hybrid nanoclay materials will have utility in catalytic, optical, biomedical, and composite materials applications.

Modeling of thermal transport in pillared-graphene architectures

Carbon nanotubes (CNT) and graphene are considered as potential future candidates for many nano/microscale integrated devices due to their superior thermal properties. Both systems, however, exhibit significant anisotropy in their thermal conduction, limiting their performance as three-dimensional thermal transport materials. From thermal management perspective, one way to tailor this anisotropy is to consider designing alternative carbon-based architectures. This paper investigates the thermal transport in one such novel architecture-a pillared-graphene (PG) network nanostructure which combines graphene sheets and carbon nanotubes to create a three-dimensional network. Nonequilibrium molecular dynamics simulations have been carried out using the AIREBO potential to calculate the thermal conductivity of pillared-graphene structures along parallel (in-plane) as well as perpendicular (out-of-plane) directions with respect to the graphene plane. The resulting thermal conductivity values for PG systems are discussed and compared with simulated values for pure CNT and graphite. Our results show that in these PG structures, the thermal transport is governed by the minimum interpillar distance and the CNT-pillar length. This is primarily attributed to scattering of phonons occurring at the CNT-graphene junctions in these nanostructures. We foresee that such architecture could potentially be used as a template for designing future structurally stable microscale systems with tailorable in-plane and out-of-plane thermal transport.

Biomimetic chemosensor: designing peptide recognition elements for surface functionalization of carbon nanotube field effect transistors

Single-wall carbon nanotube field effect transistors (SWNT-FETs) are ideal candidates for fabricating sensors due to their unique electronic properties and have been widely investigated for chemical and biological sensing applications. The lack of selectivity of SWNT-FETs has prompted extensive research on developing ligands that exhibit specific binding as selective surface coating for SWNTs. Herein we describe the rational design of a peptide recognition element (PRE) that is capable of noncovalently attaching to SWNTs as well as binding to trinitrotoluene (TNT). The PRE contains two domains, a TNT binding domain derived from the binding pocket of the honeybee odor binding protein ASP1, and a SWNT binding domain previously identified from the phage peptide display library. The PRE structure in the presence of SWNT was investigated by performing classical all-atom molecular dynamics simulations, circular dichroism spectroscopy, and atomic force microscopy. Both computational and experimental analyses demonstrate that the peptide retains two functional domains for SWNT and TNT binding. The binding motif of the peptide to SWNT and to TNT was revealed from interaction energy calculations by molecular dynamics simulations. The potential application of the peptide for the detection of TNT is theoretically predicted and experimentally validated using a SWNT-FET sensor functionalized with a designer PRE. Results from this study demonstrate the creation of chemosensors using designed PRE as selective surface coatings for targeted analytes.

Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation

Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (epsilon(ij)) matrix (residue-residue, residue-solvent) of the coefficient (fepsilon(ij)) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified-some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly(49), with the time steps show how they slow down on increasing the interaction strength.

Toward understanding amino acid adsorption at metallic interfaces: a density functional theory study

In examining adsorption of a few selected single amino acids on Au and Pd cluster models by density functional theory calculations, we have shown that specific side-chain binding affinity to the surface may occur because of a combination of effects, including charge transfer. Larger binding was calculated at the Pd interface. In addition, the interplay between amino acid solvation and adsorption at the interface was considered from first principles. This analysis serves as the first step toward gaining a more accurate understanding of specific interactions at the interface of biological-metal nanostructures than has been attempted in the past.

Enrichment of (6,5) single wall carbon nanotubes using genomic DNA

Single wall carbon nanotubes (SWNTs) have attracted attention because of their potential in a vast range of applications, including transistors and sensors. However, immense technological importance lies in enhancing the purity and homogeneity of SWNTs with respect to their chirality for real-world electronic applications. In order to achieve optimal performance of SWNTs, the diameter, type, and chirality have to be effectively sorted. Any employed strategy for sorting SWNTs has to be scalable, nondestructible, and economical. In this paper, we present a solubilization and chirality enrichment study of commercially available SWNTs using genomic DNA. On the basis of the comparison of the photoluminescence (PL) and near-infrared absorption measurements from the SWNTs dispersed with salmon genomic DNA (SaDNA) and d(GT)20, we show that genomic DNA specifically enriches (6,5) tubes. Circular dichroism and classical all-atom molecular dynamics simulations reveal that the genomic double-stranded SaDNA prefers to interact with (6,5) SWNTs as compared to (10,3) tubes, meanwhile single-stranded d(GT)20 shows no or minimal chirality preference. Our enrichment process demonstrates enrichment of >86% of (6,5) SWNTs from CoMoCat nanotubes using SaDNA.

Relation between packing density and thermal transitions of alkyl chains on layered silicate and metal surfaces

Self-assembled layers of alkyl chains grafted onto the surfaces of layered silicates, metal, and oxidic nanoparticles are utilized to control interactions with external media by tuning the packing density of the chains on the surface, head group functionality, and chain length. Characterization through experiment and simulation shows that the orientation of the alkyl layers and reversible phase transitions on heating are a function of the cross-sectional area of the alkyl chains in relation to the available surface area per alkyl chain. On even surfaces, a packing density less than 0.2 leads to nearly parallel orientation of the alkyl chains on the surface, a high degree of conformational disorder, and no reversible melting transitions. A packing density between 0.2 and 0.75 leads to intermediate inclination angles, semicrystalline order, and reversible melting transitions on heating. A packing density above 0.75 results in nearly vertical alignment of the surfactants on the surface, a high degree of crystalline character, and absence of reversible melting transitions. Curved surfaces can be understood by the same principle, taking into account a local radius of curvature and a distance-dependent packing density on the surface. In good approximation, this simple model is independent from the length of the alkyl chains (a minimum length of C10 is required to form sufficiently distinctive patterns), the chemical nature of the surface, and of the surfactant head group. These structural details primarily determine the functionality of alkyl modified surfaces and the temperature of thermal transitions.

Conformation of a coarse-grained protein chain (an aspartic acid protease) model in effective solvent by a bond-fluctuating Monte Carlo simulation

In a coarse-grained description of a protein chain, all of the 20 amino acid residues can be broadly divided into three groups: Hydrophobic (H) , polar (P) , and electrostatic (E) . A protein can be described by nodes tethered in a chain with a node representing an amino acid group. Aspartic acid protease consists of 99 residues in a well-defined sequence of H , P , and E nodes tethered together by fluctuating bonds. The protein chain is placed on a cubic lattice where empty lattice sites constitute an effective solvent medium. The amino groups (nodes) interact with the solvent (S) sites with appropriate attractive (PS) and repulsive (HS) interactions with the solvent and execute their stochastic movement with the Metropolis algorithm. Variations of the root mean square displacements of the center of mass and that of its center node of the protease chain and its gyration radius with the time steps are examined for different solvent strength. The structure of the protease swells on increasing the solvent interaction strength which tends to enhance the relaxation time to reach the diffusive behavior of the chain. Equilibrium radius of gyration increases linearly on increasing the solvent strength: A slow rate of increase in weak solvent regime is followed by a faster swelling in stronger solvent. Variation of the gyration radius with the time steps suggests that the protein chain moves via contraction and expansion in a somewhat quasiperiodic pattern particularly in strong solvent.

High-resolution electron microscopy of montmorillonite and montmorillonite/epoxy nanocomposites

With the use of high-resolution transmission electron microscopy the structure and morphology of montmorillonite (MMT), a material of current interest for use in polymer nanocomposites, was characterized. Using both imaging theory and experiment, the procedures needed to generate lattice images from MMT were established. These procedures involve careful control of the microscope's objective lens defocus to maximize contrast from features of a certain size, as well as limiting the total dose of electrons received by the sample. Direct images of the MMT lattice were obtained from neat Na+ MMT, organically modified MMT, and organically modified MMT/epoxy nanocomposites. The degree of crystallinity and turbostratic disorder were characterized using electron diffraction and high-resolution electron microscopy (HREM). Also, the extent of the MMT sheets to bend when processed into an epoxy matrix was directly visualized. A minimum radius of curvature tolerable for a single MMT sheet during bending deformation was estimated to be 15 nm, and from this value a critical failure strain of 0.033 was calculated. HREM can be used to improve the understanding of the structure of polymer nanocomposites at the nanometer-length scale.

Correlation of the β-sheet crystal size in silk fibers with the protein amino acid sequence

Low voltage transmission electron microscopy (LVTEM) and wide angle X-ray scattering (WAXS) are used to independently determine the size of the β-sheet crystalline regions in Bombyx mori silk fibers. The peak in the size distributions of the major and minor axes of the anisotropic crystallites measured from the LVTEM images compare well with the average sizes as determined by Scherrer analysis of the X-ray fiber diagrams. These values are then discussed in the context of the B. mori fibroin heavy chain amino acid sequence, and the underlying mechanism for the organism's control on fiber crystallite size, and therefore mechanical properties, is proposed.

Multiscale mode dynamics of a tethered membrane

Stochastic dynamics of a tethered membrane with a bond-fluctuating coarse-grained Monte Carlo simulation shows, in addition to diffusion, nondiffusive behavior sensitive to the type of membrane, its size, and quality of the solvent. Motion of the membrane's center node is described by the variation of the mean-square displacement (R{n}{2}) with time step (t) , i.e., R{n}{2} proportional, variantt{2nu} with the exponent nu approximately 18-16 in the short time followed by subdiffusive power laws (i.e., nu approximately 15,110 ) in the intermediate time regimes before reaching diffusion nu=1. The crossover between in-plane wrinkle modes is identified from the segmental (node) motion of the membrane.

Study of the ordered structures of poly(styrene-b-vinyl4pyridine) in a solution state by using small-angle X-ray scattering and generalized indirect Fourier transform

The structures of the mesophases and their subunits (micelles) of poly(styrene-b-vinyl4pyridine) (PS-b-P4VP) in a toluene solution were studied by using small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and generalized indirect Fourier transform (GIFT) methods. The structures of PS-b-P4VP, such as the individual micelle, the face-centered cubic (fcc) and body-centered cubic (bcc), and the lamellar, were identified. The SAXS from the PS-b-P4VP solution showed a good contrast for the micelle, even in a low concentration of 0.25 wt %. As the concentration increases, the fcc and both fcc and bcc appear for the packing of the micelles of PS(3.3K)-b-P4VP(4.7K) and PS(12K)-b-P4VP(11.8K), respectively. The lamellar structure was also identified, with a further increase in the concentration for PS(3.3K)-b-P4VP(4.7K). These structures were also identified via TEM images.

Dynamics of Alkyl Ammonium Intercalants within Organically Modified Montmorillonite: Dielectric Relaxation and Ionic Conductivity

The low-frequency (0.01 Hz-10 MHz) dynamic characteristics of alkyl quaternary ammonium exchanged montmorillonite (SC20A) were investigated to determine the correlation between temperature-dependent changes in the interlayer structure and collective mobility of the surfactant. From 25 to 165 degrees C, SC20A exhibits two interlayer transitions, one ascribed to the melting of the intercalated alkyl chains of the surfactant (20-40 degrees C) and another associated with an abrupt decrease in the interlayer's coefficient of thermal expansion (100 degrees C). For this temperature range, the excess surfactant and residual electrolytes present in commercially manufactured SC20A enhance the direct current conductivity and increase low-frequency space-charge polarization, which is believed to occur across percolation paths established by the surfaces of the SC20A crystallites. In contrast, a higher-frequency relaxation, which was less sensitive to process history and impurity content, is ascribed to relaxation within the interlayer at the surfactant-aluminosilicate interface electrostatic couple. The temperature dependence of these dielectric relaxations indicated a drastic increase in mobility as the interlayer organic phase transitions from static and glasslike into molten and mobile. Overall, SC20A displayed features of alternating current universality, including time-temperature superposition, common in other types of disordered ion-conducting media. The presence of long-range transport and its sensitivity to low amounts of impurities imply that from a dynamic perspective the local environment of the surfactants are substantially diverse and a minority fraction, such as at the edge of the crystallite (gallery and aluminosilicate layer), may dominate the lower-frequency dielectric response.

Interaction energy and surface reconstruction between sheets of layered silicates

Interactions between two layered silicate sheets, as found in various nanoscale materials, are investigated as a function of sheet separation using molecular dynamics simulation. The model systems are periodic in the xy plane, open in the z direction, and subjected to stepwise separation of the two silicate sheets starting at equilibrium. Computed cleavage energies are 383 mJ /m(2) for K-mica, 133 mJ /m(2) for K-montmorillonite (cation exchange capacity=91), 45 mJ /m(2) for octadecylammonium (C(18))-mica, and 40 mJ /m(2) for C(18)-montmorillonite. These values are in quantitative agreement with experimental data and aid in the molecular-level interpretation. When alkali ions are present at the interface between the silicate sheets, partitioning of the cations between the surfaces is observed at 0.25 nm separation (mica) and 0.30 nm separation (montmorillonite). Originally strong electrostatic attraction between the two silicate sheets is then reduced to 5% (mica) and 15% (montmorillonite). Weaker van der Waals interactions decay within 1.0 nm separation. The total interaction energy between sheets of alkali clay is less than 1 mJ /m(2) after 1.5 nm separation. When C(18) surfactants are present on the surfaces, the organic layer (>0.8 nm) acts as a spacer between the silicate sheets so that positively charged ammonium head groups remain essentially in the same position on the surfaces of the two sheets at any separation. As a result, electrostatic interactions are efficiently shielded and dispersive interactions account for the interfacial energy. The flexibility of the hydrocarbon chains leads to stretching, disorder, and occasional rearrangements of ammonium head groups to neighbor cavities on the silicate surface at medium separation (1.0-2.0 nm). The total interaction energy amounts to less than 1 mJ /m(2) after 3 nm separation.

Thermally Induced α-Helix to β-Sheet Transition in Regenerated Silk Fibers and Films

The structure of thin films cast from regenerated solutions of Bombyx mori cocoon silk in hexafluoroisopropyl alcohol (HFIP) was studied by synchrotron X-ray diffraction during heating. A solid-state conformational transition from an alpha-helical structure to the well-known beta-sheet silk II structure occurred at a temperature of approximately 140 degrees C. The transition appeared to be homogeneous, as both phases do not coexist within the resolution of the current study. Modulated differential scanning calorimetry (DSC) of the films showed an endothermic melting peak followed by an exothermic crystallization peak, both occurring near 140 degrees C. Oriented fibers were also produced that displayed this helical molecular conformation. Subsequent heating above the structural transition temperature produced oriented beta-sheet fibers very similar in structure to B. mori cocoon fibers. Heat treatment of silk films at temperatures well below their degradation temperature offers a controllable route to materials with well-defined structures and mechanical behavior.