Molecular dynamics of folding of secondary structures in Go-type models of proteins

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamics simulations with the Langevin noise. Models with the steric constraints are found to be better folders and to be more stable, especially in the case of the $\beta$-structures. Phononic spectra for vibrations around the native states have low frequency gaps that correlate with the thermodynamic stability. Folding of the secondary structures proceeds through a well defined sequence of events. For instance, $\alpha$-helices fold from the ends first. The closer to the native state, the faster establishment of the contacts. Increasing the system size deteriorates the folding characteristics. We study the folding times as a function of viscous friction and find a regime of moderate friction with the linear dependence. We also consider folding when one end of a structure is pinned which imitates instantaneous conditions when a protein is being synthesized. We find that, under such circumstances, folding of helices is faster and of the $\beta$-sequences slower.Comment: REVTeX, 14 pages, EPS figures included, JCP in pres

Probing autoionizing states of molecular oxygen with XUV transient absorption: Electronic symmetry dependent lineshapes and laser induced modification

The dynamics of autoionizing Rydberg states of oxygen are studied using attosecond transient absorption technique, where extreme ultraviolet (XUV) initiates molecular polarization and near infrared (NIR) pulse perturbs its evolution. Transient absorption spectra show positive optical density (OD) change in the case of $ns\sigma_g$ and $nd\pi_g$ autoionizing states of oxygen and negative OD change for $nd\sigma_g$ states. Multiconfiguration time-dependent Hartree-Fock (MCTDHF) calculation are used to simulate the transient absorption spectra and their results agree with experimental observations. The time evolution of superexcited states is probed in electronically and vibrationally resolved fashion and we observe the dependence of decay lifetimes on effective quantum number of the Rydberg series. We model the effect of near-infrared (NIR) perturbation on molecular polarization and find that the laser induced phase shift model agrees with the experimental and MCTDHF results, while the laser induced attenuation model does not. We relate the electron state symmetry dependent sign of the OD change to the Fano parameters of the static absorption lineshapes.Comment: 15 pages, 8 figure

Appropriately differentiated ARPE-19 cells regain phenotype and gene expression profiles similar to those of native RPE cells.

PurposeThe RPE cell line ARPE-19 provides a dependable and widely used alternative to native RPE. However, replication of the native RPE phenotype becomes more difficult because these cells lose their specialized phenotype after multiple passages. Compounding this problem is the widespread use of ARPE-19 cells in an undifferentiated state to attempt to model RPE functions. We wished to determine whether suitable culture conditions and differentiation could restore the RPE-appropriate expression of genes and proteins to ARPE-19, along with a functional and morphological phenotype resembling native RPE. We compared the transcriptome of ARPE-19 cells kept in long-term culture with those of primary and other human RPE cells to assess the former's inherent plasticity relative to the latter.MethodsARPE-19 cells at passages 9 to 12 grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum were differentiated for up to 4 months. Immunocytochemistry was performed on ARPE-19 cells grown on filters. Total RNA extracted from ARPE-19 cells cultured for either 4 days or 4 months was used for RNA sequencing (RNA-Seq) analysis using a 2 × 50 bp paired end protocol. The RNA-Seq data were analyzed to identify the affected pathways and recognize shared ontological classification among differentially expressed genes. RPE-specific mRNAs and miRNAs were assessed with quantitative real-time (RT)-PCR, and proteins with western blotting.ResultsARPE-19 cells grown for 4 months developed the classic native RPE phenotype with heavy pigmentation. RPE-expressed genes, including RPE65, RDH5, and RDH10, as well as miR-204/211, were greatly increased in the ARPE-19 cells maintained at confluence for 4 months. The RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of the genes in the differentiated ARPE-19 cells. Of the 16,757 genes with detectable signals, nearly 1,681 genes were upregulated, and 1,629 genes were downregulated with a fold change of 2.5 or more differences between 4 months and 4 days of culture. Gene Ontology analysis showed that the upregulated genes were associated with visual cycle, phagocytosis, pigment synthesis, cell differentiation, and RPE-related transcription factors. The majority of the downregulated genes play a role in cell cycle and proliferation.ConclusionsThe ARPE-19 cells cultured for 4 months developed a phenotype characteristic of native RPE and expressed proteins, mRNAs, and miRNAs characteristic of the RPE. Comparison of the ARPE-19 RNA-Seq data set with that of primary human fetal RPE, embryonic stem cell-derived RPE, and native RPE revealed an important overall similar expression ratio among all the models and native tissue. However, none of the cultured models reached the absolute values in the native tissue. The results of this study demonstrate that low-passage ARPE-19 cells can express genes specific to native human RPE cells when appropriately cultured and differentiated

Lightweight, flaw-tolerant, and ultrastrong nanoarchitected carbon

It has been a long-standing challenge in modern material design to create low-density, lightweight materials that are simultaneously robust against defects and can withstand extreme thermomechanical environments, as these properties are often mutually exclusive: The lower the density, the weaker and more fragile the material. Here, we develop a process to create nanoarchitected carbon that can attain specific strength (strength-to-density ratio) up to one to three orders of magnitude above that of existing micro- and nanoarchitected materials. We use two-photon lithography followed by pyrolysis in a vacuum at 900 °C to fabricate pyrolytic carbon in two topologies, octet- and iso-truss, with unit-cell dimensions of ∼2 μm, beam diameters between 261 nm and 679 nm, and densities of 0.24 to 1.0 g/cm^3. Experiments and simulations demonstrate that for densities higher than 0.95 g/cm^3 the nanolattices become insensitive to fabrication-induced defects, allowing them to attain nearly theoretical strength of the constituent material. The combination of high specific strength, low density, and extensive deformability before failure lends such nanoarchitected carbon to being a particularly promising candidate for applications under harsh thermomechanical environments

Sequencing of folding events in Go-like proteins

We have studied folding mechanisms of three small globular proteins: crambin (CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3) which are modelled by a Go-like Hamiltonian with the Lennard-Jones interactions. It is shown that folding is dominated by a well-defined sequencing of events as determined by establishment of particular contacts. The order of events depends primarily on the geometry of the native state. Variations in temperature, coupling strengths and viscosity affect the sequencing scenarios to a rather small extent. The sequencing is strongly correlated with the distance of the contacting aminoacids along the sequence. Thus $\alpha$-helices get established first. Crambin is found to behave like a single-route folder, whereas in CI2 and SH3 the folding trajectories are more diversified. The folding scenarios for CI2 and SH3 are consistent with experimental studies of their transition states.Comment: REVTeX, 12 pages, 11 EPS figures, J. Chem. Phys (in press

An Exotic Species Is the Favorite Prey of a Native Enemy

Although native enemies in an exotic species' new range are considered to affect its ability to invade, few studies have evaluated predation pressures from native enemies on exotic species in their new range. The exotic prey naiveté hypothesis (EPNH) states that exotic species may be at a disadvantage because of its naïveté towards native enemies and, therefore, may suffer higher predation pressures from the enemy than native prey species. Corollaries of this hypothesis include the native enemy preferring exotic species over native species and the diet of the enemy being influenced by the abundance of the exotic species. We comprehensively tested this hypothesis using introduced North American bullfrogs (Lithobates catesbeianus, referred to as bullfrog), a native red-banded snake (Dinodon rufozonatum, the enemy) and four native anuran species in permanent still water bodies as a model system in Daishan, China. We investigated reciprocal recognition between snakes and anuran species (bullfrogs and three common native species) and the diet preference of the snakes for bullfrogs and the three species in laboratory experiments, and the diet preference and bullfrog density in the wild. Bullfrogs are naive to the snakes, but the native anurans are not. However, the snakes can identify bullfrogs as prey, and in fact, prefer bullfrogs over the native anurans in manipulative experiments with and without a control for body size and in the wild, indicating that bullfrogs are subjected to higher predation pressures from the snakes than the native species. The proportion of bullfrogs in the snakes' diet is positively correlated with the abundance of bullfrogs in the wild. Our results provide strong evidence for the EPNH. The results highlight the biological resistance of native enemies to naïve exotic species

Simple scheme for implementing the Deutsch-Jozsa algorithm in thermal cavity

We present a simple scheme to implement the Deutsch-Jozsa algorithm based on two-atom interaction in a thermal cavity. The photon-number-dependent parts in the evolution operator are canceled with the strong resonant classical field added. As a result, our scheme is immune to thermal field, and does not require the cavity to remain in the vacuum state throughout the procedure. Besides, large detuning between the atoms and the cavity is not necessary neither, leading to potential speed up of quantum operation. Finally, we show by numerical simulation that the proposed scheme is equal to demonstrate the Deutsch-Jozsa algorithm with high fidelity.Comment: 7 pages, 4 figure