Search results for "Dynamics"

Ubiquitous Structural Signaling in Bacterial Phytochromes

2015

The phytochrome family of light-switchable proteins has long been studied by biochemical, spectroscopic and crystallographic means, while a direct probe for global conformational signal propagation has been lacking. Using solution X-ray scattering, we find that the photosensory cores of several bacterial phytochromes undergo similar large-scale structural changes upon red-light excitation. The data establish that phytochromes with ordinary and inverted photocycles share a structural signaling mechanism and that a particular conserved histidine, previously proposed to be involved in signal propagation, in fact tunes photoresponse.

Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes

2013

Gold nanoparticles (AuNps) are used in nanomedicine in, e.g., drug delivery and bio-imaging. However, it is regrettable that the understanding of nanoparticle properties in cellular surroundings is incompletely understood. Here, we have complemented our previous studies [1] by performing extensive atomistic molecular dynamics simulations of lipid membranes interacting with charged gold nanoparticles. We have elucidated the action of these nanoparticles on membranes characterized by lipid compositional asymmetry in the two leaflets, thereby unraveling the interactions of AuNPs with both the extracellular and the cytosolic sides of plasma membranes of eukaryotic cells. We have found that ther…

An exploration of digital ride-hailing multisided platforms' market dynamics: empirical evidence from the Uber case study

2020

PurposeThe purpose of this paper is to experiment a dynamic performance management (DPM) approach to explore and assess the business dynamics of digital ride-hailing platforms with a focus on both supply and demand sides, and related interplays.Design/methodology/approachThe research adopts the DPM framework supported by simulation-based experimentations for developing a systemic case interpretation of Uber Inc. and its specific business complexity.FindingsThe emerging scenario analysis reveals that changes in the commission percentage for drivers and cutting prices for customers (car hailers) by competitors have significant impacts on the car-hailing industry.Originality/valueDPM and assoc…

Paving the way for synthetic biology-based bioremediation in Europe

2009

Synthetic biology (SB) has a dual definition. It is both the design and construction of new biological parts, devices and systems, and also the re‐design of existing, natural systems for useful purposes. The latter field is maybe one of the major challenges within this discipline, since the promising prospect that biological systems may be used as biomachines will certainly be exploited in the near future. Synthetic biology has challenging conceptual possibilities (Moya et al., 2009a) and impressive progress has already been made in biotechnology following SB approaches (de Lorenzo and Danchin, 2008). Much more is expected in the near future from current efforts aiming to make synthetic gen…

2021

A substantial body of research has shown worse health conditions for East- vs. West-Germany in the wake of reunification. In the present study, we investigate how these differences between the two formerly divided regions developed and what maintains them. Specifically, we consider the associations between health status, income satisfaction, and health-related locus of control. In a quasi-experimental and longitudinal study design, we are particularly interested in the differences between individuals who stayed in East-Germany and those who were born in the East but migrated to West-Germany. To this end, we examined data from seven waves of the Saxony Longitudinal Study (2003–2009). Specifi…

Author Correction: On the thermodynamic origin of metabolic scaling

2018

The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument predicts. The universality of exponent 3/4 -claimed in terms of the fractal properties of the nutrient network- has recently been challenged according to empirical evidence that observed a wealth of robust exponents deviating from 3/4. Here we present a conceptually simple thermodynamic framework, where the dependence of metabolic rate with body mass emerges from a trade-off between the energy dissipated as heat and the energy efficiently used by the organi…

Dynamics of liking for flavoured crackers: Test of predictive value of a boredom test

1998

Abstract The principal aim of this study was to compare two experimental conditions for measuring the effect of repeated consumption on liking: a laboratory boredom test and a home use test. Another goal was to investigate the impact of perceived familiarity, appropriateness and complexity on the dynamics of liking. Two groups of consumers were recruited, one for each condition. Five variants of salty crackers, each with a different flavour, were tested. The laboratory condition did not show any difference in the dynamics of liking among the flavours. The home condition revealed a significant increase in liking for only one flavour. This increase could not be related to the level of complex…

Modeling of Particle Number Fluctuations in Entire Cells

2012

In a recent study we developed a method to model protein diffusion in cells [1], where special attention was given to generating from image data of the measured cell a realistic digital model cell in which protein dynamics were simulated. The method was shown to be well suited for modeling non-equilibrium situations that arise, e.g., in photobleaching experiments, and to be capable of producing more detailed information about protein motion than traditional modeling.Another experimental way to assess protein dynamics is to study fluctuations in the local protein number, as it is done, e.g., in fluorescence correlation spectroscopy (FCS), or in similar measurements that apply single-plane il…

A Microscopic Description of SARS-CoV-2 Main Protease Inhibition with Michael Acceptors. Strategies for Improving Inhibitors Design

2020

The irreversible inhibition of the main protease of SARS-CoV-2 by a Michael acceptor known as N3 has been investigated using multiscale methods. The noncovalent enzyme–inhibitor complex was simulated using classical molecular dynamics techniques and the pose of the inhibitor in the active site was compared to that of the natural substrate, a peptide containing the Gln–Ser scissile bond. The formation of the covalent enzyme–inhibitor complex was then simulated using hybrid QM/MM free energy methods. After binding, the reaction mechanism was found to be composed of two steps: (i) the activation of the catalytic dyad (Cys145 and His41) to form an ion pair and (ii) a Michael addition where the …

2019

So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution…