Search results for "interaction [dark matter]"

Experimental-Like Affinity Constants and Enantioselectivity Estimates from Flexible Docking

2012

Experimental-like affinity constants and enantioselectivity estimates, not predicted so far computationally, were obtained using a novel flexible modeling/docking combined strategy. The S- and R-warfarin-human serum albumin (HSA, site I) complexes were used as an interaction model. The process for a verified estimation includes the following: (i) ionized open chain forming at physiological pH (a recent focus); (ii) conformational search (molecular mechanics and Monte Carlo methods); (iii) rigid protein-flexible ligand docking (GlideXP) generating low energy paired S- and R-poses; (iv) graphical comparison against the X-ray crystal structure (unsatisfactory verification step); (v) quantum po…

Multi-scale theoretical investigation of molecular hydrogen adsorption over graphene: coronene as a case study

2014

The physisorption of molecular hydrogen onto coronene is studied using a multi-scale theoretical approach with Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations. We consider two different kinds of model conformation for the approach of hydrogen towards the coronene i.e., systematic and random. For the systematic attack of hydrogen over coronene, the resulting potential energy profiles from DFT analysis are further found to resemble the Morse potential, and even the highly flexible Murrell–Sorbie (M–S) potential. The resulting M–S fitting also shows a zero-point energy correction of ∼16–17%. On the other hand, the potential energies from the random approach…

Msb2 is a Ste11 membrane concentrator required for full activation of the HOG pathway.

2015

The high osmolarity glycerol (HOG) pathway, composed of membrane-associated osmosensors, adaptor proteins and core signaling kinases, is essential for the survival of yeast cells under hyper-osmotic stress. Here, we studied how the MAPKKK Ste11 might change its protein interaction profile during acute stress exposure, with an emphasis on the sensory system of the so-called Sho1/Msb2 signaling branch. To characterize the transience of protein-protein interactions we utilized a recently described enzymatic in vivo protein proximity assay (M-track). Accordingly, interaction signals between Ste11 and many of its signaling partners can already be detected even under basal conditions. In most cas…

Membrane-insertion fragments of Bcl-xL, Bax, and Bid.

2004

Apoptosis regulators of the Bcl-2 family associate with intracellular membranes from mitochondria and the endoplasmic reticulum, where they perform their function. The activity of these proteins is related to the release of apoptogenic factors, sequestered in the mitochondria, to the cytoplasm, probably through the formation of ion and/or protein transport channels. Most of these proteins contain a C-terminal putative transmembrane (TM) fragment and a pair of hydrophobic alpha helices (alpha5-alpha6) similar to the membrane insertion fragments of the ion-channel domain of diphtheria toxin and colicins. Here, we report on the membrane-insertion properties of different segments from antiapopt…

Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets

2008

Total Internal Reflection Fluorescence Microscopy (TIRFM) allows us to image fluorescenttagged proteins near the plasma membrane of living cells with high spatial-temporal resolution. Using TIRFM imaging of GFP-tagged clathrin endocytic proteins, areas of fluorescence are observed as overlapping spots of different sizes and durations. Standard procedures to measure protein-protein colocalization of dual labeled samples threshold the original graylevel images to segment areas covered by different proteins. This binary logic is not appropriate as it leaves a free tuning parameter which can influence the conclusions. Moreover, these procedures rely on simple statistical analysis based on corre…

NordiCHI 2014 Workshop : Human-Technology Choreographies : re-thinking body, movement and space in interaction design

2014

Testing Hadronic Interactions at Ultrahigh Energies with Air Showers Measured by the Pierre Auger Observatory

2016

Ultrahigh energy cosmic ray air showers probe particle physics at energies beyond the reach of accelerators. Here we introduce a new method to test hadronic interaction models without relying on the absolute energy calibration, and apply it to events with primary energy 6-16 EeV (ECM=110-170 TeV), whose longitudinal development and lateral distribution were simultaneously measured by the Pierre Auger Observatory. The average hadronic shower is 1.33±0.16 (1.61±0.21) times larger than predicted using the leading LHC-tuned models EPOS-LHC (QGSJetII-04), with a corresponding excess of muons.

Halogen bonds with coordinative nature: halogen bonding in a S–I+–S iodonium complex†

2015

A detailed study of unexpectedly strong iodonium–sulfur halogen bonds in [I(2-imidazolidinethione)2]+ is presented. The interactions are characterized by single-crystal X-ray diffraction, charge density analysis based on QTAIM calculations, mass spectrometry, and NMR spectroscopy. The results, small RIS = 0.7 and high interaction energy of −60 kJ mol−1, support a coordinative nature of the halogen bond between the iodonium ion and the sp2 hybridized sulfur atoms.

FIRST experiment: Fragmentation of Ions Relevant for Space and Therapy

2013

International audience; Nuclear fragmentation processes are relevant in different fields of basic research and applied physics and are of particular interest for tumor therapy and for space radiation protection applications. The FIRST (Fragmentation of Ions Relevant for Space and Therapy) experiment at SIS accelerator of GSI laboratory in Darmstadt, has been designed for the measurement of different ions fragmentation cross sections at different energies between 100 and 1000 MeV/nucleon. The experiment is performed by an international collaboration made of institutions from Germany, France, Italy and Spain. The experimental apparatus is partly based on an already existing setup made of the …

A Protein-Interaction Array Inside a Living Cell

2013

Cell phenotype is determined by protein network states that are maintained by the dynamics of multiple protein interactions.1 Fluorescence microscopy approaches that measure protein interactions in individual cells, such as by Forster resonant energy transfer (FRET), are limited by the spectral separation of fluorophores and thus are most suitable to analyze a single protein interaction in a given cell. However, analysis of correlations between multiple protein interactions is required to uncover the interdependence of protein reactions in dynamic signal networks. Available protein-array technologies enable the parallel analysis of interacting proteins from cell extracts, however, they can …