Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.

Protein-RNA docking is hampered by the high flexibility of RNA, and particularly single-stranded RNA (ssRNA). Yet, ssRNA regions typically carry the specificity of protein recognition. The lack of methodology for modeling such regions limits the accuracy of current protein-RNA docking methods.

A Simple Approach for Molecular Controlled Release based on Atomic Layer Deposition Hybridized Organic-Inorganic Layers.

On-demand release of bioactive substances with high spatial and temporal control offers ground-breaking possibilities in the field of life sciences. However, available strategies for developing such release systems lack the possibility of combining efficient control over release with adequate storage capability in a reasonably compact system. In this study we present a new approach to target this deficiency by the introduction of a hybrid material.

Mechanism of Reversible Peptide-Bilayer Attachment: Combined Simulation and Experimental Single-Molecule Study.

The binding of peptides and proteins to lipid membrane surfaces is of fundamental importance for many membrane-mediated cellular processes. Using closely matched molecular dynamics simulations and atomic force microscopy experiments, we study the force-induced desorption of single peptide chains from phospholipid bilayers to gain microscopic insight into the mechanism of reversible attachment. This approach allows quantification of desorption forces and decomposition of peptide-membrane interactions into energetic and entropic contributions.

Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step.

Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments.

Stochastic Approach to Phonon-Assisted Optical Absorption.

We develop a first-principles theory of phonon-assisted optical absorption in semiconductors and insulators which incorporates the temperature dependence of the electronic structure. We show that the Hall-Bardeen-Blatt theory of indirect optical absorption and the Allen-Heine theory of temperature-dependent band structures can be derived from the present formalism by retaining only one-phonon processes. We demonstrate this method by calculating the optical absorption coefficient of silicon using an importance sampling Monte Carlo scheme, and we obtain temperature-dependent line shapes and band gaps in good agreement with experiment.

Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase.

The enzyme adenylate kinase (ADK) features two substrate binding domains that undergo large-scale motions during catalysis. In the apo state, the enzyme preferentially adopts a globally open state with accessible binding sites. Binding of two substrate molecules (AMP + ATP or ADP + ADP) results in a closed domain conformation, allowing efficient phosphoryl-transfer catalysis.

Clinical epidemiology of heart failure with preserved ejection fraction (HFpEF) in comparatively young hospitalized patients.

Background: While heart failure with preserved ejection fraction (HFpEF) is primarily a disease of old age, risk factors that contribute to HFpEF are not limited to older patients. The objectives of this population-based observational study were to describe the clinical epidemiology of HFpEF in younger (<65 years) as compared with older (≥65 years) patients hospitalized with acute decompensated heart failure.

Methods And Results: We reviewed the medical records of residents of central Massachusetts hospitalized with HFpEF at all 11 greater Worcester (MA) medical centers during the 5 study years of 1995, 2000, 2002, 2004, and 2006.

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.

Double stranded helical DNA and RNA are flexible molecules that can undergo global conformational fluctuations. Their bending, twisting and stretching deformabilities are of similar magnitude. However, recent single-molecule experiments revealed a striking qualitative difference indicating an opposite sign for the twist-stretch couplings of dsDNA and dsRNA [Lipfert et al.

Connecting marine productivity to sea-spray via nanoscale biological processes: Phytoplankton Dance or Death Disco?

Bursting bubbles at the ocean-surface produce airborne salt-water spray-droplets, in turn, forming climate-cooling marine haze and cloud layers. The reflectance and ultimate cooling effect of these layers is determined by the spray's water-uptake properties that are modified through entrainment of ocean-surface organic matter (OM) into the airborne droplets. We present new results illustrating a clear dependence of OM mass-fraction enrichment in sea spray (OMss) on both phytoplankton-biomass, determined from Chlorophyll-a (Chl-a) and Net Primary Productivity (NPP).

The Antibody Light-Chain Linker Is Important for Domain Stability and Amyloid Formation.

The association of light chains (LCs) and heavy chains is the basis for functional antibodies that are essential for adaptive immune responses. However, in some cases, LCs and especially fragments consisting of the LC variable (VL) domain are pathologically deposited in fatal aggregation diseases. The two domains of the LC are connected by a highly conserved linker.

RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity.

Aptamers are an emerging class of highly specific targeting ligands. They can be selected in vitro for a large variety of targets, ranging from small molecules to whole cells. Most aptamers selected are nucleic acid-based, allowing chemical synthesis and easy modification.

The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study.

Major histocompatibility complex (MHC) class I molecules (proteins) bind peptides of eight to ten amino acids to present them at the cell surface to cytotoxic T cells. The class I binding groove binds the peptide via hydrogen bonds with the peptide termini and via diverse interactions with the anchor residue side chains of the peptide. To elucidate which of these interactions is most important for the thermodynamic and kinetic stability of the peptide-bound state, we have combined molecular dynamics simulations and experimental approaches in an investigation of the conformational dynamics and binding parameters of a murine class I molecule (H-2Kb) with optimal and truncated natural peptide epitopes.

Quantum Critical Elasticity.

We discuss elastic instabilities of the atomic crystal lattice at zero temperature. Because of long-range shear forces of the solid, at such transitions the phonon velocities vanish, if at all, only along certain crystallographic directions, and, consequently, the critical phonon fluctuations are suppressed to a lower dimensional manifold and governed by a Gaussian fixed point. In the case of symmetry-breaking elastic transitions, a characteristic critical phonon thermodynamics arises that is found, e.

Exploring biomolecular dynamics and interactions using advanced sampling methods.

Molecular dynamics (MD) and Monte Carlo (MC) simulations have emerged as a valuable tool to investigate statistical mechanics and kinetics of biomolecules and synthetic soft matter materials. However, major limitations for routine applications are due to the accuracy of the molecular mechanics force field and due to the maximum simulation time that can be achieved in current simulations studies. For improving the sampling a number of advanced sampling approaches have been designed in recent years.

Fully Blind Peptide-Protein Docking with pepATTRACT.

Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. Here, we present a new fully blind flexible peptide-protein docking protocol, pepATTRACT, which combines a rapid coarse-grained global peptide docking search of the entire protein surface with a two-stage atomistic flexible refinement.

Assessing the clinical benefit of a nomogram to predict specimen-confined disease at radical prostatectomy in patients with high-risk prostate cancer: An external validation.

Objective: The objective of the current study was to test generalizability and clinical value of a recently published nomogram to predict specimen-confined disease (SCD, pT2-pT3a+R0+pN0) at radical prostatectomy (RP) in patients with clinical high-risk prostate cancer (HRPCa). The nomogram allows improved decision making with curative intent within this heterogeneous patient cohort, which is important, as RP in patients with clinical HRPCa remains a topic of controversy.

Methods: We externally validated the nomogram in 1,669 men with clinical HRPCa who underwent RP and extended pelvic lymph node dissection between 1992 and 2011.

Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.

The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures.

Location and Electronic Nature of Phosphorus in the Si Nanocrystal--SiO2 System.

Up to now, no consensus exists about the electronic nature of phosphorus (P) as donor for SiO2-embedded silicon nanocrystals (SiNCs). Here, we report on hybrid density functional theory (h-DFT) calculations of P in the SiNC/SiO2 system matching our experimental findings. Relevant P configurations within SiNCs, at SiNC surfaces, within the sub-oxide interface shell and in the SiO2 matrix were evaluated.

Observing the morphology of single-layered embedded silicon nanocrystals by using temperature-stable TEM membranes.

We use high-temperature-stable silicon nitride membranes to investigate single layers of silicon nanocrystal ensembles by energy filtered transmission electron microscopy. The silicon nanocrystals are prepared from the precipitation of a silicon-rich oxynitride layer sandwiched between two SiO2 diffusion barriers and subjected to a high-temperature annealing. We find that such single layers are very sensitive to the annealing parameters and may lead to a significant loss of excess silicon.

Structural parameters effect on the electrical and electroluminescence properties of silicon nanocrystals/SiO2 superlattices.

The effect of the oxide barrier thickness (tSiO2) reduction and the Si excess ([Si]exc) increase on the electrical and electroluminescence (EL) properties of Si-rich oxynitride (SRON)/SiO2 superlattices (SLs) is investigated. The active layers of the metal-oxide-semiconductor devices were fabricated by alternated deposition of SRON and SiO2 layers on top of a Si substrate. The precipitation of the Si excess and thus formation of Si nanocrystals (NCs) within the SRON layers was achieved after an annealing treatment at 1150 °C.

An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA.

Oligomeric macromolecules in the cell self-organize into a wide variety of geometrical motifs such as helices, rings or linear filaments. The recombinase proteins involved in homologous recombination present many such assembly motifs. Here, we examine in particular the polymorphic characteristics of RecA, the most studied member of the recombinase family, using an integrative approach that relates local modes of monomer/monomer association to the global architecture of their screw-type organization.

Constraints on an annihilation signal from a core of constant dark matter density around the milky way center with H.E.S.S.

An annihilation signal of dark matter is searched for from the central region of the Milky Way. Data acquired in dedicated on-off observations of the Galactic center region with H.E.

Dielectrophoretic investigation of Bi₂Te₃ nanowires-a microfabricated thermoelectric characterization platform for measuring the thermoelectric and structural properties of single nanowires.

In this article a microfabricated thermoelectric nanowire characterization platform to investigate the thermoelectric and structural properties of single nanowires is presented. By means of dielectrophoresis (DEP), a method to manipulate and orient nanowires in a controlled way to assemble them onto our measurement platform is introduced. The thermoelectric platform fabricated with optimally designed DEP electrodes results in a yield of nanowire assembly of approximately 90% under an applied peak-to-peak ac signal Vpp = 10 V and frequency f = 20 MHz within a series of 200 experiments.