Molecular modeling and structural characterization of a high glycine–tyrosine hair keratin associated protein

Physical Chemistry Chemical Physics
High glycine–tyrosine (HGT) proteins are an important constituent of the keratin associated proteins (KAPs) present in human hair. The glassy state physics of hair fibres are thought to be largely regulated by KAPs, which exist in an amorphous state and are readily affected by environmental conditions. However, there are no studies characterizing the individual KAPs. In this paper, we present the first step to fill this gap by computational modeling and experimental studies on a HGT protein, KAP8.1. In particular, we have modeled the three-dimensional structure of this 63-residue protein using homology information from an anti-freeze protein in snow flea. The model for KAP8.1 is characterized by four strands of poly-proline II (or PPII) type helical secondary structures, held together by two cysteine disulphide bridges. Computer simulations confirm the stability of the modelled structure and show that the protein largely samples the PPII and β-sheet conformations during the...  Read more

Phase transformation in two-dimensional crystalline silica under compressive loading

Physical Chemistry Chemical Physics
Using molecular dynamics simulations, we report a novel phase transformation from the hexagonal structure to the distorted structure in two-dimensional (2D) crystalline bilayer silica under uniaxial compression. In particular, the transformed distorted structures are found to be topographically different when the 2D silica is compressed in the zigzag and armchair directions, respectively. The compression-induced phase transformation has important implications for the physical responses of 2D silica. It is shown that the Young's modulus, Poisson's ratio and thermal conductivity of 2D silica are all greatly reduced after it transitions from the parent hexagonal phase to the transformed distorted phase. Moreover, we also find that the aforementioned material properties of 2D silica become strongly anisotropic after the phase transformation, in contrast to the isotropic material properties observed in the parent hexagonal phase of 2D silica.Read more

Theoretical and Experimental Examination on SFG Polarization Analysis at Acetonitrile-Water Solution Surfaces

Physical Chemistry Chemical Physics
Sum frequency generation (SFG) spectroscopy is widely used to observe molecular orientation at interfaces through combination of various polarizations. The present work thoroughly examines the relation between the polarization dependence of SFG signals and the molecular orientation, by comparing SFG measurement and molecular dynamics (MD) simulation of acetonitrile/water solutions. The present SFG experiment and MD simulation yield quite consistent results on the ratios of χ(2) elements, supporting the reliability of both means. However, the subsequent polarization analysis tends to derive more upright tilt angles of acetonitrile than the direct MD calculation. The reasons of discrepancy are examined in terms of three issues; (i) anisotropy of Raman tensor, (ii) cross correlation, and (iii) orientational distribution. The analysis revealed that the issues (i) and (iii) are the main causes of errors in the conventional polarization analysis of SFG spectra. In...  Read more

Atomic structure of Mg-based metallic glasses from molecular dynamics and neutron diffraction

Physical Chemistry Chemical Physics
We use a combination of classical molecular dynamics simulation and neutron diffraction to identify the atomic structure of five different Mg–Zn–Ca bulk metallic glasses, covering a range of compositions with substantially different behaviour when implanted in vitro. There is very good agreement between the structures obtained from computer simulation and those found experimentally. Bond lengths and the total correlation function do not change significantly with composition. The zinc and calcium bonding shows differences between composition: the distribution of Zn–Ca bond lengths becomes narrower with increasing Zn content, and the preference for Zn and Ca to avoid bonding to themselves or each other becomes less strong, and, for Zn–Ca, transforms into a positive preference to bond to each other. This transition occurs at about the same Zn content at which the behaviour on implantation changes, hinting at a possible structural connection. A very broad distribution of...  Read more

Negative Poisson's ratio in rippled graphene

In this work, we perform molecular dynamics (MD) simulations to study the effect of rippling on the Poisson's ratio of graphene. Due to the atomic scale thickness of graphene, out-of-plane ripples are generated in free standing graphene with topological defects (e.g. heptagons and pentagons) to release the in-plane deformation energy. Through MD simulations, we have found that the Poisson's ratio of rippled graphene decreases upon increasing its aspect ratio η (amplitude over wavelength). For the rippled graphene sheet η = 0.188, a negative Poisson's ratio of −0.38 is observed for a tensile strain up to 8%, while the Poisson's ratio for η = 0.066 is almost zero. During uniaxial tension, the ripples gradually become flat, thus the Poisson's ratio of rippled graphene is determined by the competing factors of the intrinsic positive Poisson's ratio of graphene and the negative Poisson's ratio due to the de-wrinkling effect. Besides, the rippled...  Read more

Spontaneous NaCl-Doped Ice at Seawater Conditions: Focus on the Mechanisms of Ions Inclusion

Physical Chemistry Chemical Physics
Molecular dynamics simulations on microsecond time scale have been performed on an aqueous solution of TIP4P/2005 water and NaCl by using the direct coexistence technique to study the ice growth and the interface ice/liquid water. At ambient pressure, for temperatures above the eutectic point of the salt and at seawater concentration the brine rejection phenomenon and the spontaneous growth of a ice slab doped by the salt are obtained, as found in natural terrestrial and planetary environments. Experiments indicate that Cl- goes substitutional to ice sites. In line with these evidences we find a new result: the Cl- ion included in the lattice always substitutes not one but two water molecules leaving the ice structure around not distorted. The Na+ ion shows lower probability to be included in the ice and it occupies an interstitial site, causing a local distortion of the lattice. No sign of significative ions diffusion is observed in the lattice.Read more

Thermally-Induced Softening of PNIPAm-Based Nanopillar Arrays

Soft Matter
The surface properties of soft nanostructured hydrogels are crucial in the design of responsive materials that can be used as platforms to create adaptive devices. The lower critical solution temperature (LCST) of thermo-responsive hydrogels such as poly(N-isopropylacrylamide) (PNIPAm) can be modified by introducing a hydrophilic monomer to create a wide range of thermo-responsive micro-nanostructures in a large temperature range. Using surface initiation atom-transfer radical polymerization in synthesized anodized aluminum oxide templates, we designed, fabricated, and characterized thermo-responsive nanopillars based on PNIPAm hydrogels with tunable mechanical properties by incorporating acrylamide monomers (AAm). In addition to their LCST, the incorporation of a hydrophilic entity in the nanopillars based on PNIPAm has abruptly changed the topological and mechanical properties of our system. To gain insight on the mechanical properties of the nanostructure, its...  Read more

On the coupling between the dynamics of protein and water

Physical Chemistry Chemical Physics
Interactions between water and biomolecules can significantly change the former's structural, dynamic, and thermodynamic properties relative to the bulk. Experimental, theoretical, and computational studies show that changes in water properties can be observed at distances of more than 10 Å from a biomolecule. The effects of biopolymers on hydration water molecules can be attributed to several factors: the chemical nature of the amino acid residues involved, the spatial arrangement of the biomolecule, and its conformational flexibility. In the current study, we concentrate on the effect of protein chain flexibility on the properties of hydration water, using short peptides as a model. We constructed 18 linear peptides with the sequence (XXGG) × 5, where X represents one of the common amino acids, other than glycine and proline. Using molecular dynamics (MD) simulations, we studied how restricting the chain flexibility can affect the structural, dynamic, and thermodynamic properties...  Read more

Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations

Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems. We study the structure and dynamics of this DNA icosahedron using fully atomistic molecular dynamics (MD) simulation in explicit water and ions. The major modes of internal motion have been identified using principal component analysis. We provide a quantitative estimate of the radius of gyration (Rg), solvent accessible surface area (SASA) and volume of the icosahedron which is essential to estimate its...  Read more

Modulation of electronic and mechanical properties of phagraphene via hydrogenation and fluorination

Physical Chemistry Chemical Physics
Recently, a new carbon sheet, phagraphene, was proposed by theoretical calculations [Nano Lett. 2015, 15, 6182]. In this paper, the hydrogenated and fluorinated phagraphene (denoted as H-PHA and F-PHA) sheets have been systematically studied using first-principles calculations. The results of formation energy, ab initio molecular dynamics, phonon dispersion and elastic constants confirm that the modified phagraphene sheets are thermodynamically and dynamically as well as mechanically stable. We find that hydrogenation or fluorination is an effective way to modulate the bandgap, and we also find that adsorption-induced semimetal-semiconductor transition and adsorption-induced semimetal-insulator transition occur. Configuration-dependent bandgap for partially H-PHA and configuration-independent bandgap for fully H-PHA are determined. Adsorption-ratio-dependent bandgaps of H-PHA and F-PHA are also identified. Calculated bandgaps from HSE06 and PBE functionals of fully H-PHA are larger...  Read more

Adsorption of the natural protein surfactant Rsn-2 onto liquid interfaces

Physical Chemistry Chemical Physics
To stabilize foams, droplets and films at liquid interfaces a range of protein biosurfactants have evolved in nature. Compared to synthetic surfactants, these combine surface activity with biocompatibility and low solution aggregation. One recently studied example is Rsn-2, a component of the foam nest of the frog Engystomops pustulosus, which has been predicted to undergo a clamshell-like opening transition at the air–water interface. Using atomistic molecular dynamics simulations and surface tension measurements we study the adsorption of Rsn-2 onto air–water and cyclohexane–water interfaces. The protein adsorbs readily at both interfaces, with adsorption mediated by the hydrophobic N-terminus. At the cyclohexane–water interface the clamshell opens, due to the favourable interaction between hydrophobic residues and cyclohexane molecules and the penetration of cyclohexane molecules into the protein core. Simulations of deletion mutants showed that removal of the...  Read more

Anisotropic ion diffusion in α-Cr2O3: an atomistic simulation study

Physical Chemistry Chemical Physics
Chromia α-Cr2O3 is one of the most technologically important oxides, as it is the basis behind the passivation of many structural materials like stainless steel. It both resists oxygen ingress and slows the release of metals from its substrate by its high density and very low diffusivities. Were any further improvement to the protectiveness of chromia to be realized, no matter how small, it would have an enormous impact due to its ubiquitousness. Here we use molecular dynamics (MD) in conjunction with nudged elastic band (NEB) calculations to study oxygen and chromium ions diffusion mechanisms in α-Cr2O3 . Significant anisotropic diffusion between the ab-plane and the c-axis are observed for both oxygen and chromium ions. We find that vacancy-mediated ion diffusion in the ab-plane is faster than diffusion along c-axis, while interstitial-mediated diffusion along the c-axis is...  Read more

Oligomerization process of Bcl-2 associated X protein revealed from intermediate structures in solution

Physical Chemistry Chemical Physics
Upon apoptotic stress, Bcl-2 associated X (BAX) protein undergoes conformational changes and oligomerizes, leading to the mitochondrial membrane permeabilization and cell death. While structures of the resultant oligomer have been extensively studied, little is known about the intermediates that describe the reaction pathway from the inactive monomers to activated oligomers. Here we characterize the intermediate structures of BAX using combined small-angle X-ray scattering (SAXS) with on-line gel-filtration and electron spin resonance (ESR). The intermediates, including monomers, dimers, and tetramers, are reconstructed via integrating the SAXS-envelopes and ESR-determined skeleton structures. The hence revealed structures suggest a linear oligomerization of BAX utilizing the extended dimers with the two flexible α6 chains protruded out as ditopic ligands. The results of molecular dynamics simulation also support the ditopic dimer conformation with mobile α6. The ditopic...  Read more

Asymmetric Charge Separation and Recombination in Symmetrically Functionalized σ-π Hybrid Oligosilanes

Dalton Transactions
The flexibility of σ-conjugated silanes presents new opportunities for manipulating charge generation, transport, and non-linear optical properties of materials. Recently we synthesized a series of acceptor-donor-acceptor (ADA) compounds in which a methylated oligosilane core (D) is flanked by electron-deficient cyanovinyl-substituted arenes (A). Based on a detailed characterization of the photophysics of ADA and donor-acceptor (DA) architectures using both steady state and ultrafast spectroscopic measurements we illustrate that asymmetric charge separation occurs directly following light absorption. Lippert analysis of solvatochromic emission indicates large changes in dipole moments on excitation consistent with the formation of dipolar emissive states. Time resolved absorption measurements reveal common excited-state relaxation behavior across molecular structures: spectral dynamics associated with the relaxation of nascent excited states occur on a common timescale for all...  Read more

Models for biomedical interfaces: a computational study of quinone-functionalized amorphous silica surface features

Physical Chemistry Chemical Physics
A density functional theory (PBE functional) investigation is carried out, in which a model of an amorphous silica surface is functionalized by ortho-benzoquinone. Surface functionalization with catechol and quinone-based compounds is relevant in biomedical fields, from prosthetic implants to dentistry, to develop multifunctional coatings with antimicrobial properties. The present study provides atomistic information on the specific interactions between the functionalizing agent and the silanol groups at the silica surface. The distinct configurations of the functional groups, the hydrogen bond pattern, the role of dispersion forces and the simulated IR spectra provide detailed insight into the features of this model surface coating. Ab initio molecular dynamics gives further insights into the mobility of the functionalizing groups. As a final step, we studied the condensation reaction with allylamine, via Schiff base formation, to ground subsequent...  Read more

Graphene flakes obtained by local electro-exfoliation of graphite with a STM tip

Physical Chemistry Chemical Physics
Graphite surfaces can be manipulated by several methods to create graphene structures of different shapes and sizes. Scanning tunneling microscopy (STM) can be used to create these structures either through mechanical contact between the tip and the surface or through electro-exfoliation. In the latter, the mechanisms involved in the process of exfoliation at an applied voltage are not fully understood. Here, we show how a graphite surface can be locally exfoliated in a systematic manner by applying an electrostatic force with a STM tip at the edge of a terrace, forming triangular flakes several nanometers in length. We demonstrate, through experiments and simulations, how these flakes are created by a two-step process: first a voltage ramp must be applied at the edge of the terrace, and then the tip must be scanned perpendicular to the edge. Ab initio electrostatic calculations reveal that the presence of charges on the graphite surface weakens the interaction between layers...  Read more

Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors

Physical Chemistry Chemical Physics
Globular denatured proteins have structural properties similar to those of random coils. Experiments on denatured proteins have shown that when the temperature is increased thermal compaction may take place, resulting in a reduction of their radius of gyration Rg to range between 5% and 35% of its initial value. This phenomenon has been attributed to various causes, namely entropic, hydrophobic, and structural factors. The intrinsically disordered protein tau, which helps in nucleating and stabilizing microtubules in the axons of the neurons, also undergoes a relevant compaction process: when its temperature is increased from 293 K to 333 K its gyration radius decreases by 18%. We have performed an atomistic simulation of this molecule, at the lowest and highest temperatures of the mentioned interval, using both standard molecular dynamics and metadynamics, in parallel with small-angle X-ray scattering experiments. Using the fit of the experimental...  Read more

An insight into methanol oxidation mechanisms on RuO2(100) under an aqueous environment by DFT calculations

Physical Chemistry Chemical Physics
In this work, we have studied methanol oxidation mechanisms on RuO2(100) by using density functional theory (DFT) calculations and ab initio molecular dynamics (MD) simulations with some explicit interfacial water molecules. The overall mechanisms are identified as: CH3OH* → CH3O* → HCHO* → HCH(OH)2* → HCHOOH* → HCOOH* → mono-HCOO* → CO2*, without CO formation. This study provides a theoretical insight into C1 molecule oxidation mechanisms at atomic levels on metal oxide surfaces under an aqueous environment.Read more

Tunable phenol remediation from wastewater using SWCNT-based, sub-nanometer porous membranes: reactive molecular dynamics simulations and DFT calculations

Physical Chemistry Chemical Physics
The importance and impact of the application of CNT membranes with sub-nanometer pores for effective water purification are marvelous. Here we demonstrate, by reactive MD simulations, that CNT membranes can efficiently reject phenol due to molecular size exclusion effects and yield high permeability of water. The water flux in armchair CNTs with a pore diameter of about 7 Å is 1.3 orders of magnitude greater than that of the zigzag counterparts, and pore chemistry plays an important role in moderating the water flux. Nanotubes with H-capped atoms on their rims lead to higher fluxes (50 times) than that of the C-passive counterpart. In nanotubes of larger diameters (8 Å), the pore size is large enough to permit phenol molecules to permeate without any restraint. A series of evidence-based investigations on the interaction nature of the systems under consideration was performed to explain the specific molecular factors as well as systematically reliable relationships for water...  Read more

Clustering of hydroxyapatite on a super-twisted collagen microfibril under mechanical tension

Journal of Materials Chemistry B
It is well-known that nucleation and growth of the mineral phase in bone are intimately linked to the interaction between the apatite phase and the collagen matrix at the molecular scale. The exact mechanism of this interaction, however, is not clear due to the challenges involved in experimental characterization at the small size-scale. Herein, we employed molecular dynamics (MD) simulations to investigate the early state of nucleation (i.e. clustering) and growth of apatite clusters on a super-twisted collagen microfibril under mechanical tension in an aqueous solution. The results reveal that mechanical tension (force) facilitates the clustering and growth of the mineral phase on collagen. These results contribute to the understanding of hydroxyapatite (HAP)-collagen interaction and bone biomechanics at the microfibril level.Read more